WO2010141143A2

WO2010141143A2 - Engineered avirulent bacteria strains and use in medical treatments

Info

Publication number: WO2010141143A2
Application number: PCT/US2010/027245
Authority: WO
Inventors: Nabil Arrach; Michael Mcclelland
Original assignee: Vivocure, Inc.
Priority date: 2009-04-21
Filing date: 2010-03-12
Publication date: 2010-12-09
Also published as: WO2010141143A3

Abstract

Provided in part herein are avirulent bacterial compositions suitable for use as medicaments for the treatment of various tumors. Also provided in part are methods for identifying and/or generating avirulent bacterial strains or engineered avirulent bacterial strains that can be formulated as medicaments. Also provided in part are methods of cancer treatment utilizing engineered avirulent bacteria as described herein. Engineered strains as described herein show normal or increased fitness in tumor tissue, while exhibiting reduced fitness in normal tissue. Compositions described herein may prove useful for the treatment of other medical conditions.

Description

PATENT VIV-1002-PC

ENGINEERED AVIRULENT BACTERIA STRAINS AND USE IN MEDICAL TREATMENTS

Related Patent Application(s)

This application claims the benefit of U.S. provisional patent application no. 61/171 ,330 filed on April 21 , 2009, entitled METHOD OF ENGINEERING AVIRULENT BACTERIA STRAINS TO TREAT SOLID TUMORS, naming Nabil Arrach and Michael McClelland as inventors and designated by Attorney Docket No. VIV-1002-PV. The entire content of the foregoing patent application is incorporated herein by reference, including, without limitation, all text, tables and drawings.

Statement of Government Support

This technology was developed in part with government support under the following Grants. NIH grants R01AI034829, R01AI052237, R21AI057733, TRDRP 16KT-0045, DOD grant W81XWH-06- 1-0117 and grant ADI-08/2006 from PBCT-CONICYT (Chile) and The World Bank. The government has certain rights in this technology.

Field

The technology relates in part to engineering bacterial strains for use in anti-cancer therapies.

Background

Use of bacteria for medical treatments has been investigated and bacteria have been administered as medicaments for the treatment of various medical conditions. Bacteria with favorable characteristics for use in medical therapies can be isolated or engineered. For treatment of cancer, bacteria that are attenuated can used to preferentially target and colonize tumor tissue. Engineered bacteria may prove suitable for the treatment of other non-cancer medical conditions.

Summary

Provided are modified bacteria that invade cancer cells and/or extracellular spaces in cancer tissues and have reduced activity in normal cells and/or extracellular spaces in normal tissues. In PATENT VIV-1002-PC

some embodiments, provided are orally active pharmaceutical compositions that include a mutant bacterium containing a genetic mutation, where the wild type counterpart of the mutant bacterium is virulent against non-cancer cells and/or non-cancer tissues, the virulence of the mutant bacterium against non-cancer cells and/or non-cancer tissues is substantially reduced compared to the virulence of the wild type counterpart bacterium against non-cancer cells and/or non-cancer tissues, and the virulence of the mutant bacterium against cancer cells and/or cancer tissues is not substantially reduced compared to the virulence of the wild type counterpart bacterium against cancer cells and/or cancer tissues. Cancer tissues generally include a population of cancer cells, and non-cancer tissues generally include no detectable amount of cancer cells. A cancer tissue sometimes comprises one or more tumors, and sometimes a cancer tissue is a tumor. Certain mutant bacteria can be "avirulent" bacteria, which as referred to herein, have no virulence or substantially no virulence against non-cancer cells and non-cancer tissues.

In certain embodiments, provided are methods that include administering a mutant bacterium that contains one or more genetic mutations to a subject having a tumor in an amount effective to treat the tumor, where the wild type counterpart of the mutant bacterium is virulent against non-cancer cells and/or non-cancer tissues, the virulence of the mutant bacterium against non-cancer cells and/or non-cancer tissues is substantially reduced compared to the virulence of the wild type counterpart bacterium against non-cancer cells and/or non-cancer tissues, and the virulence of the mutant bacterium against cancer cells and/or cancer tissues is not substantially reduced compared to the virulence of the wild type counterpart bacterium against cancer cells and/orcancer tissues. In some embodiments, the mutant bacterium is administered via oral delivery.

In some embodiments, provided are high throughput methods to identify a bacterial strain that will selectively infect tumor tissue in comparison to normal tissue, that include (a) providing an input library of bacteria that are mutants of a wild type strain, (b) administering the library to tumor- bearing subjects and to normal subjects, (c) recovering DNA from bacteria that have survived in tumor tissue of the tumor-bearing subject and that have survived in the tissues of the normal subject, and (d) analyzing the DNA obtained in (c) to determine the relative representation of mutants in tumor and normal tissues. In some embodiments, the DNA obtained in (c) is analyzed by microarray analysis and/or sequencing analysis. In certain embodiments, the DNA obtained in (c) is analyzed against a panel containing open reading frames of wild type bacterial genes. In some embodiments, the analysis in (d) determines mutations in genes and/or associated PATENT VIV-1002-PC

regulatory elements of bacterial that preferentially survive in tumor tissue as compared to normal tissue.

In certain embodiments, provided are bacterial mutants selective for tumor tissue identified by a method that includes (a) providing an input library of bacteria that includes mutants of a wild type strain, (b) administering the library to tumor-bearing subjects and to normal subjects, (c) recovering DNA from bacteria that have survived in tumor tissue of the tumor-bearing subject and that have survived in the tissues of the normal subject, and (d) analyzing the DNA obtained in (c) to determine the relative representation of mutants in tumor and normal tissues. In some embodiments, the DNA obtained in (c) is analyzed by microarray analysis and/or sequencing analysis. In some embodiments, the analysis in (d) determines mutations in genes and/or associated regulatory elements of bacterial that preferentially survive in tumor tissue as compared to normal tissue.

In some embodiments, provided are methods to obtain an attenuated strain of bacteria that include administering a library of mutant bacteria to a multiplicity of subjects and identifying a mutant strain that is present in the tissues of a subject having a predetermined survival time.

In certain embodiments, provided are attenuated strains of bacteria identified by a method that includes administering a library of mutant bacteria to a multiplicity of subjects and identifying a mutant strain that is present in the tissues of a subject having a predetermined survival time.

In some embodiments, provided is a library of mutant bacteria obtainable by transfecting a bacterial culture with transposons that result in disruption of genes and/or associated regulatory elements in transfected bacteria. In some embodiments, provided is a library of mutant bacteria obtained by homologous recombination that result in disruption of genes and/or associated regulatory elements in transfected bacteria. In some embodiments, provided is a library of mutant bacteria obtained by random mutagenesis, including the use of mutagenic chemicals, that result in disruption of genes and/or associated regulatory elements in transfected bacteria. In some embodiments, transposons are fused to an expression system for a selectable marker that includes a promoter (e.g., T7 promoter) where the fused expression system results in disruption of genes and/or associated regulatory elements. PATENT VIV-1002-PC

Virulence sometimes is determined in vitro or ex vivo (e.g., using a cell culture). In some embodiments, virulence is assessed in vivo (e.g., against cells and/or tissues from an animal (e.g., rodent, dog, cat, monkey, ape) or human to which a bacterium described herein has been administered).

In certain embodiments, the mutant and/or attenuated bacteria include a genetic mutation. In some embodiments, the genetic mutation includes two or more genetic mutations. In certain embodiments, the two or more mutations can be in the same gene or associated regulatory element, and in some embodiments, the two or more mutations can be in different genes or associated regulatory element.

In some embodiments, the mutation modulates an activity encoded by a gene. In certain embodiments, the genetic mutation modulates an activity selected from the group consisting of: a secretion system activity (e.g., bacterial type III secretion system); a bacterial transcriptional regulator activity, a magnesium transport activity; a amino acid ligase activity (e.g., D-alanine-D- alanine ligase); a protease activity (e.g., serine protease (e.g., periplasmic, cytoplasmic, organelle associated), other known or putative proteases); an oxidase activity (e.g., Cytochrome o ubiquinol oxidase); a structural protein activity; a polymerase activity (e.g., O-antigen polymerase); a reductase activity (e.g., CDP-6-deoxy-delta3,4-glucose reductase); a pyrophosphorylase activity (e.g., dTDP-glucose pyrophosphorylase); a sugar synthetase activity (e.g., TDP-rhamnose synthetase); a sugar transferase activity (e.g., a glucose or galactose sugar transferase, UDP-D- glucose:(galactosyl)lipopolysaccharide glucosyltransferase, UDP-D- galactose:(glucosyl)lipopolysaccharide-alpha-1 ,3-D-galactosyltransferase); an oxidase activity (e.g., a monoamine oxidase); an activity that suppresses mutants of outer membrane protein assembly (e.g., a suppressor of porin (ompF) assembly mutants); a hydrolase activity (e.g., acetyl- CoA hydrolase); a phosphatase activity (e.g., phosphohistidine phosphatase); a transcriptional repressor activity (e.g., a glucitol operon transcriptional repressor); a protein synthesis chain elongation activity (e.g., protein synthesis chain elongation factor EF-Tu); a potassium uptake activity (e.g., potassium transport); a chemotaxis activity (e.g., methyl-accepting chemotaxis protein (MCP)); an exporter activity (e.g., an ABC-type bacteriocin/antibiotic exporter); a dehydrogenase activity (e.g., succinate dehydrogenase); a redox factor activity (e.g., thioredoxin 1); a polysaccharide chain length modulator activity (e.g., enterobacterium common antigen (ECA) polysaccharide chain length modulator); and a Hes-B like domain activity. PATENT VIV-1002-PC

In certain embodiments, the genetic mutation includes an alteration to a gene. In some embodiments, the genetic mutation includes an alteration to a gene selected from ddlB, htrA, cyoA, sdhA, sifA, phoP, rfc, sufA, ssrA, ssaB, ssaC, ssaD, sseB, sscA, sseC, sseD, sseE, ssaJ.ssaK, ssaL, ssaM, ssaV, ssaN, ssaP, ssaQ, yscR, ssaT, yebC, rfbl, rfbA, rfbD, asmA, sixA, srlR, yhdP, tufA, rfaK, rfaJ, rfal, rfaB, mgtC, trxA, wzzE, ubiB, trkH, purH, STM1410, STM0278, STM4262, STM4258, STM3118, STM3119, STM3120, STM3121 , a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes. In certain embodiments, the genetic mutation comprises an alteration to a gene in the SPI-2 gene family (i.e., an "SPI-2 gene").

In some embodiments, the genetic mutation includes an alteration to a nucleotide sequence. In certain embodiments, the genetic mutation includes an alteration to the nucleotide sequence of a gene, with respect to the nucleotide sequence of the wild type counterpart, selected from ddlB, htrA, cyoA, sdhA, sifA, phoP, rfc, sufA, ssrA, ssaB, ssaC, ssaD, sseB, sscA, sseC, sseD, sseE, ssaJ.ssaK, ssaL, ssaM, ssaV, ssaN, ssaP, ssaQ, yscR, ssaT, yebC, rfbl, rfbA, rfbD, asmA, sixA, srlR, yhdP, tufA, rfaK, rfaJ, rfal, rfaB, mgtC, trxA, wzzE, ubiB, trkH, purH, STM1410, STM0278, STM4262, STM4258, STM3118, STM3119, STM3120, STM3121 , a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes.

In some embodiments the mutant bacterium is a mutant pathogenic bacterium. In certain embodiments, the mutant bacterium is a mutant enteric bacterium. In some embodiments the mutant bacterium is a mutant Salmonella bacterium. Sometimes the Salmonella bacterium is S. typhimurium, and at times the S. typhimurium is strain 14028.

Certain embodiments are described further in the following description, examples, claims and drawings.

Brief Description of the Drawings

The drawings illustrate certain embodiments of the technology and are not limiting. For clarity and ease of illustration, the drawings are not made to scale and, in some instances, various aspects may be shown exaggerated or enlarged to facilitate an understanding of particular embodiments. PATENT VIV-1002-PC

FIG.1 illustrates steps used to prepare labeled nucleic acid, isolated from input and/or output pool mutants, for microarray analysis. Steps involved in preparation of nucleic acid (e.g., RNA and/or DNA, either labeled or unlabeled) are described in further detail herein and in Example 1. The portion of the method illustrated is applicable to libraries generated using transposon-mediated mutagenesis or knockout mutagenesis.

FIGS. 2A and 2B present fitness data for class 1 and class 2 Salmonella mutants, identified and/or generated as described herein, having fitness phenotypes measurable by microarray analysis. Data represents the log base 2 calculations of the ratios of output pool or library after selection in a tissue versus the control or input pool (library generated by mutagenesis prior to selection). FIG. 2A presents the fitness data for class 1 Salmonella mutants, in normal and tumor tissue. FIG. 2B presents the fitness data for class 2 Salmonella mutants, in normal and tumor tissues. Large negative numbers indicate reduced fitness, small negative numbers indicate little or no difference in phenotype, and positive numbers indicate an increase in fitness in that tissue. In some embodiments, a loss of fitness is indicated by at least a three-fold reduction in signal intensity in the experimental or output pool as compared to the input or control pool. PC3 refers to subcutaneous prostate tumors and MDA refers to melanoma tumors. Raw microarray data is presented in Table 1 , and microarray data for select class 1 mutants presented with known or putative gene functions for the selected class 1 mutants is presented in Table 2. Some of the Tables present data filtered to show only the largest changes, which was arbitrarily set at a threshold of a 2.25-fold change [Log2(2.25)= -1.5]. These changes are marked in grey in Table 1 , Table 2, and Figure 2A. Division by zero is marked by ####.

FIG. 3 presents virulence data for sixteen selected class 1 and class 2 Salmonella mutants. The experimental conditions utilized for investigating the virulence of Salmonella identified and/or mutagenized using the present technology are described herein and in Example 1. In general microarray fitness was positively correlated with mouse survival and mutant virulence. Those mutants with reduced fitness tended to show the most reduced virulence and longest mouse survival times. In the results the microarray phenotypes are; NT, reduced fitness in normal tissues; TUM, reduced fitness in tumors. Panel A presents the results of each of the selected mutants. Panel B groups the mutants by class.

FIG. 4 presents the competitive fitness data between a selected class 1 mutant (STM3120) and aroA and aroD mutants. The experimental conditions utilized for comparing the fitness of PATENT VIV-1002-PC

STM3120 against aroA and aroD are described herein and in Example 1. The numbers presented on the X axis represent the number of colony forming units counted in biopsies taken at the indicated time point following inoculation (e.g., 2 days, 4 days, 7 days).

FIG. 5 presents data illustrating the ability of Salmonella mutant STM3120 to target and colonize tumor tissue, when given orally to BALB/c mice. The experimental conditions utilized for investigating the ability of STM3120 to target and colonize tumors are described herein and in Example 1. The number of colony forming units from each biopsy is presented in the Figure. The number of bacteria counted in the biopsies represents an amount of bacteria known to be therapeutically effective. Dashes indicate a level of bacteria below the level of detection.

Detailed Description

Certain bacteria have the ability to colonize tissue or cells of a host or subject. Bacteria that colonize the tissue or cells of a host frequently are beneficial, and occasionally are pathogenic. Pathogenic bacteria cause disease and or death in the infected host, and sometimes are known to preferentially target or colonize certain types of cells or tissue (e.g., lung, spleen, stomach, skin, tumors).

Bacteria, including pathogenic bacteria, which colonize the cells and/or tissues of infected hosts, could prove useful for certain medical therapies. To protect against disease or death to the treated subject, pathogenic bacteria used in medical therapies typically are selected for reduced or attenuated virulence. Strains of pathogenic bacteria with attenuated virulence and the ability to target and/or colonize certain cell or tissue types could provide additional avenues for bacterially directed medical therapies

Naturally occurring or engineered bacteria with attenuated virulence can be isolated, identified and/or generated, using methods described herein. Naturally occurring or engineered bacteria with attenuated virulence and the ability to target and/or colonize certain cell or tissue types (e.g., tumors) can be isolated, identified and/or generated, using methods described herein. Thus, provided herein are methods and compositions designed to isolate, identify and/or generate attenuated and/or mutant bacteria that can be utilized in medical treatments (e.g., cancer therapies). PATENT VIV-1002-PC

In some embodiments, technology described herein provides methods for screening mutations in non-essential genes in Salmonella and identifying mutants displaying an enhanced ability to colonize and grow in solid tumors and are unable to grow well in normal host tissues. In certain embodiments, the technology described herein provides methods for selection of a library of bacterial mutants with one or more DNA insertions or alterations.

In some embodiments, technology described herein identifies genes and proteins (or variants thereof) of gram-negative bacteria with improved targeting, enhanced growth, and reduced virulence in solid tumors and reduce growth in non-tumor tissue. In certain embodiments, the technology described herein also provides bacterial strains with one or more genetically altered genes that promote enhanced bacterial colonization, accumulation and/or growth in solid tumors. In some embodiments, the technology described herein also provides bacterial strains with one or more genetically altered genes that promote reduced bacterial colonization, accumulation and/or growth in non-tumor cells and tissue while retaining their growth potential in solid tumors. In certain embodiments, the technology described herein also provides for the therapeutic use of mutant bacteria for growth inhibition and/or reduction in volume of solid tumors.

Engineering and Alteration Methods

Methods and compositions described herein can be used to identify and/or generate attenuated and/or engineered bacteria suitable for use in medical therapies (e.g., cancer treatments). The term "attenuated bacteria" as used herein refers to a bacteria that has one or more reduced or eliminated activities with respect to a wild type counterpart. The term "engineered bacteria" as used herein refers to a modified bacteria that includes one or more gene or regulatory sequences (e.g., nucleic acid sequences) or activities distinct from a nucleic acid sequence or activity present in a bacteria utilized as a starting point for modification or alteration (e.g., wild type counterpart). Engineered bacteria typically arise as a result of a genetic modification, usually introduced or selected for, using readily available techniques. Any suitable method for generating attenuated and/or mutant bacteria having an altered activity may be used. Non-limiting examples of methods useful for generating an altered activity include, chemical mutagenesis, ultra violet light (UV) mutagenesis, introducing a heterologus polynucleotide (e.g., nucleic acid or gene integration, also referred to as "knock in"), removing an endogenous polynucleotide, altering the sequence of an existing endogenous nucleic acid sequence ( e.g., site-directed mutagenesis), disruption of an existing endogenous nucleic acid sequence (e.g., knock outs and transposon or insertion element PATENT VIV-1002-PC

mediated mutagenesis), selection for an altered activity where the selection causes a change in a naturally occurring activity that can be stably inherited (e.g., causes a change in a nucleic acid sequence in the genome of the organism or in an epigenetic nucleic acid that is replicated and passed on to daughter cells), PCR-based mutagenesis, and the like. The term "mutagenesis" as used herein refers to any modification to a nucleic acid (e.g., nucleic acid sequence, gene sequence or host chromosome) that is subsequently used to generate a mutant bacteria suitable for use in medical treatments. Non-limiting examples of mutagenesis include deletion, insertion, substitution, rearrangement, point mutations, suppressor mutations and the like. Mutagenesis methods are known and readily available to a user. Non-limiting examples of mutagenesis methods are described herein and can also be found in Maniatis, T., E. F. Fritsch and J. Sambrook (1982) Molecular Cloning: a Laboratory Manual; Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.

The term "genetic modification," "genetic alteration" and grammatical equivalents thereof as used herein refers to any suitable nucleic acid addition, removal or alteration that results in a bacteria that can be utilized in medical treatments (e.g., has attenuated virulence and/or maintains the ability to preferentially target or colonize tumors (e.g., substantially identical fitness in tumors when compared to the starting bacteria), when introduced into a host organism or subject. A genetic modification can be performed on a wild type bacteria or a modified or attenuated bacteria, in some embodiments. In certain embodiments, a previously attenuated or engineered bacteria can be the starting organism for further genetic modification (e.g., used as a starting point or background to add additional modifications or construct mutant libraries in (e.g., transposon or knockout libraries)). Genetic modifications include, without limitation, insertion of one or more nucleotides in a native nucleic acid of a host organism in one or more locations, deletion of one or more nucleotides in a native nucleic acid of a host organism in one or more locations, modification or substitution of one or more nucleotides in a native nucleic acid of a host organism in one or more locations, insertion of a non-native nucleic acid into a host organism (e.g., insertion of an autonomously replicating vector), and removal of a non-native nucleic acid in a host organism (e.g., removal of a vector). In some embodiments, the genetic mutation or modification includes two or more genetic mutations or modifications. In certain embodiments, the two or more genetic mutations or modifications can be in one or more genes and/or associated regulatory element.

The term "heterologus polynucleotide" as used herein refers to a nucleotide sequence not present in a wild type bacterium in some embodiments (e.g., transposable elements used as a PATENT VIV-1002-PC

mutagenesis agent to generate mutant libraries). In certain embodiments, a heterologus polynucleotide is present in a different amount (e.g., different copy number) than in a unaltered host or wild type bacteria (e.g., wild type counter part), which can be accomplished, for example, by introducing more copies of a particular nucleotide sequence to a host microorganism (e.g., the particular nucleotide sequence may be in a nucleic acid autonomous of the host chromosome or may be inserted into a chromosome). A heterologus polynucleotide is from a different organism in some embodiments, and in certain embodiments, is from the same type of organism but from an outside source (e.g., a recombinant source).

The term "altered activity," "modulated activity" and grammatical equivalents thereof as used herein refer to an activity in an attenuated and/or engineered bacterium that is modified or modulated relative to the wild type counterpart activity (e.g., added, increased, reduced, inhibited or removed activity). An activity can be altered by introducing a genetic modification to a bacterium that yields an engineered bacterium having added, increased, reduced, inhibited or removed activity. In some embodiments, an attenuated bacteria has one or more activities that are modified relative to a wild type counterpart. In certain embodiments, the modified activity or activities may directly or indirectly alter a bacterial system or component associated with virulence and/or tumor targeting and/or colonization. In some embodiments, a genetic mutation or modification modulates an activity.

An altered activity sometimes is an activity not detectable in a host bacterium (e.g., starting bacteria, wild type bacteria) and is added to an engineered bacterium. An altered activity also may be an activity detectable in a host bacterium and is increased in an engineered bacterium. An activity may be added or increased by increasing the number of copies of a polynucleotide that encodes a polypeptide having a target activity, in some embodiments. An altered activity sometimes is an activity detectable in a host bacterium and is reduced, inhibited or removed (i.e., not detectable) in an engineered bacterium. An activity may be reduced or removed by decreasing the number of copies of a polynucleotide that encodes a polypeptide having a target activity, in some embodiments.

An activity also can be reduced or removed by (i) inhibiting a polynucleotide that encodes a polypeptide having the activity or (ii) inhibiting a polynucleotide operably linked to another polynucleotide that encodes a polypeptide having the activity. A polynucleotide can be inhibited by any suitable technique known, such as by contacting an RNA encoded by the polynucleotide with a PATENT VIV-1002-PC

specific inhibitory RNA (e.g., RNAi, siRNA, ribozyme). An activity also can be reduced or removed by contacting a polypeptide having the activity with a molecule that specifically inhibits the activity (e.g., enzyme inhibitor, antibody). In certain embodiments, an activity can be reduced or removed by subjecting a host bacterium to a selective environment and screening for bacterium that have a reduced level or removal of an activity that affects of is associated with virulence and/or tumor targeting and/or colonization.

In certain embodiments, a gene includes an open reading frame and the gene may be in effective connection with one or more associated regulatory elements (e.g., promoter sequences, 5' untranslated regions (5'UTR), 3' untranslated regions (3' UTR), enhancer sequences, operator sequences, the like or combinations thereof). In some embodiments a regulatory element is adjacent to or abuts an open reading frame, and in certain embodiments a regulatory element is located at a distance from the open reading frame. In some embodiments, an activity can be altered by modifying the nucleotide sequence of an open reading frame (ORF). An ORF sometimes is mutated or modified (for example, by point mutation, deletion mutation, insertion mutation, homologous recombination, PCR based mutagenesis and the like) to alter, enhance or increase, reduce, substantially reduce or eliminate the activity of the encoded protein or peptide. The protein or peptide encoded by a modified ORF sometimes is produced in a lower amount or may not be produced at detectable levels, and in other embodiments, the product or protein encoded by the modified ORF is produced at a higher level (e.g., codons sometimes are modified so they are compatible with tRNA's preferentially used in the host organism or engineered organism). To determine the relative activity, the activity from the product of the mutated ORF (or cell containing it) can be compared to the activity of the product or protein encoded by the unmodified ORF (or cell containing it).

In some embodiments, an untranslated ribonucleic acid, or a cDNA can be used to reduce the expression of a particular activity or enzyme. For example, a bacteria can be engineered by genetic modification to express a nucleic acid reagent that reduces the expression of an activity by producing an RNA molecule that is partially or substantially homologous to a nucleic acid sequence of interest which encodes the activity of interest. The RNA molecule can bind to the nucleic acid sequence of interest and inhibit the nucleic acid sequence from performing its natural function, in certain embodiments. In some embodiments, the RNA may alter the nucleic acid sequence of interest which encodes the activity of interest in a manner that the nucleic acid PATENT VIV-1002-PC

sequence of interest is no longer capable of performing its natural function (e.g., the action of a ribozyme for example).

In certain embodiments, an alteration (e.g., by mutagenesis, introduction or deletion) to a nucleic acid sequence or gene can alter a given activity by (i) increasing or decreasing feedback inhibition mechanisms, (ii) increasing or decreasing promoter initiation, (iii) increasing or decreasing translation initiation, (iv) increasing or decreasing translational efficiency, (v) modifying localization of peptides or products expressed from nucleic acid reagents described herein, or (vi) increasing or decreasing the copy number of a nucleotide sequence of interest, (vii) expression of an anti-sense RNA, RNAi, siRNA, ribozyme and the like. In some embodiments, alteration of a nucleic acid or nucleotide sequence can alter a region involved in feedback inhibition (e.g., 5' UTR, promoter and the like). A modification sometimes is made that can add or enhance binding of a feedback regulator and sometimes a modification is made that can reduce, inhibit or eliminate binding of a feedback regulator.

In certain embodiments, alteration of a nucleic acid or gene sequence can alter sequences involved in transcription initiation (e.g., promoters, 5¹ UTR, and the like). A modification sometimes can be made that can enhance or increase initiation from an endogenous or heterologus promoter element. A modification sometimes can be made that removes or disrupts sequences that increase or enhance transcription initiation, resulting in a decrease or elimination of transcription from an endogenous or heterologus promoter element.

In some embodiments, alteration of a nucleic acid nucleic acid or gene sequence can alter sequences involved in translational initiation or translational efficiency (e.g., 5' UTR, 3' UTR, coάon triplets of higher or lower abundance, translational terminator sequences and the like, for example). A modification sometimes can be made that can increase or decrease translational initiation, modifying a ribosome binding site for example. A modification sometimes can be made that can increase or decrease translational efficiency. Removing or adding sequences that form hairpins and changing codon triplets to a more or less preferred codon are non-limiting examples of genetic modifications that can be made to alter translation initiation and translation efficiency.

In certain embodiments, alteration of a nucleic acid nucleic acid or gene sequence can alter sequences involved in localization of peptides, proteins or other desired products. A modification sometimes can be made that can alter, add or remove sequences responsible for targeting a PATENT VIV-1002-PC

polypeptide, protein or product to an intracellular organelle, the periplasm, cellular membranes, or extracellularly.

In some embodiments, alteration of a nucleic acid nucleic acid or gene sequence can alter sequences involved in increasing or decreasing the copy number of a nucleotide sequence of interest. A modification sometimes can be made that increases or decreases the number of copies of an ORF stably integrated into the genome of an organism or on an epigenetic nucleic acid vector. Non-limiting examples of alterations that can increase the number of copies of a sequence of interest include, adding copies of the sequence of interest by duplication of regions in the genome (e.g., adding additional copies by recombination or by causing gene amplification of the host genome, for example), cloning additional copies of a sequence onto a nucleic acid reagent, or altering an ORI to increase the number of copies of an epigenetic nucleic acid reagent. Non- limiting examples of alterations that can decrease the number of copies of a sequence of interest include, removing copies of the sequence of interest by deletion or disruption of regions in the genome, removing additional copies of the sequence from epigenetic nucleic acid reagents, or altering an ORI to decrease the number of copies of an epigenetic nucleic acid reagent.

In certain embodiments, increasing or decreasing the level of an activity associated directly or indirectly with virulence or fitness in tumors can also be accomplished by altering, adding or removing sequences involved in the expression of an anti-sense RNA, RNAi, siRNA, ribozyme and the like. The methods described herein can be used to modify expression of anti-sense RNA, RNAi, siRNA, ribozyme and the like.

Engineered bacteria can be prepared by altering, introducing or removing nucleotide sequences in the host genome, in some embodiments. In some embodiments, the nucleotide sequences can be carried on stably maintained epigenetic nucleic acids. Any suitable mutagenic technique can be used to alter, introduce or remove nucleotide sequences in the genome of a host bacteria or in an epigenetic nucleic acid in a host bacteria. Attenuated and/or mutant bacteria and libraries including attenuated and/or mutant bacteria, suitable for use in medical treatments, can be prepared utilizing nucleic acid mutagenesis methods described herein or other known nucleic acid mutagenesis methods. PATENT VIV-1002-PC

Generating libraries

Any suitable method can be used to generate a library. In some embodiments, transposon mutagenesis is used to generate mutated bacteria. Transposon mutagenesis has been utilized to generate a library of greater than 40,000 kanamycin (Kan) resistant transposon insertion mutants in Salmonella typhimurium strain 14028 (see Examples section hereafter). A transposon insertion library can be generated by transforming or transfecting a bacterial culture with a nucleic acid vector (sometimes also referred to as a nucleic acid reagent, for example) comprising transposons that optionally further comprise a selectable marker, as described herein in the Examples. Transposon-mediated mutagenesis makes use of naturally occurring or modified naturally occurring mobile genetic elements. Transposon mutagenesis is a type of random mutagenesis, although some transposable elements can have specific targeting sequences. A wild type strain, attenuated strain or strain that was previously mutagenized can be used as the starting strain for the mutagenesis described herein. A transposon-mediated mutagenesis procedure described in the Examples section herein generated, on average, in the range of about 10 transposon insertions per gene in the Salmonella genome. This level of mutagenesis often is desirable to ensure each gene in the genome contains at least one insertion (e.g., mutation).

Methods described herein can identify genes, that when mutated, result in a bacterial strain that is avirulent or has reduced virulence when compared to the wild type counterpart or attenuated strain used as the starting point for mutagenesis. Methods described herein can be used to identify avirulent strains that have unchanged or increased fitness in tumor tissue (e.g., preferentially targeted or colonized tumor tissue). In some embodiments, methods described herein facilitate screening of all non-essential bacterial genes (e.g., Salmonella genes) to identify mutants that show an enhanced ability to colonize and grow in solid tumors and a reduced ability to grow well in normal or non-tumor tissues, in some embodiments. In certain embodiments, methods described herein facilitate selection of a library of bacterial mutants with one or more DNA insertions or alterations. In some embodiments, methods described herein can generate and/or identify genetically engineered bacterial strains with enhanced fitness including one or more of the following properties: (i) enhanced accumulation of bacterial cells in solid tumors; (ii) enhanced colonization and growth in solid tumors; (iii) improved tumor killing; (iv) reduced colonization of bacterial strains in non-tumor cells and/or non-tumor tissues; and (v) increased therapeutic efficacy. PATENT VIV-1002-PC

Subjecting a library of transposon insertion mutants to selection sometimes results in the loss of genes from the population that contributes to the fitness of the bacteria in that selective environment. The transposons sometimes effect disruptions of various genes by virtue of insertions in the genome. In some embodiments, genes disrupted are essential genes and in certain embodiments, genes disrupted are non-essential genes.

The term "essential gene" as described herein refers to a gene whose function or activity is necessary for cell viability, and therefore loss of the function or activity results in a non-viable cell. The term "non-essential" gene as described herein refers to a gene whose function or activity is not necessary for cell viability (e.g., the cell can obtain the product or activity from the environment or a host), and therefore results in a cell that is viable, but may exhibit a mutant phenotype (e.g., reduced virulence, slow growth, requirement for nutrient, and the like). The transposon mutagenesis vector utilized in certain methods described herein can include a T7 promoter sequence in the transposon insert that allows analysis of individual genes/mutants and measurement of their fitness in a complex mutant library.

The term "library" as used herein refers to a collection of nucleic acids representative of part or all of the genome of a subject (e.g., bacteria). Nucleic acid in a library can be in any suitable form, including, without limitation, linear, circular, plasmid, artificial chromosome and the like. A library can include any suitable number of nucleic acid species, and can include, without limitation, in some embodiments about 2 to about 10,000,000 nucleic acid species (e.g., about 2, 5, 10, 15, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 5000, 10000, 50000, 100000, 500000, 5,000,000 nucleic acid species). There may be multiple copy numbers of each nucleic acid species in a library. Nucleic acid species in a library may be separated for further analysis. For example, a nucleic acid library (e.g., "input" library) may be inserted into a population of organisms, and DNA isolated from each organism (e.g., "output" library) in the population to identify the position of the genomic insertions that make up the library. In some embodiments, the output library is a selective library.

A mutagenized bacterial culture, including transposon-mediated mutagenized bacteria, can be analyzed using microarray analysis to identify which genes are present in the population after mutagenesis. The mutagenized bacteria collectively form a "mutant" library due to the occurrence of inserted mutagenic elements throughout the host genome. An initial mutant library, or "input" library of mutagenized (e.g., transposon-mediated mutagenesis) bacteria can be analyzed to identify the mutants present in the library. In some embodiments, the analysis is performed prior to PATENT VIV-1002-PC

generating an output library, and in certain embodiments, the analysis is performed concurrently with analysis of the output library. An "output" library also can be analyzed to identify the mutants present after passage in normal tissue or tumor tissue, in some embodiments. The term "input library" as used herein refers to the initial population of mutants obtained after mutagenesis of the starting bacterial strain. The term "output library" as used herein refers to the population of mutants after passage or selection of the "input library" in normal tissue or tumor tissue.

In some embodiments, a library of mutant bacteria can be generated by transfecting a bacterial culture with transposons fused to an expression system for a selectable marker including a T7 promoter, where, the fused expression system results in disruption of genes in transfected bacteria. In certain embodiments a library of mutant bacteria is generated by transfecting a bacterial culture with a nucleic acid vector that includes a homologous recombination cassette fused to an expression system for a selectable marker including a T7 promoter, where, the fused expression system results in disruption of genes in transfected bacteria.

A library also can be generated in vivo. A non-limiting example of a method for generating an output library (a library of Salmonella mutants with therapeutic value, for example) includes intravenously injecting the input library generated by mutagenesis of a wild type, attenuated or previously mutagenized strain (e.g., starting strain mutagenized using any suitable method of nucleic acid mutagenesis; transposon-mediated mutagenesis, for example) into tumor-free mice nude mice and into human PC3 prostate and MDA melanoma tumors growing subcutaneously in nude mice (e.g., xenografts), as described in embodiments described herein. The mutant bacteria in the library are allowed to propagate in the host for a predetermined period of time (e.g., 2 days, 4 days, 7 days, 14 days and the like).

Construction and analysis of knockout mutants

In addition to the mutant libraries described above, one or more knockout mutants can be generated and can be included in a library. As described in the Examples section hereafter, a knockout mutant library was generated having greater than about 1200 knockout mutants. The term "knockout" mutant" as used herein refers to a partial or complete deletion of a nucleic acid sequence associated with a particular gene, which results in loss of the activity associated with and/or encoded by the deleted nucleic acid sequences, when compared to a native or wild type counterpart. As described herein, the term "native sequence" refers to an unmodified nucleotide PATENT VIV-1002-PC

sequence as found in its natural setting (e.g., a nucleotide sequence as found in an organism). The deleted sequence sometimes includes a promoter element, a regulatory element (e.g., upstream or downstream untranslated regions (UTR's), ribosome binding sites, termination sequences, polyadenylation signals, enhancer sequences, repressor sequences and the like), an open reading frame (e.g., ORF, sequence that encodes a given protein or activity), and the like and combinations thereof.

Knockout mutants can be generated by specific homologous recombination of a target gene by a selection cassette (e.g., kanamycin or chloramphenicol cassette). A cassette can be configured to be adapted to any targeting sequence desired and sometimes includes a T7 promoter sequence to allow analysis of the deletion boundaries using methods substantially similar to those described above for the transposon-mediated mutant library. Using such procedures, specific details of genes disrupted by knockout are presented in the Examples section hereafter and FIG. 4.

Mutant bacteria analysis and identification

Any suitable method to identify or analyze (e.g., screen) the resultant mutant population in generated libraries can be used. Non-limiting examples of methods suitable for use in identifying or screening mutant libraries include microarray analysis, sequencing methods (e.g., high throughput sequencing (e.g., pyrosequencing, nanopore based sequencing methods (e.g., sequencing by synthesis)), sequencing by ligation, sequencing by hybridization, microsequencing (primer extension based polymorphism detection), and conventional nucleotide sequencing (e.g., dideoxy sequencing using conventional methods)), mass spectrometry analysis, microarray analysis (e.g., microarray primer extension methods (e.g., microarray sequence determination methods)), and the like and combinations thereof.

Microarray analysis often allows a user to rapidly screen large numbers or pools of nucleic acids, to identify the presence, absence or quantity of a particular nucleic acid species (e.g., gene, genome or nucleic acid of interest). Microarray analysis can be, and often is, used in conjunction with or combined with other screening methods (e.g., sequencing, primer extension, mass spectrometry, the like and combinations thereof). Embodiments described herein sometimes combine microarray analysis and T7 polymerase directed nucleic acid synthesis to determine both the fitness of mutants in a library and the nature and/or position of the disrupted gene. PATENT VIV-1002-PC

Microarray analysis can be used to identify mutants present in a mutant library (e.g., transposon- mediated mutant "input" library). An input library is a library that represents the entire population of mutagenized non-essential genes. Such a method, described briefly here and in further detail in Example 1 , includes (1) extracting DNA from the bacteria in the library; (2) contacting the extracted DNA with RNA polymerase operable on the T7 promoters contained in the transposon insert to obtain RNA, which is then amplified using primers appropriate to the sequences contained in the transposon inserts (see FIG. 1); and (3) contacting the amplified nucleic acid (e.g., RNA, DNA) with a microarray on which is displayed the various genetic components of the starting or host bacterial strain (e.g., the strain on which mutagenesis was performed). The amplified RNA frequently contains at least a remnant of the gene that has been disrupted, such that the disrupted gene often can be identified. In some embodiments, the RNA is labeled directly during amplification (e.g., a 1 step process) or amplified and then labeled by a fluorophore during reverse transcription (e.g., a 2 step process).

A similar method can be used to identify mutants present in an "output" library, with the addition of a step involving passage through normal or tumor tissue prior to extraction of DNA in step (1 ), described above. As noted above, output libraries contain the surviving mutagenized bacteria after exposure to selective pressure (e.g., antibiotic, environment or microenvironment, targeting and/or colonization of a specific favorable environment, the like and combinations thereof). Any selection suitable for isolating mutant bacteria with a desired phenotype or characteristic can be used. In some embodiments, the selection used is survival in a specific tissue. Any suitable normal or tumor tissue can be used to generate an output library. Non-limiting examples of cells or tissue in which output libraries can be generated include normal tissues (e.g., spleen, lung, liver and the like) and tumor specific tissues (e.g., PC3 human prostate cells, MDA-MB-455 human melanoma cells, 4T1 breast tumor cells and the like).

Tissues often are isolated from subjects (e.g., normal tissue or tumor tissue) after a mutated bacteria are administered. Tissues sometimes are isolated after a predetermined growth or incubation period, homogenized and treated with culture broth containing the appropriate selective marker (e.g., kanamycin or chloramphenicol), and the supernatants (e.g., containing bacteria) are recovered. Steps (2) and (3) described above are then performed to identify the surviving mutants in the "output" library. In certain embodiments, a single subject can provide normal and tumor specific tissue (e.g., subjects bearing xenografts). In some embodiments, the labeled RNA or cDNA from the input and output libraries are mixed together and are simultaneously contacted with PATENT VIV-1002-PC

a microarray on which is displayed the various genetic components of the bacterial strain. For each gene, signals of the input library and/or output library can be directly compared on a 2-color microarray system. Microarray analysis as described above can be used to quantify the fitness of each individual mutant in tumors and normal tissues, in certain embodiments. Spontaneous and orthotopic tumors could also be used, in some embodiments.

As noted above, the transposon-mediated mutants and knockout mutants were generated using nucleic acid vectors that included T7 promoters. The T7 promoters were included to provide a method for RNA production from a site at or near the boundary of the disruption caused by the transposon or homologous recombination cassette. The RNA produced can be directly sequenced and/or used in hybridization analysis, in some embodiments, or can serve as the template for cDNA synthesis, which can then be further analyzed (e.g., sequencing, hybridization, mass spectrometry, and the like and combinations thereof), in certain embodiments.

The mutant genes remaining in the library populations (e.g., input library or output library of knockout or transposon-mediated mutants) are contacted with a microarray representative of the genome of the desired host organism (e.g., wild type, attenuated or previously isolated mutant organism; Salmonella, for example). A microarray can be utilized for determining whether a particular nucleotide species is present or absent in a nucleic acid sample. Methods for making a microarray suitable for use with methods and compositions described herein are known and often involve immobilizing nucleic acids representative of the genome of the desired organism to a solid support. The nucleic acids may be linked to the solid support by covalent bonds or by non- covalent interactions. The nucleic acids may also be linked to the solid support directly or by a spacer molecule. In certain embodiments, the nucleic acids extracted from mutant bacteria are contacted with the microarray under conditions of low, medium or high stringency.

Mutagenized bacteria that fail to survive, or survive only poorly, can be identified because there is a low level or non-existent level (e.g., below the level of detection by microarray) of nucleic acid derived from the T7 promoter in the nucleic acid used for mutagenesis, in that bacteria. That is, the disrupted gene detected in the input library microarray is not present or is present at a low level (e.g., the signal generated at the location of the relevant gene is diminished), in the output library or when compared to a non-mutagenized or native gene, and therefore will not produce a hybridization signal for that particular gene. In those rare cases where the fitness or survival of a mutant is enhanced, the signal (e.g., hybridization signal) seen in the microarray will be greater PATENT VIV-1002-PC

than that of the input library control. Examples of results typical of microarray analysis of a library of mutants selected for decreased virulence and increased tumor fitness are shown in FIGS. 2 and 3, and are described further herein.

The data provided in the tables presented in FIGS. 2 and 3 are representative of an input library of greater than about 40,000 random transposon insertion mutants prepared in Salmonella (e.g., approximately 10 insertions per gene), and generally show the base 2 logarithm of the ratio of the intensity of the signal obtained from the mutant in the test sample (e.g. output library after passage through a host) divided by the signal from the corresponding mutant in the input library. Large negative numbers represent poor survival and smaller negative numbers represent essentially no change in ability to survive. A positive value represents enhanced fitness.

Competitive growth fitness assay

Analytical methods described above (e.g., microarray analysis, sequencing analysis) can be used with other methods of analysis, virulence assays or competitive growth assays, for example. In some embodiments, bacterial fitness of mutant strains when compared to each other as measured by microarray can be predictive of bacterial growth in vivo, when competitive growth fitness assays are performed. Competitive growth fitness assays are described herein and below in Example 1.

As with the microarray fitness assays performed on the output libraries, virulence assays, and/or survivability or competitive growth assays described herein can be performed on pools of mutants, in some embodiments. The fitness assays described herein offer advantageous features (e.g., the ability to screen pooled mutants, while simultaneously monitoring the relative ability to survive in tumors) that facilitate screening thousands of candidates and evaluating individual mutants in parallel, in certain embodiments. A competitive fitness assay can be performed using a modification of the virulence assay described herein and in Example 1.

The competitive fitness of a class 1 mutant, STM3120, identified also as being severely attenuated was evaluated against severely attenuated class 2 mutants aroA and aroD. Equal amounts of each strain were mixed (e.g., 1 :1 ratio of STM3120:aroA or STM3120:aroD) and about 1X10⁶ CFU of the mixture were injected in nude mice bearing human PC3 prostate tumors growing subcutaneously. The inoculated bacteria were allowed to propagate and input ratios were compared with output ratios recovered from tumor biopsies performed 2 days, 4 days or 7 days after inoculation. The results of the competitive fitness assay are presented in FIG. 5 and PATENT VIV-1002-PC

described in further detail in the examples. Strains altered in STM3120 out competed (e.g., are more fit) aroA and aroD mutants (e.g., STM3120>aroA>aroD; see FIG. 5), consistent with microarray data showing that STM3120 is more fit than aroA and aroD in tumors (e.g., STM3120>aroA>aroD; see FIG. 2). STM3120 was chosen as a proof of concept for showing the feasibility of engineering Salmonella strains for cancer therapies, however other class 1 mutants (e.g., SPI-2 genes, htrA, and the like) can be used, in some embodiments.

Characteristics of mutant bacteria

As noted above, any suitable mutagenesis method can be used to generate mutant bacteria or mutant bacterial libraries. In certain embodiments described herein, transposon-mediated mutagenesis is utilized to generate a mutagenized "input" library. Transposon mediated mutagenesis sometimes disrupts essential genes and sometimes disrupts non-essential genes. Mutants disrupted in essential genes generally are non-viable and are lost from the population. Non-essential genes grown under non-selective conditions are maintained in the population and can be screened for desire phenotypes. Non-limiting examples of phenotypes desirable for use in medical therapies include reduced virulence, reduced general fitness, substantially normal or increased fitness in a desired tissue or environment in a subject (e.g., blood, tumor, lungs, gastrointestinal tract, pancreas, liver, kidneys, brain, muscle, vascular system, heart, and the like and combinations thereof), altered responsiveness to the environment or microenvironment (e.g., increased or decreased responsiveness to conditions in various organs and/or tissues, such as oxygen, nutrients, protection from the immune system of the subject, and the like), altered motility, altered chemotaxic response, and capability to act as an engineered delivery vehicle, the like and combinations thereof. Mutant libraries generated using methods described herein, or generated using other mutagenesis methods known, can be screened for mutagenized bacteria disrupted in a gene that encodes a function or activity that is directly or indirectly involved with a phenotype or characteristic desirable for use in bacteria-based medicaments.

In certain embodiments, disrupted genes sometimes directly or indirectly increase in function or activity. Mutations sometimes, increase the production of an activity or function, increase the efficacy of an activity or function (e.g., increase the kinetics of a reaction associated with an activity or function (e.g., binding, catalysis or turnover, and the like and combinations thereof)), decrease turnover of the function or activity, and the like and combinations thereof. In some embodiments, disrupted genes sometimes directly or indirectly decrease in function or activity. Mutations PATENT VIV-1002-PC

sometimes decrease the production of an activity or function, decrease the efficacy of an activity or function (e.g., decrease the kinetics of a reaction associated with an activity or function (e.g., binding, catalysis or turnover, and the like and combinations thereof)), increase turnover of the function or activity, and the like and combinations thereof. The nucleic acids from disrupted genes with desirable phenotypes sometimes can be isolated by recombinant DNA methods for use on nucleic acid vectors.

Any disrupted nucleic acid having suitable phenotypic characteristics for use as a bacterial based medicament, can be isolated for use in nucleic acid vectors, in some embodiments. Non-limiting examples of disrupted nucleic acids (or their native counterparts) that can be isolated include aral (arabinose polymer transporter), araC (bacterial regulatory helix-turn-helix proteins), cheZ (CheY protein phosphatase), cheY (chemotaxis regulator), cheB (response regulator for chemotaxis (cheA sensor)), uvrY (putative response regulator) and yfcH (putative sugar nucleotide epimerase). In some embodimentsprovided are isolated nucleic acid molecules that encode polypeptides selected from the group including aral (arabinose polymer transporter), araC (bacterial regulatory helix-turn-helix proteins), cheZ (CheY protein phosphatase), cheY (chemotaxis regulator), cheB (response regulator for chemotaxis (cheA sensor)), uvrY (putative response regulator) and yfcH (putative sugar nucleotide epimerase).

Mutations identified in mutagenized bacterial libraries

Methods described herein can be used to identify any genes potentially useful for a bacterial based medicament. The methods described herein can be used with any bacterial genus or species. Embodiments described herein use Salmonella Typhimurium strain 14028 as the basis for generating a mutant bacterial library. Data presented in FIGS. 2 and 3, and described further in the examples, show that the surviving mutants (e.g., output library mutants) can be categorized into distinct classes of phenotypes: class 1 mutants, which contains mutants with reduced fitness in organs (spleen, liver and lung) and unchanged fitness in tumors. 19 class 1 mutants are localized to a region of the Salmonella chromosome known as the Salmonella pathogenicity island 2 (SPI-2); class 2 mutants, which contains mutants with reduced fitness both in organs (spleen, liver and lung) and in tumors; class 3 mutants, which contains mutants with enhanced fitness in tumors and no apparent effect in normal tissues; and class 4 mutants, which contain mutants with the same fitness as wild type in normal tissues but reduced fitness in tumors, and not discussed further herein. Class 1 mutants and combinatorial class 1/ class 3 mutants (e.g., mutations of each PATENT VIV-1002-PC

class combined in a single bacterial genome) may provide mutant bacteria (e.g., attenuated and/or engineered bacteria) suitable for use in cancer therapies described herein.

Non-limiting examples of genes altered (e.g., mutagenized, deleted) in class 1 mutants include genes from the SPI-1 gene family (e.g., ssrA, ssaB, ssaC, ssaD, sseB, sscA, sseC, sseD, sseE, ssaJ.ssaK, ssaL, ssaM, ssaV, ssaN, ssaP, ssaQ, yscR, ssaT and STM1410), OmpF, yebC, rfbl, rfbA, rfbD, asmA, sixA, srlR, yhdP, tufA, rfaK, rfaJ, rfal, rfaB, mgtC, trxA, wzzE, ubiB, trkH, purH, STM1410, STM0278, STM4262, STM4258, STM3118, STM3119, STM3120, STM3121 , ddlB, htrA, cyoA, sdhA, sifA, phoP, rfc, sufA, a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes.. In some embodiments, a genetic mutation includes an alteration to a gene selected from ssrA, ssaB, ssaC, ssaD, sseB, sscA, sseC, sseD, sseE, ssaJ.ssaK, ssaL, ssaM, ssaV, ssaN, ssaP, ssaQ, yscR, ssaT, STM1410, ompF, yebC, rfbl, rfbA, rfbD, asmA, sixA, srlR, yhdP, tufA, rfaK, rfaJ, rfal, rfaB, mgtC, trxA, wzzE, ubiB, trkH, purH, STM1410, STM0278, STM4262, STM4258, STM3118, STM3119, STM3120, STM3121 , ddlB, htrA, cyoA, sdhA, sifA, phoP, rfc, sufA, a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes. In certain embodiments, a genetic mutation includes an alteration to a gene in the SPI-2 gene cluster, a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes. In some embodiments, a genetic mutation includes an alteration to a gene in the SPI-3 gene cluster, a substantially identical gene of a gene in the cluster, or an associated regulatory element of a gene in the cluster or a substantially identical gene thereof.

Activities encoded by genes in Class 1 have a wide variety of functions. Non-limiting examples of activities encoded by genes of class 1 include; a secretion system activity (e.g., bacterial type III secretion system); a bacterial transcriptional regulator activity, a magnesium transport activity; a amino acid ligase activity (e.g., D-alanine-D-alanine ligase); a protease activity (e.g., serine protease (e.g., periplasmic, cytoplasmic, organelle associated), other known or putative proteases); an oxidase activity (e.g., Cytochrome o ubiquinol oxidase); a structural protein activity; a polymerase activity (e.g., O-antigen polymerase); a reductase activity (e.g., CDP-6-deoxy- delta3,4-glucose reductase); a pyrophosphorylase activity (e.g., dTDP-glucose pyrophosphorylase); a sugar synthetase activity (e.g., TDP-rhamnose synthetase); a sugar transferase activity (e.g., a glucose or galactose sugar transferase, UDP-D- PATENT VIV-1002-PC

glucose:(galactosyl)lipopolysaccharide glucosyltransferase, UDP-D- galactose:(glucosyl)lipopolysaccharide-alpha-1 ,3-D-galactosyltransferase); an oxidase activity (e.g., a monoamine oxidase); an activity that suppresses mutants of outer membrane protein assembly (e.g., a suppressor of porin (ompF) assembly mutants); a hydrolase activity (e.g., acetyl- CoA hydrolase); a phosphatase activity (e.g., phosphohistidine phosphatase); a transcriptional repressor activity (e.g., a glucitol operon transcriptional repressor); a protein synthesis chain elongation activity (e.g., protein synthesis chain elongation factor EF-Tu); a potassium uptake activity (e.g., potassium transport); a chemotaxis activity (e.g., methyl-accepting chemotaxis protein (MCP)); an exporter activity (e.g., an ABC-type bactehocin/antibiotic exporter); a dehydrogenase activity (e.g., succinate dehydrogenase); a redox factor activity (e.g., thioredoxin 1); a polysaccharide chain length modulator activity (e.g., enterobacterium common antigen (ECA) polysaccharide chain length modulator); and a Hes-B like domain activity. In some embodiments, a genetic mutation modulates one or more of such activities.

Non-limiting examples of genes altered in class 2 mutants include: rfbK, rfbM, rfbC, rfaQ, aroM, aroD and aroA. Non-limiting examples of activities encoded by genes of class 2 include aromatic compound synthesis activities and lipo-polysaccharide synthesis activities. Non-limiting examples of genes altered in class 3 mutants include; barA, sirA and cheZ. Non-limiting examples of activities encoded by genes of class 3 include a sensory histidine kinase activity, response regulator activity and chemotaxis activities.

In certain embodiments, a high throughput method for identifying a bacterial strain that selectively infects tumor tissue in comparison to normal tissue, includes: (a) providing an input library of bacteria that are mutants of a wild type strain, (b) administering the library to tumor-bearing subjects and to normal subjects, (c) recovering DNA from bacteria that have survived in tumor tissue of the tumor-bearing subject and that have survived in the tissues of the normal subject, and (d) analyzing the DNA obtained in (c) by microarray analysis against a panel containing parts or all of the genome of a bacteria that preferentially survive in tumor as compared to normal tissue. In some embodiments, bacteria (e.g., attenuated bacteria, engineered bacteria, attenuated and engineered bacteria) that selectively infect tumor tissue, in comparison to normal tissue, are identified by a high throughput method including (a) providing an input library of bacteria that are mutants of a wild type strain, (b) administering the library to tumor-bearing subjects and to normal subjects, (c) recovering DNA from bacteria that have survived in tumor tissue of the tumor-bearing subject and that have survived in the tissues of the normal subject, and (d) analyzing the DNA PATENT VIV-1002-PC

obtained in (c) by microarray analysis against a panel containing probes encompassingpart or all of the genome of the wild type bacterial genome to determine mutations in genes or associated regulatory elements of bacteria that preferentially survive in tumor as compared to normal tissue.

In certain embodiments, a method to identify a bacterial strain that will selectively infect tumor tissue, with respect to normal tissue, includes (a) providing an input library of mutant bacteria comprising transposons fused to an expression system for a selectable marker; wherein said fused expression system results in disruption of genes in said mutants; (b) administering the input library to tumor-bearing laboratory animals and normal control laboratory animals; (c) extracting DNA from bacteria grown under selection conditions recovered from tumor tissue of the tumor-bearing animals and from the organs of the normal control animals and optionally from the input library to obtain extracted DNAs; (d) contacting the each of the extracted. DNAs with a polymerase operable on the expression system to obtain RNA containing segments of the disrupted genes; (e) amplifying and labeling said RNA, or amplifying, reverse transcribing and labeling resulting cDNA; (f) analyzing the RNA or cDNA of (e) by comparison to a genomic library characteristic of said bacteria to determine the genes that have been disrupted in the input library and in the bacteria that have been recovered from tumor tissue and in the bacteria that have been recovered from normal organs in (c); and (g) identifying disrupted genes that are present at higher levels in bacteria recovered from tumor tissue as compared to normal organs as characteristic of bacteria that selectively infect tumor tissue.

In some embodiments, a method for obtaining an attenuated strain of bacteria includes administering a library of mutant bacteria to a multiplicity of subjects, and identifying a mutant strain that is present in the tissues of a subject having a predetermined survival time. In certain embodiments, an attenuated bacteria is identified by a method that includes, administering a library of mutant bacteria to a multiplicity of subjects, and identifying a mutant strain that is present in the tissues of a subject having a predetermined survival time.

In some embodiments, a sequence is a substantially identical gene, substantially identical nucleic acid sequence or substantially identical amino acid sequence. In certain embodiments, a substantially identical gene or nucleotide sequence may include a polynucleotide sequence or amino acid sequence 80% or more identical to a particular nucleotide sequences (or to the complementary sequence), and/or amino acid sequence associated with an activity described herein. In some embodiments, a substantially identical nucleotide sequence is about 80% or more, PATENT VIV-1002-PC

81% or more, 82% or more, 83% or more, 84% or more, 85% or more, 86% or more, 87% or more, 88% or more, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more, or 99% or more identical to a particular nucleotide sequence and/or amino acid sequence associated with an activity described herein. The term "identical" as used herein refers to two or more nucleotide sequences having substantially the same nucleotide sequence when compared to each other. One test for determining whether two nucleotide sequences or amino acids sequences are substantially identical is to determine the percent of identical nucleotide sequences or amino acid sequences shared.

Calculations of sequence identity can be performed as follows. Sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The length of a reference sequence aligned for comparison purposes is sometimes 30% or more, 40% or more, 50% or more, often 60% or more, and more often 70% or more, 80% or more, 90% or more, or 100% of the length of the reference sequence. The nucleotides or amino acids at corresponding nucleotide or polypeptide positions, respectively, are then compared among the two sequences. When a position in the first sequence is occupied by the same nucleotide or amino acid as the corresponding position in the second sequence, the nucleotides or amino acids are deemed to be identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, introduced for optimal alignment of the two sequences.

Comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. Percent identity between two amino acid or nucleotide sequences can be determined using the algorithm of Meyers & Miller, CABIOS 4: 11-17 (1989), which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. Also, percent identity between two amino acid sequences can be determined using the Needleman & Wunsch, J. MoI. Biol. 48: 444-453 (1970) algorithm which has been incorporated into the GAP program in the GCG software package (available at the http address www.gcg.com), using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1 , 2, 3, 4, 5, or 6. Percent identity between two nucleotide sequences can be determined using the GAP PATENT VIV-1002-PC

program in the GCG software package (available at http address www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1 , 2, 3, 4, 5, or 6. A set of parameters often used is a Blossum 62 scoring matrix with a gap open penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.

Sequence identity can also be determined by hybridization assays conducted under stringent conditions. As use herein, the term "stringent conditions" refers to conditions for hybridization and washing. Stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y., 6.3.1-6.3.6 (1989). Aqueous and non- aqueous methods are described in that reference and either can be used. An example of stringent hybridization conditions is hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45⁰C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 5O⁰C. Another example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45⁰C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 55⁰C. A further example of stringent hybridization conditions is hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45⁰C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 6O⁰C. Often, stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45⁰C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 65⁰C. More often, stringency conditions are 0.5M sodium phosphate, 7% SDS at 65⁰C, followed by one or more washes at 0.2X SSC, 1% SDS at 65⁰C.

Virulence assay

Bacteria suitable for use as cancer therapeutics sometimes have normal or increased fitness with respect to tumor cells or tissue with decreased fitness with respect to normal tissue, and are relatively safe for the intended subject. Bacterial strains generated for cancer therapies generally do not have a deleterious affect on the infected subject. Many wild type bacterial strains having suitable characteristics for host organism colonization often are virulent and therefore capable of negatively affecting the infected subject.

Methods described herein can be used to identify any bacterial strain (e.g., native, attenuated or engineered) with reduced virulence (e.g., avirulent strains, attenuated strains) can be identified using methods described herein. A starting bacterial strain can be mutagenized using known methods or isolated using genetic selection, serial passage, mating, the like and combinations PATENT VIV-1002-PC

thereof. The mutagenized or isolated strain can then be used to infect a suitable host to determine the level of virulence reduction achieved by mutagenesis or selection. The level of virulence can be determined by observation of the level of distress, or the death of the infected host. Additionally, multiply mutant strains (e.g., strains that have been engineered and/or mated to accumulate two or more mutations that are suitable for use in a bacterial medicament), can be tested for additional or synergistic affects of the multiply mutant background by a substantially similar method. The term "avirulent bacteria" as used herein refers to bacteria that do not cause significant, substantial, or detectable distress or condition, and do not cause death, in an infected host and do not cause a significant competitive disadvantage to infected non-cancer cells and/or non-tumor tissues when compared to uninfected non-cancer cells and/or non-tumor tissues. In certain embodiments, an avirulent bacteria can be virulent to a target cell and/or target tissue (e.g., a diseased cell, a cancer cell, a tumor tissue). The term "attenuated bacteria" as used herein refers to bacteria with reduction in one or more activities. Avirulence sometimes is a form of attenuation, in some embodiments, and in certain embodiments, attenuation sometimes is a form of avirulence.

A non-limiting embodiment of a method for identifying bacterial strains with reduced virulence, and the results typically obtained using the method is described briefly herein, and presented in more detail in FIG. 4 and the examples. Knockout mutants of sixteen genes identified as class 1 or class 2 mutants and three genes identified as having no observable phenotype (e.g., null phenotype mutant), were generated as described herein (see FIG. 4 for a listing of the deleted genes, tissue specificity and virulence). Each mutant was injected (e.g., about 1x10⁵ colony forming units (CFU)) into mice known to be particularly sensitive to Salmonella infection (e.g., C57BU6 mice). The use of C57BL/6 mice ensured a stringent test of virulence. The mice were observed over the course of infection, and each mutant assigned to one of three categories based on survival of the infected mice: virulent, mildly attenuated or severely attenuated (e.g., avirulent).

Based on the Salmonella strain used in the embodiment described herein, strains categorized as virulent typically caused distress, dehydration and death within about one or two days after inoculation. Wild type Salmonella used as a control and strains with deletions of genes having no observable phenotype (e.g., STM1459, ybnJ and feoB) caused death within about one or two days. Mildly attenuated strains caused signs of distress two to six days after inoculation. Strains with deletions of STM3119, rfbl, rfaQ, rfbK, rfbM, phoP, and sfiA caused signs of distress within about two to six days after inoculation. Severely attenuated or avirulent strains did not cause signs of distress and infected mice survived for up to four weeks. Strains with deletions of genes in SPI-2, PATENT VIV-1002-PC

htrA, STM3120, aroA and aroD showed no signs of distress and survived up to four weeks. Therefore, several class 1 mutants (reduced fitness in normal tissue and normal fitness in tumor tissue) also are severely attenuated.

Tumor targeting

As noted above, bacteria suitable for use as cancer therapeutics sometimes have normal or increased fitness in tumor cells with decreased fitness in normal tissue and should also be safe for the intended subject. Of additional benefit as a cancer therapeutic is the ability of mutated bacteria to preferentially target and/or colonize tumor tissue. Methods described herein can be used to identify, isolate and/or generate mutant bacteria with increased tumor targeting ability, increased capability for chemotaxis, increase tumor colonization capability, the like and combinations thereof. The method can also be used with multiply mutant strains (e.g., strains that have been engineered and/or mated to accumulate two or more mutations that are suitable for use in a bacterial medicament), to test for additional or synergistic affects of the multiply mutant background.

A non-limiting embodiment of a method for identifying bacterial strains with increased tumor targeting, chemotaxis and/or tumor colonization, and the results typically obtained using the method is described briefly herein, and presented in more detail in FIG. 5 and the examples. A strain identified as having reduced virulence was chosen to investigate tumor targeting and colonization fitness. The chosen strain (e.g., class 1 mutant STM3120) was inoculated into five BALB/c mice bearing 4T1 breast tumors orthotopically grown for ten days. Mice were gavaged with 7X10⁸ CFU of STM3120, and tumor biopsies taken at 2, 5, 7, and 9 days. Bacterial counts were determined on the biopsies. Bacteria were detected in tumor biopsies of 3 mice after 7 days and in all 5 mice after 9 days (see FIG. 5), suggesting that intragastric delivery of a class 1 mutant allows a sufficient number of bacteria to target and multiply in the tumor environment, to levels known to effectively reduce tumor size after injection intratumorally or intravenously. Additional details are presented below in the examples.

In some embodiments, the method for identifying and/or selecting bacterial strains and mutants that selectively target and/or colonize tumors can be used to identify and/or select strains and mutants that target any specific tissue (e.g., spleen, lung, liver, kidney and colon). In certain embodiments, engineered bacteria can be used to treat tissue-specific disease conditions such as anoxic ischemia. In some embodiments, the selection method includes (a) construction of a library PATENT VIV-1002-PC

of bacterial mutants each carrying one or more DNA insertions in tumors; (b) production of RNA from an RNA polymerase promoter in such inserts; (c) hybridization of nucleic acids derived from an RNA polymerase promoter; (d) comparing this data to that obtained from bacteria growing in other parts of the body to identify mutations that demonstrate enhanced fitness in tumors and reduced fitness in tissues. In certain embodiments, sequencing can be performed directly to the DNA sample recovered from tumors and tissues, or any other method that amplifies DNA or RNA directly adjacent to the site of DNA insertion. In some embodiments, bacteria engineered as described herein can be administered orally and preferentially propagate inside tumor tissue to reach an effective amount to have a therapeutic affect on a tumor.

Bacteria

Methods described herein can be utilized to identify and/or generate bacteria (e.g., engineered bacteria, attenuated bacteria, or engineered and attenuated bacteria) useful for various medical treatments, including cancer therapy. Methods described herein can be used to identify and/or generate bacteria that are substantially avirulent (e.g., virulence is severely reduced or substantially eliminated), have reduced fitness in normal tissues and substantially normal fitness or increased fitness in tumor tissues and preferentially target and/or colonize tumor tissue. The starting bacteria can be a wild type strain, an attenuated strain (e.g., a strain with a reduction in an activity, where the activity may or may not be related to virulence, fitness in normal and tumor tissues or tumor targeting) or a mutant strain (e.g., engineered or naturally occurring).

The term "engineered bacteria", "engineered bacterium", "mutagenized bacteria" or "mutagenized bacterium", derivatives and grammatical equivalents thereof, as used herein refers to a modified bacteria that includes one or more gene sequences (e.g., nucleic acid sequences) or activities distinct from a nucleic acid sequence or activity present in the bacteria utilized as a starting point for modification or alteration (e.g., host bacteria, wild type counterpart). An engineered bacteria includes a heterologus polynucleotide in some embodiments, and in certain embodiments, an engineered bacteria has been subjected to selective conditions that alter an activity, or introduce an activity, relative to the host bacteria. Thus, an engineered bacteria has been altered directly or indirectly by a human being. A host bacteria sometimes is a native or wild type bacteria, and at times is a bacteria that has been engineered to a certain point. PATENT VIV-1002-PC

Many bacteria are known to exist on or within organisms, sometimes in a beneficial capacity and sometimes in a pathogenic capacity. Any suitable bacteria that can survive in a subject can be used as a starting point for generating bacteria useful for medical treatment. Pathogenic bacteria have evolved mechanisms for cell and tissue infiltration and survival in an infected host, making 5. them useful candidates for modification for use in medical treatments. Enteric bacteria generally are rod-shaped Gram-negative bacteria. Most enteric bacteria occur normally or pathogenically in intestines of humans and other animals. Many enteric bacteria are anaerobic. Enteric bacteria include the genus Eschericia, Salmonella, Klebsiella, Shigella, and Erwinia, for example. Non- limiting examples of bacterial genus suitable for use with methods and as compositions described0 herein include Erwinia Lactobacillus, Bifidobacteria, Streptococus, Clostridium, Listeria, Vibrio, Eschericia, Salmonella, Bacillus, Ruminococcus, Bacteroides, Mycobacterium, Pseudomonas, Shigella, Campylobacter, Corynebacterium, Streptomyces, Klebsiella and the like.

A bacteria selected often is suitable for genetic manipulation. In some embodiments, the 5 bacterium selected for engineering is a pathogenic bacterium. In certain embodiments the bacterium selected for engineering is an enteric bacterium. In some embodiments, the bacterium selected for engineering is a Salmonella bacterium. Non-limiting examples of Salmonella species include S. enterica (subspecies, I (e.g., enterica), Il (e.g., salmae), HIa (e.g., arizonae), IHb (e.g., diarizonae), IV (e.g., houtenae), Vl (e.g., indica)), S. bongori, (e.g., formerly known as S. enterica,0 subspecies V), S. typhimurium (and strains, serovars and or subspecies). The selected bacterium can be attenuated and/or mutagenized (e.g., engineered), as described herein, in certain embodiments. In some embodiments the selected bacterium is a wild type bacterium. In certain embodiments, the selected bacterium can be an attenuated bacterium, and in some embodiments, the selected bacterium can be a mutant bacterium. 5

In certain embodiments, technology described herein provides genetically engineered bacterial strains with enhanced fitness including one or more of the following properties: (i) enhanced accumulation of bacterial cells in solid tumors; (ii) enhanced colonization and growth in solid tumors; (iii) improved tumor killing; (iv) reduced colonization of bacterial strains in non-tumor cells0 or tissue; and (v) increased therapeutic efficacy.

In some embodiments, technology described herein provides genetically engineered bacterial strains that contain genetic disruption of one or more bacterial genes selected from the group including araJ (arabinose polymer transporter), araC (bacterial regulatory helix-turn-helix proteins), PATENT VIV-1002-PC

cheZ (CheY protein phosphatase), cheY (chemotaxis regulator), cheB (response regulator for chemotaxis (cheA sensor)), uvrY (putative response regulator) and yfcH (putative sugar nucleotide epimerase) which results in bacteria, possessing an enhanced fitness as compared to the host bacteria.

In certain embodiments, technology described herein provides genetically engineered bacterial strains that contain genetic disruption of one or more bacterial genes selected from the group including aral (arabinose polymer transporter), araC (bacterial regulatory helix-turn-helix proteins), cheZ (CheY protein phosphatase), cheY (chemotaxis regulator), cheB (response regulator for chemotaxis (cheA sensor)), uvrY (putative response regulator) and yfcH (putative sugar nucleotide epimerase) which results in bacteria, possessing an enhanced fitness as compared to the host bacteria. Engineered bacteria generated as described herein also may have enhanced fitness with respect to accumulation and replication in tumor tissues, may be useful for inhibiting the growth and/or reducing the tumor volume of sarcomas, carcinomas, lymphomas or other solid tumor cancers, such as germ line tumors and tumors of the central nervous system, including, but not limited to, breast cancer, prostate cancer, cervical cancer, uterine cancer, lung cancer, ovarian cancer, testicular cancer, thyroid cancer, astrocytoma, glioma, pancreatic cancer, stomach cancer, liver cancer, colon cancer, and melanoma.

In some embodiments, a Salmonella is provided having a disrupted gene or gene product selected from the group including araJ (arabinose polymer transporter), araC (bacterial regulatory helix-turn- helix proteins), cheZ (CheY protein phosphatase), cheY (chemotaxis regulator), cheB (response regulator for chemotaxis (cheA sensor)), uvrY (putative response regulator) and yfcH (putative sugar nucleotide epimerase), and co-expresses a chemotherapeutic agent or DNA damaging agent. In certain embodiments, the chemotherapeutic agent is cytosine deaminase (CodA) and/or other protein based drugs including cytokines and toxins.

In some embodiments, genetically engineered bacterial strains having a disrupted gene or gene product selected from the group including araJ (arabinose polymer transporter), araC (bacterial regulatory helix-turn-helix proteins), cheZ (CheY protein phosphatase), cheY (chemotaxis regulator), cheB (response regulator for chemotaxis (cheA sensor)), uvrY (putative response regulator) and yfcH (putative sugar nucleotide epimerase), is more resistant to a chemotherapeutic agent. In certain embodiments, the chemotherapeutic agent is 5-fluorouracil (5-FU). PATENT VIV-1002-PC

In certain embodiments, genetically engineered bacterial strains having a disrupted gene or gene product selected from the group including aral (arabinose polymer transporter), araC (bacterial regulatory helix-turn-helix proteins), cheZ (CheY protein phosphatase), cheY (chemotaxis regulator), cheB (response regulator for chemotaxis (cheA sensor)), uvrY (putative response regulator) and yfcH (putative sugar nucleotide epimerase), expresses another biological agent that generates a microenvironment adverse to tumor growth. In some embodiments, the microenvironment has a non-physiological pH or is hypoxic. In certain embodiments, the biological agent is a prodrug. In some embodiments, the biological agent is a therapeutically relevant protein for intracellular assembly, and in certain embodiments, the biological agent is a biological pump.

In some embodiments, technology described herein provides genetically engineered bacteria with reduced accumulation, colonization and/or growth of bacterial cells in non-tumor cells or tissue. In certain embodiments, the reduced accumulation, colonization and/or growth of bacterial cells in non-tumor cells or tissue results in one or more properties selected from (i) reduced toxicity (non- tumor cell killing), (ii) improved tumor specificity and (iii) increased therapeutic efficacy. In some embodiments, genetically engineered bacterial strains have increased therapeutic efficacy (e.g., more (or larger) effective dosages of bacteria can be used and for extended time periods).

In certain embodiments, technology described herein provides genetically engineered bacterial strains that contain a genetic disruption of one or more bacterial genes selected from the group including ssrA, ssaB, ssaC, ssaD, sseB, sscA, sseC, sseD, sseE, ssaJ.ssaK, ssaL, ssaM, ssaV, ssaN, ssaP, ssaQ, yscR, ssaT and STM1410, OmpF, yebC, rfbl, rfbA, rfbD, asmA, sixA, srlR, yhdP, tufA, rfaK, rfaJ, rfal, rfaB, mgtC, trxA, wzzE, ubiB, trkH, purH, STM1410, STM0278, STM4262, STM4258, STM3118, STM3119, STM3120, STM3121 , ddlB, htrA, cyoA, sdhA, sifA, phoP, rfc, and sufA. Such mutations often result in bacteria, possessing a reduced fitness as compared to the wild type or host bacteria.

Pharmaceutical Compositions and Formulations

Engineered bacterial compositions can be prepared as pharmaceutically acceptable medicament. The term "pharmaceutically acceptable medicament" as used here refers to a medicament that includes engineered bacteria as described herein prepared as a freeze dried formulation including a therapeutically effective amount or dosage of bacteria. In some embodiments, the engineered PATENT VIV-1002-PC

bacteria are freeze dried over a glucose carrier. In some embodiments, the engineered bacterial composition is administered orally.

Non-limiting examples of pharmaceutically acceptable medicaments include pill, lozenge, capsule, gel-cap, oral suspension, enema, suppository, nasal spray, and the like. The term

"pharmaceutically acceptable" as used herein refers to compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication commensurate with a reasonable benefit/risk ratio.

In certain embodiments, engineered bacterial compositions as described herein can be formulated in combination with one or more other agents. The one or more other agents can include, without limitation, another compound described herein, an anti-cell proliferative agent (e.g., chemotherapeutic), an anti-inflammatory agent, an immunosuppressant and an antigen. In certain embodiments, engineered bacterial compositions as described herein can be formulated as a pharmaceutical composition and administered to a mammalian host, such as a human patient or animal, in a variety of forms adapted to the chosen route of administration, e.g., orally or parenterally, by intravenous, intramuscular, topical or subcutaneous routes. In some embodiments, an engineered bacterial composition is locally administered, e.g., intravesicularly. Engineered bacterial compositions often include a diluent as well as, in some cases, an adjuvant, buffer, preservative and the like. Engineered bacterial compositions can be administered also in a liposomal composition or as a microemulsion, in certain embodiments. Various sustained release systems for drugs have also been devised, and can be applied to a compound described herein. See, for example, U.S. Patent No. 5,624,677, the methods of which are incorporated herein by reference.

Thus, engineered bacterial compositions may be systemically administered, e.g., orally, in combination with a pharmaceutically acceptable vehicle such as an inert diluent or an assimilable edible carrier. Engineered bacterial compositions described herein may be enclosed in hard or soft shell gelatin capsules, may be compressed into tablets, or may be incorporated directly with the food of the patient's diet. For oral therapeutic administration, the active composition may be combined with one or more excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like. Such compositions and preparations should contain at least 0.1% of active compound. The percentage of the compositions PATENT VIV-1002-PC

and preparations may, of course, be varied and may conveniently be between about 2 to about 60% of the weight of a given unit dosage form. The amount of active compound in such therapeutically useful compositions is such that an effective dosage level will be obtained.

Tablets, troches, pills, capsules, and the like may also contain the following: binders such as gum tragacanth, acacia, corn starch or gelatin; excipients such as dicalcium phosphate; a disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; and a sweetening agent such as sucrose, fructose, lactose or aspartame or a flavoring agent such as peppermint, oil of wintergreen, or cherry flavoring may be added. When the unit dosage form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier, such as a vegetable oil or a polyethylene glycol. Various other materials may be present as coatings or to otherwise modify the physical form of the solid unit dosage form. For instance, tablets, pills, or capsules may be coated with gelatin, wax, shellac or sugar and the like. A syrup or elixir may contain the active compound, sucrose or fructose as a sweetening agent, methyl and propylparabens as preservatives, a dye and flavoring such as cherry or orange flavor. Of course, any material used in preparing any unit dosage form should be pharmaceutically acceptable and substantially non-toxic in the amounts employed. In addition, the active compound may be incorporated into sustained-release preparations and devices.

An active engineered bacterial composition may be administered by infusion or injection. Solutions of an active compound or a pharmaceutically acceptable salt thereof can be prepared in water, optionally mixed with a nontoxic surfactant. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, triacetin, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.

A pharmaceutical dosage form can include an aqueous solution free from unwanted organisms or dispersion or sterile powder comprising an active ingredient, which are adapted for the extemporaneous preparation of sterile solutions or dispersions, and optionally encapsulated in liposomes. The ultimate dosage form sometimes is an aqueous solution free from unwanted organisms and stable under the conditions of manufacture and storage. A liquid carrier or vehicle can be a solvent or liquid dispersion medium comprising, for example, water, ethanol, a polyol (for example, glycerol, propylene glycol, liquid polyethylene glycols, and the like), vegetable oils, nontoxic glyceryl esters, and suitable mixtures thereof. The proper fluidity can be maintained, for PATENT VIV-1002-PC

example, by the formation of liposomes, by the maintenance of the required particle size in the case of dispersions or by the use of surfactants. The prevention of the action of unwanted microorganisms (e.g., microorganisms other than the desired attenuated and/or mutant bacteria) can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. An isotonic agent, for example, a sugar, buffer or sodium chloride is included in some embodiments. Prolonged absorption of an injectable composition can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin. In the case of sterile powders for the preparation of sterile injectable solutions, preparation methods sometimes utilized are vacuum drying and the freeze drying techniques, which yield a powder of an active ingredient in addition to any additional desired ingredient present in the previously sterile-filtered solutions.

For topical administration, engineered bacterial compositions herein may be applied in pure form, e.g., when in liquid form. However, it is generally desirable to administer a compound as a composition or formulation, in combination with an acceptable carrier, which may be a solid or a liquid. Useful solid carriers include finely divided solids such as talc, clay, microcrystalline cellulose, silica, alumina and the like. Useful liquid carriers include water, alcohols or glycols or water-alcohol/glycol blends, in which the present compounds can be dissolved or dispersed at effective levels, optionally with the aid of non-toxic surfactants. Adjuvants such as fragrances and additional antimicrobial agents can be added to optimize the properties for a given use. The resultant liquid compositions can be applied from absorbent pads, used to impregnate bandages and other dressings, or sprayed onto the affected area using pump-type or aerosol sprayers.

Thickeners such as synthetic polymers, fatty acids, fatty acid salts and esters, fatty alcohols, modified celluloses or modified mineral materials can also be employed with liquid carriers to form spreadable pastes, gels, ointments, soaps, and the like, for application directly to the skin of the user. Useful dosages of the compounds can be determined by comparing their in vitro activity, and in vivo activity in animal models. Methods for the extrapolation of effective dosages in mice, and other animals, to humans are known; for example, see U.S. Patent No. 4,938,949.

The amount of the engineered bacterial composition, or medicament derivative thereof, required for use in treatment will vary not only with the particular medicament selected but also with the route of administration, the nature of the condition being treated and the age and condition of the patient and will be ultimately at the discretion of the attendant physician or clinician. In general a PATENT VIV-1002-PC

suitable dose sometimes contains in the range of from about 1X10³ to about 1x10⁹ colony forming units (CFU's) per day, administered in any suitable format (e.g., pill form, oral suspension, nasal spray and the like, or combinations thereof). A desired dose may conveniently be presented in a single dose or as divided doses administered at appropriate intervals, for example, as two, three, four or more sub-doses per day. A sub-dose itself may be further divided, e.g., into a number of discrete loosely spaced administrations; such as multiple inhalations from an insufflator or by application of a plurality of drops into the eye.

Medical Treatments

Engineered bacteria compositions identified and/or generated using methods described herein, can be used in the treatment of various types of cancers and other conditions. Non-limiting examples of cancers that can be treated using engineered bacterial compositions described herein include sarcomas, carcinomas, lymphomas or other solid tumor cancers, such as germ line tumors and tumors of the central nervous system, brain cancer, breast cancer, prostate cancer, cervical cancer, uterine cancer, lung cancer, ovarian cancer, testicular cancer, thyroid cancer, astrocytoma, glioma, pancreatic cancer, stomach cancer, liver cancer, colon cancer, and melanoma. Bacterial compositions engineered and prepared as described herein may be useful for treatment of other disease conditions (e.g., drug delivery vehicles, bacterial mediated genetic therapies and the like), in certain embodiments. Engineered bacteria compositions identified and/or generated using methods described herein may have beneficial uses in the treatment of disease conditions other than cancer (e.g., autoimmune disease, parasitic, bacterial or fungal infection, delivery of drugs or prodrugs to a target site).

In some embodiments, engineered bacteria described herein can be further modified by mating or recombinant DNA techniques to combine disrupted genes that are advantageous for generating engineered bacteria suitable for use in cancer therapeutics. Combination of two or more mutations known to decrease virulence, decrease fitness in normal tissue, increase tumor targeting and fitness in tumors can be employed and result in strains with further beneficial characteristics with respect to cancer treatment (e.g., increased fitness in tumors, decreased fitness in normal tissues, increased or decreased responsiveness to the tumor microenvironment, and the like and combinations there of). PATENT VIV-1002-PC

In certain embodiments, engineered bacteria or libraries thereof can be transfected with nucleic acids having therapeutic value for cancer therapies. Any suitable nucleic acid vector or agent that encodes an activity or nucleic acid that directly or indirectly inhibits growth of a tumor or causes tumor necrosis and/or death can be used. In some embodiments, a nucleic acid vector or agent includes a promoter preferentially active in cancer cells and/or tumor cells. In certain embodiments the nucleic acid vector or agent encodes an activity effective as a cancer therapeutic (e.g., a toxin, a prodrug, a peptide, an enzyme, an antibody fragment, a binding moiety, and the like and combinations thereof), and in some embodiments the nucleic acid vector or agent encodes a nucleic acid (e.g., RNAi, RNAsi, ribozyme, anti-sense nucleic acid, and the like and combinations thereof) effective as a cancer therapeutic. In certain embodiments, the activity and/or the nucleic acid is functionally linked to a tumor-specific or cancer cell-specific promoter. Salmonella promoter sequences preferentially active in tumors or tumor cells are described in commonly owned international patent application PCT/US2009/047285, filed 12 June, 2009, entitled "METHODS TO TREAT SOLID TUMORS", the entire contents of which is incorporated herein by reference, including, without limitation, all text, tables and drawings. In some embodiments, mutant bacteria can be used to deliver drugs or prodrugs to a desired target, and in certain embodiments, mutant or engineered bacteria can be further modified to actively seek specific targets and/or tissues (e.g., modified chemotaxis or recognition of molecules, compounds or moieties on a cell surface).

Engineered bacteria compositions described herein sometimes can be formulated for oral delivery. Data presented herein illustrate orally active engineered bacterial strains proliferating to levels known to have a therapeutic effect in tumors, when delivered intratumorally or intravenously. Thus, engineered bacterial generated using methods described herein can form the basis for orally active pharmaceutical compositions. In some embodiments, technology described herein provides an orally active pharmaceutical composition, including a mutant bacterium that contains a genetic mutation, where the wild type counterpart of the mutant bacterium is virulent against non-cancer cells and/or tissues, the virulence of the mutant bacterium against non-cancer cells and/or tissues is substantially reduced compared to the virulence of the wild type counterpart bacterium against non-cancer cells and/or tissues, and the virulence of the mutant bacterium against cancer cells and/or tissues is not substantially reduced compared to the virulence of the wild type counterpart bacterium against cancer cells and/or tissues.

The terms "treat" and "treating" as used herein refer to (i) preventing a pathologic condition from occurring (e.g. prophylaxis); (ii) inhibiting the pathologic condition or arresting its development; (iii) PATENT VIV-1002-PC

relieving the pathologic condition; and/or (iv) ameliorating, alleviating, lessening, and removing symptoms of a disease or condition. A candidate engineered bacteria, bacterial library or bacterial composition described herein may be in a therapeutically effective amount in a formulation or medicament, which is an amount that can lead to a biological effect (e.g., inhibiting inflammation), or lead to ameliorating, alleviating, lessening, relieving, diminishing or removing symptoms of a disease or condition, for example. The terms also can refer to reducing or stopping a cell proliferation rate (e.g., slowing or halting tumor growth) or reducing the number of proliferating cancer cells (e.g., removing part or all of a tumor), or reducing the spread of tumor cells to other parts of the body. Subjects suffering from certain disease conditions, including cancer, sometimes suffer from secondary infection by microbes. Thus, these terms also are applicable to reducing a titre of a microorganism in a system (i.e., cell, tissue, or subject) infected with a microorganism, . reducing the rate of microbial propagation, reducing the number of symptoms or an effect of a symptom associated with the microbial infection, and/or removing detectable amounts of the microbe from the system. Examples of microorganism include but are not limited to virus, bacterium and fungus.

Engineered bacteria as described herein can be administered to a subject in need thereof to potentially treat one or more medical conditions, including but not limited to a variety of proliferative disorders (e.g., various cancers). In such treatments, the terms "treating," "treatment" and "therapeutic effect" can refer to reducing or stopping a cell proliferation rate (e.g., slowing or halting tumor growth), reducing the number of proliferating cancer cells (e.g., ablating part or all of a tumor) and alleviating, completely or in part, a cell proliferation condition. Cell proliferative conditions and tumor conditions include, but are not limited to, cancers of the colorectum, breast, lung, liver, pancreas, lymph node, colon, prostate, brain, head and neck, skin, liver, kidney, and heart. Non-limiting examples of cancers include hematopoietic neoplastic disorders, which are diseases involving hyperplastic/neoplastic cells of hematopoietic origin (e.g., arising from myeloid, lymphoid or erythroid lineages, or precursor cells thereof). The diseases can arise from poorly differentiated acute leukemias, e.g., erythroblastic leukemia and acute megakaryoblastic leukemia. Additional myeloid disorders include, but are not limited to, acute promyeloid leukemia (APML), acute myelogenous leukemia (AML) and chronic myelogenous leukemia (CML) (reviewed in

Vaickus, Crit. Rev. in Oncol./Hemotol. 11 :267-297 (1991)); lymphoid malignancies include, but are not limited to acute lymphoblastic leukemia (ALL), which includes B-lineage ALL and T-lineage ALL, chronic lymphocytic leukemia (CLL), prolymphocytic leukemia (PLL), hairy cell leukemia (HLL) and Waldenstrom's macroglobulinemia (WM). Additional forms of malignant lymphomas PATENT VIV-1002-PC

include, but are not limited to non-Hodgkin lymphoma and variants thereof, peripheral T cell lymphomas, adult T cell leukemia/lymphoma (ATL), cutaneous T-cell lymphoma (CTCL), large granular lymphocytic leukemia (LGF), Hodgkin's disease and Reed-Sternberg disease. In a particular embodiment, the cell proliferative disorder is non-endocrine tumor or endocrine tumors. Illustrative examples of non-endocrine tumors include but are not limited to adenocarcinomas, acinar cell carcinomas, adenosquamous carcinomas, giant cell tumors, intraductal papillary mucinous neoplasms, mucinous cystadenocarcinomas, pancreatoblastomas, serous cystadenomas, solid and pseudopapillary tumors. An endocrine tumor may be an islet cell tumor. In some embodiments, the mutant bacteria (e.g., engineered bacteria) used to treat a cancer or proliferative disorder is a mutant pathogenic bacteria. In certain embodiments, the mutant bacteria used to treat a cancer or proliferative disorder is a mutant enteric bacteria. In some embodiments, the mutant bacteria used to treat a cancer or proliferative disorder is a mutant Salmonella bacteria.

Cell proliferative conditions also include inflammatory conditions, such as inflammation conditions of the skin, including, for example, eczema, discoid lupus erythematosus, lichen planus, lichen sclerosus, mycosis fungoides, photodermatoses, pityriasis rosea, psoriasis. Also included are cell proliferative conditions related to obesity, such as proliferation of adipocytes, for example.

Cell proliferative conditions also include viral diseases, including for example, Acquired Immunodeficiency Syndrome, Adenoviridae Infections, Alphavirus Infections, Arbovirus Infections, Borna Disease, Bunyaviridae Infections, Caliciviridae Infections, Chickenpox, Coronaviridae Infections, Coxsackievirus Infections, Cytomegalovirus Infections, Dengue, DNA Virus Infections, Ecthyma, Contagious, Encephalitis, Arbovirus, Epstein-Barr Virus Infections, Erythema Infectiosum, Hantavirus Infections, Hemorrhagic Fevers, Viral, Hepatitis, Viral, Human, Herpes Simplex, Herpes Zoster, Herpes Zoster Oticus, Herpesvihdae Infections, Infectious Mononucleosis, Influenza in Birds, Influenza, Human, Lassa Fever, Measles, Molluscum Contagiosum, Mumps, Paramyxoviridae Infections, Phlebotomus Fever, Polyomavirus Infections, Rabies, Respiratory Syncytial Virus Infections, Rift Valley Fever, RNA Virus Infections, Rubella, Slow Virus Diseases, Smallpox, Subacute Sclerosing Panencephalitis, Tumor Virus Infections, Warts, West Nile Fever, Virus Diseases and Yellow Fever. For example, Large T antigen of the SV40 transforming virus acts on UBF, activates it and recruits other viral proteins to Pol I complex, and thereby stimulates cell proliferation to ensure virus propagation. Cell proliferative conditions also include conditions related to angiogenesis (e.g., cancers) and obesity caused by proliferation of adipocytes and other fat cells. PATENT VIV-1002-PC

In some embodiments, a medical condition is treated, using engineered bacterial compositions described herein, by a method including administering a mutant bacterium that contains a genetic mutation to subject having a tumor in an amount effective to treat the tumor, where the wild type counterpart of the mutant bacterium is virulent against non-cancer cells and/or tissues, the virulence of the mutant bacterium against non-cancer cells and/or tissues is substantially reduced compared to the virulence of the wild type counterpart bacterium against non-cancer cells and/or tissues, and the virulence of the mutant bacterium against cancer cells and/or tissues is not substantially reduced compared to the virulence of the wild type counterpart bacterium against cancer cells and/or tissues. In some embodiments, the mutant bacterium is administered orally.

Examples

The examples set forth below illustrate certain embodiments and do not limit the technology.

Example 1: High-throughput screening for Salmonella avirulent mutants that retain targeting of solid tumors

The relative fitness of 41 ,000 Salmonella transposon insertion mutants growing in mouse models of human prostate cancer and melanoma was measured in an effort to identify mutant strains that were avirulent yet maintained tumor targeting ability. Two classes of potentially safe mutants were identified. Class 1 mutants showed reduced fitness in normal tissues and unchanged fitness in tumors (e.g., mutants in htrA, SPI-2, and STM3120). Class 2 mutants showed reduced fitness in tumors and normal tissues (e.g., mutants in aroA and aroD). In a competitive fitness assay in human PC3 tumors growing in mice, class 1 mutant STM3120 had a fitness advantage over class 2 mutants aroA and aroD, validating the findings of the initial screening of a large pool of transposon mutants and indicating a potential advantage of class 1 mutants for delivery of cancer therapeutics. In addition, an STM3120 mutant successfully targeted tumors after intragastric delivery, opening up the oral route as an option for therapy administration.

Salmonella enterica serovar Typhimurium is a facultative anaerobic bacterium that infects a wide variety of animal hosts and naturally accumulates in most solid murine tumors versus normal murine tissues at a ratio of 1000. Described herein is a high-throughput fitness screening of Salmonella mutants in all non-essential genes to determine which mutants accumulated in tumors PATENT VIV-1002-PC

while being disabled for growth in normal tissues. Mutants with reduced fitness in normal tissues but unchanged fitness in tumors were identified and have potential use as cancer therapeutics.

Results and Discussion

Microarray analysis determined fitness in normal tissues and tumors

A library of greater than about 40,000 Salmonella mutants containing mini-Tn5 transposon insertions was constructed and pooled. The pool was injected into six human prostate (PC3) and six melanoma (MDA-MB-435) tumors growing subcutaneously in nude mice, and injected intravenously into three tumor-free mice. Bacteria were recovered after two days from tumors and spleens, livers, and lungs of tumor-free mice.

During in vivo selection, defective mutants in genes contributing to fitness in the selective environment are lost from the pool. Differences in the mutant pool composition before (input pool) and after selection (output pool) can be detected using microarray hybridization. Transposons were used that carry the T7 promoter sequence, allowing the specific amplification of genomic sequences adjacent to each insertion, which are then mapped on the Salmonella genome using a gene microarray (see FIG. 1 and the section below entitled "Transposon library sampling for microarray and data analysis"). The present study revealed two distinct classes of mutant phenotypes (see FIGS. 2A-2B and Table 1).

Class 1 mutants. This class contains mutants with reduced fitness in normal tissues (spleen, liver and lung) and unchanged fitness in tumors. Mutants affecting at least 19 distinct genes within the SPI-2 island (i.e., ssrA, ssaB, ssaC, ssaD, sseB, sscA, sseC, sseE, ssaJ, STM1410, ssaK, ssaL, ssaM, ssaV, ssaN, ssaP, ssaQ, yscR and ssaT) were identified. In addition, mutants in genes involved in a number of cellular functions were identified (FIGS. 2A and 2B). These include htrA, phoP, sifA and a hypothetical operon composed of a putative acetyl-CoA hydrolase (STM3118), a putative monoamine oxidase (STM3119) and two putative transcriptional regulators (STM3120 and STM3121 ).

Class 2 mutants. This class contains mutants with reduced fitness both in normal and tumor tissues. Three mutants of the same operon involved in the synthesis of aromatic compounds were identified: aroM, aroD and aroA. Mutants in genes related to lipopolysacchahde biosynthesis were PATENT VIV-1002-PC

also identified in this class (e.g., rfbK, rfbM, rfbC, rfaQ). The ability of mutants to directly kill tumors was not tested because the study was designed only to identify mutants with reduced fitness in spleen but unchanged or improved fitness in tumors. Regardless of any ability to kill tumors, such mutants will be able to deliver and express therapeutics under the control of tumor-specific promoters.

Virulence assay of specific knockout mutants in immunocompetent mice

Individual gene knockouts of class 1 and class 2 Salmonella genes were constructed using the Lambda-Red recombination technique. These deletion mutants were tested for virulence in immunocompetent mice. Each mutant was injected (10⁵ cfu) intravenously into five C57BL/6 mice, which are particularly sensitive to Salmonella infection, and are thus a stringent test of virulence. Additional deletions were made in three genes that had no observable fitness phenotype in our microarray screen and used as controls (STM1459, ybjN and feoB). Each mutant strain was assigned to one of three categories based on virulence level: virulent, mildly attenuated, or severely attenuated (see FIG. 3). Virulent strains cause distress, dehydration and death within 2 days post inoculation, which was observed with all three control mutants. In contrast, class 1 and class 2 mutants were either mildly or severely attenuated. Exposure to the mildly attenuated mutants STM31 19, rfbl, rfaQ, rfbK, rfbM, sifA and phoP caused signs of distress 2 to 6 days post inoculation (see FIG. 3). The C57BL/6 strain of mouse also presents similar symptoms within 2 days following the same dose of wild-type Salmonella administration (data not shown). All other mutants were severely attenuated and did not cause any distress during the 2-week experiment. These strains include SPI-2, htrA, STM3120, aroA and aroD (see FIG. 3). Assays with SPI-2 and STM3120 mutants were repeated three times, each with five mice. No signs of distress or death were observed for four weeks, after which all mice were sacrificed.

In summary, fitness assays on pools of mutants can be used as a primary screen for candidate attenuated mutants while simultaneously monitoring the relative ability to survive in tumors.

Competitive fitness assay in nude mice bearing human prostate tumors

The competitive fitness of the class 1 mutant STM3120 in the tumor environment was tested in vivo against the class 2 mutants aroD and aroA. Input bacterial mixes were prepared in an approximately 1 :1 ratio of STM3120 to aroD or aroA. Approximately 10^s cfu of the mixture were PATENT VIV-1002-PC

injected into human PC3 tumors growing subcutaneously in nude mice. Input ratios were compared with output ratios recovered from tumor biopsies 2, 4, and 7 days after injection.

Two days after injection, the level of viable aroD mutants was 2 logs lower than that of STM3120. After 1 week, aroD was undetectable whereas STM3120 counts increased slightly. When

STM3120 was competed against aroA, the aroA count was initially reduced by about two logs 2 days following injection but maintained the same level 1 week after injection (1 to 2 logs less than STM3120). These results suggest that STM3120 out competed aroD to a greater extent than it out competed aroA (see FIG. 4), consistent with the microarray data showing that aroA is more fit in tumors than aroD, but not as fit as STM3120.

Tumor-targeting of STM3120 mutants using syngeneic orthotopic 4T1 breast tumors

The tumor-targeting capability of STM3120 was tested in five 6-week old BALB/c mice bearing 4T1 breast tumors grown orthotopically for 10 days. Mice were gavaged with 7 x 10⁸ cfu of STM3120, tumor biopsies were taken 2, 5, 7 and 9 days later and bacterial counts determined. Bacteria were detected in three mice 7 days after administration. At day 9, bacterial counts ranged from 2 x 10" to 9 x 10⁵ cfu per biopsy in all 5 mice (see FIG. 5).

These results suggest that intragastric delivery of STM3120 allows a sufficient number of bacteria (approximately 1X10⁷ to 5 x 10⁸ cfu per tumor) to target and multiply in the tumor environment to levels known to effectively reduce tumor size after intratumoral or intravenous injection. Intragastric delivery of therapeutic strains may offer improved safety over intravenous delivery. Recently, VNP20009 administered orally to mice bearing syngeneic subcutaneous B16F10 melanoma and Lewis lung carcinoma also was shown to have an anticancer effect. Tumor- targeting after oral delivery to BALB/c mice is likely due to the ability of Typhimurium to produce a typhoid-like systemic infection in this mice strain. The ability to efficiently enter the bloodstream of humans after oral delivery may require additional engineering or the use of strains that are naturally efficient at this transition such as Typhi strain Ty21.

Screenings in the original study lasted only 2 days, a period of time necessary to ensure sufficient complexity in the mutant library without random loss of mutants that would confound the high- throughput analysis. As a result mutants such as STM3120 were selected based on the fitness PATENT VIV-1002-PC

phenotype not the tumor killing targeting. Nevertheless, tumor necrosis was occasionally observed, likely associated with the injection of STM3120.

High-throughput screening of a pool of transposon mutants can allow the identification of novel Salmonella mutants with potential therapeutic value and the re-evaluation of those previously used in cancer therapy. Mutants that retain tumor-targeting while being poor colonizers of normal tissue are candidates for delivery of cancer therapeutics. Further characterization of the mutants can be carried out in suitable host organisms. The method described herein can be adapted to any host and tumor model and a wide variety of bacterial species.

Materials and Methods

Bacterial strains

Specific knockout mutants described in Table 2 were generated in the S. typhimurium strain 14028 background using the Lambda-Red recombination method, with modifications. A transposon library in 14028 was constructed using the EZ-Tn5™ <T7/KAN-2> kit (Epicenter). The library had greater than about 40,000 kanamycin-resistant mutants.

Animal experiments

PC3 human prostate and human MDA-MB-435 recently redefined as melanoma, were grown in nude mice by injecting approximately 1X10⁶ cancer cells subcutaneously. In the 4T1 breast syngeneic model, 4T1 tumors were grown in BALB/c immunocompetent mice by injecting 2 x 10⁶ cells at the second mammary gland on the right side.

Sample preparation for the microarray and data analysis

A frozen aliquot of the initial library was used to inoculate 100 ml of LB. After overnight growth, bacteria (input library) were pelleted, washed three times with PBS and 107 cfu injected intratumorally into twelve 6-week old nude mice (six mice bearing subcutaneous human PC3 prostate, six mice bearing subcutaneous human MDA-MB-435 melanoma) and intravenously into three tumor-free nude mice. Two days after injection, tumors and normal tissues (spleen, liver and lung) from tumor-free mice were recovered and homogenized in PBS. An aliquot was plated on PATENT VIV-1002-PC

kanamycin-containing LB plates to determine the cfu. The remainder of the sample was added to kanamycin-containing LB and incubated overnight at 37⁰C (output libraries). The DNA adjacent to transposon insertions in library samples was amplified. PCR amplifications were carried out using the primers DOPR2 (CAACGCAGACCGTTCCGTGGCA) and CCT₂₄VN (CCTTTTTTTTTTTTTTTTTTTTTTTTVN). Nested PCR amplifications were carried out using primers CCT24VN and KAN2FP1-B (GTCCACCTACAACAAAGCTCTCATCAACC).

Transposon library sampling for microarray and data analysis

Each transposon insertion queries a T7 RNA polymerase promoter (PT7) that is used to generate a unique transcript for each mutant. Each genomic sequence adjacent to Tn insertion is sampled in 3 steps:

Polyadenylation: PoIyA tails were added to fragmented genomic DNA using terminal transferase (TdT) as follows: 1.5 μg of DNA fragments were incubated for 30 min at 37⁰C in a total reaction volume of 50 μl containing 40 U TdT (New England BioLabs), CoCI2 0.25 mlvl, and dATP 0.4 mM. Terminal transferase was subsequently inactivated at 70⁰C for 10 min and the tailed product was purified using the QIAquick PCR purification kit (Qiagen).

A two step PCR reaction was used to amplify the polyA-tailed DNA fragments containing the insert PT7 and the flanking inserted region: In the first PCR reaction, 50 ng of purified polyA-tailed DNA was used as template for a PCR reaction using primer DOPR2

(CAACGCAGACCGTTCCGTGGCA), and a primer designed to anneal to the polyA-tail (CCT₂₄VN). The reaction mixture consisted of 1 x PCR buffer, 0.2 mM of each dNTP, 1.5 mM MgCI2, 0.05 U Taq polymerase (Promega), and 0.2 μM of each forward and reverse primer in a total reaction volume of 25 μl. The PCR reaction was performed under the following conditions: initial denaturation at 94°C for 1 min followed by 30 cycles with denaturation at 94°C for 10 s, annealing at 50⁰C for 10 s, and extension at 72⁰C for 5 s. The last cycle was followed by a final extension for 3 min at 72°C. In the second amplification step, a nested PCR was performed using 1 μl of the amplified product from the initial PCR in a total volume of 50 μl. Internal primer KAN2FP1-B (GTCCACCTACAACAAAGCTCTCATCAACC) and primer CCT₂₄VN were used under identical cycling conditions as during the initial PCR reaction. PCR products were analyzed on 1% agarose gels. PATENT VIV-1002-PC

cDNA synthesis and labeling

8 μl of the nested PCR reaction were used as template for a 20 μl in vitro transcription reaction using the AmpliScribe T7 transcription kit (Epicentre). The RNA was purified through RNeasy spin columns (Qiagen) and used as template to synthesize labeled cDNA by incorporation of Cy5-dCTP or Cy3-dCTP (GE Healthcare) using Superscript Il reverse transcriptase (Invitrogen). The labeled cDNA was purified through a spin column (Qiagen). 2 μg of labeled cDNA from the output library (Cy3 label) and the input library (Cy5 label) were mixed 1 :1 and hybridized to slides containing a Salmonella ORF microarray printed in triplicate. Signal intensities were quantified using the QuantArray 3.0 software package, and normalized based on total signal in each' channel. The ratio of the signal from tumor and from normal tissue was compared to the input library. The Tables present data filtered to show only the largest changes, which was arbitrarily set at a threshold of a 2.25-fold change [Log2(2.25)= -1.5] to show a few of the most dramatic changes.

Example 2: Embodiments

Provided hereafter are examples of certain non-limiting embodiments of the technology.

A1. An orally active pharmaceutical composition, comprising: a mutant bacterium that contains a genetic mutation, wherein: the wild type counterpart of the mutant bacterium is virulent against non-cancer cells and/or non-cancer tissues, the virulence of the mutant bacterium against non-cancer cells and/or non-cancer tissues is substantially reduced compared to the virulence of the wild type counterpart bacterium against non-cancer cells and/or non-cancer tissues, and the virulence of the mutant bacterium against cancer cells and/or cancer tissues is not substantially reduced compared to the virulence of the wild type counterpart bacterium against cancer cells and/or cancer tissues.

A2. The orally active pharmaceutical composition of embodiment A1 , wherein the genetic mutation comprises two or more genetic alterations.

A3. The orally active pharmaceutical composition of embodiments A1 or A2, wherein the genetic mutation modulates an activity selected from the group consisting of: a secretion system activity; bacterial type III secretion system activity; a bacterial transcriptional regulator activity; a PATENT VIV-1002-PC

magnesium transport activity; an amino acid ligase activity; a D-alanine-D-alanine ligase activity; a protease activity; a serine protease activity; an oxidase activity; a cytochrome activity; an ubiquinol oxidase activity; a structural protein activity; a polymerase activity; an O-antigen polymerase activity; a reductase activity; a CDP-6-deoxy-delta3,4-glucose reductase activity; a pyrophosphorylase activity; a dTDP-glucose pyrophosphorylase activity; a sugar synthetase activity; a TDP-rhamnose synthetase activity; a sugar transferase activity; a glucose or galactose sugar transferase activity, UDP-D-glucose:(galactosyl)lipopolysaccharide glucosyltransferase activity, UDP-D-galactose:(glucosyl)lipopolysaccharide-alpha-1 ,3-D-galactosyltransferase activity; an oxidase activity; a monoamine oxidase activity; an activity that suppresses mutants of outer membrane protein assembly; a suppressor of porin (ompF) assembly mutant activity; a hydrolase activity; acetyl-CoA hydrolase activity; a phosphatase activity; phosphohistidine phosphatase activity; a transcriptional repressor activity; a glucitol operon transcriptional repressor activity; a protein synthesis chain elongation activity; a protein synthesis chain elongation factor EF-Tu activity; a potassium uptake activity; a potassium transport activity; a chemotaxis activity; methyl- accepting chemotaxis protein (MCP) activity; an exporter activity; an ABC-type bactehocin/antibiotic exporter activity; a dehydrogenase activity; succinate dehydrogenase activity; a redox factor activity; a thioredoxin 1 activity; a polysaccharide chain length modulator activity; an enterobacterium common antigen (ECA) polysaccharide chain length modulation activity); and a Hes-B like domain activity.

A4. The orally active pharmaceutical composition of embodiments A1 or A2, wherein the genetic mutation modulates a secretion system activity.

A5. The orally active pharmaceutical composition of embodiment A4, wherein the genetic mutation modulates a bacterial type III secretion system activity.

A5. The orally active pharmaceutical composition of embodiments A1 or A2, wherein the genetic mutation modulates a bacterial transcriptional regulator activity.

A6. The orally active pharmaceutical composition of embodiments A1 or A2, wherein the genetic mutation modulates a protease activity.

A7. The orally active pharmaceutical composition of embodiments A1 or A2, wherein the genetic mutation modulates a periplasmic serine protease activity. PATENT VIV-1002-PC

A8. The orally active pharmaceutical composition of any one of embodiments A1 to A7, wherein the genetic mutation comprises an alteration to a gene selected from the group consisting of: ddlB gene, htrA gene, cyoA gene, sdhA gene, sifA gene, phoP gene, rfc gene, sufA gene, ssrA gene, ssaB gene, ssaC gene, ssaD gene, sseB gene, sscA gene, sseC gene, sseD gene, sseE gene, ssaJ gene, ssaK gene, ssaL gene, ssaM gene, ssaV gene, ssaN gene, ssaP gene, ssaQ gene, yscR gene, ssaT gene, yebC gene, rfbl gene, rfbA gene, rfbD gene, asmA gene, sixA gene, srlR gene, yhdP gene, tufA gene, rfaK gene, rfaJ gene, rfal gene, rfaB gene, mgtC gene, trxA gene, wzzE gene, ubiB gene, trkH gene, purH gene, STM 1410 gene, STM0278 gene, STM4262 gene, STM4258 gene, STM3118 gene, STM3119 gene, STM3120 gene, STM3121 gene, a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the ffoorreeαgooiinnαg α geenneess o orr o onnee o off t thhee s suubbssttaannttiiaallllyy i iddeennttiiccaall α geenneess..

A9. The orally active pharmaceutical composition of any one of embodiments A1 to A3, A5 and A8, wherein the genetic mutation comprises an alteration to a STM3120 gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A10. The orally active pharmaceutical composition of any one of embodiments A1 to A3 and A6 to A8, wherein the genetic mutation comprises an alteration to a htrA gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A11. The orally active pharmaceutical composition of any one of embodiments A1 to A5 and A8, wherein the genetic mutation comprises an alteration to a SPI-2 gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A12. The orally active pharmaceutical composition of embodiment A11 , wherein the genetic mutation comprises an alteration to a gene selected from the group consisting of: ssrA gene, ssaB gene, ssaC gene, ssaD gene, sseB gene, sscA gene, sseC gene, sseD gene, sseE gene, ssaJ gene, ssaK gene, ssaL gene, ssaM gene, ssaV gene, ssaN gene, ssaP gene, ssaQ gene, yscR gene, ssaT gene, a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes. PATENT VIV-1002-PC

A13. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssrA gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene..

A14. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaB gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A15. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaC gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A16. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaD gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A17. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a sseB gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A18. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a sscA gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A19. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a sseC gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A20. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a sseD gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene. PATENT VIV-1002-PC

A21. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaJ gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A22. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaK gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A23. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaL gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A24. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaM gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A25. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaV gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A26. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaN gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A27. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaP gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A28. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaQ gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene. PATENT VIV-1002-PC

A29. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a ssaT gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A30. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a yscR gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A31. The orally active pharmaceutical composition of embodiment A12, wherein the genetic mutation comprises an alteration to a STM1410 gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

A32. The orally active pharmaceutical composition of any one of embodiments A1 to A31 , wherein the mutant bacterium is a mutant pathogenic bacterium.

A33. The orally active pharmaceutical composition of embodiment A32, wherein the mutant bacterium is a mutant enteric bacterium.

A34. The orally active pharmaceutical composition of embodiment A32, wherein the mutant bacterium is a mutant Salmonella bacterium.

A35. The method of embodiment A34, wherein the Salmonella bacterium is S. typhimurium.

A36. The method of embodiment A35, wherein the S. typhimurium is strain 14028.

B1. A method, comprising: administering a mutant bacterium that contains a genetic mutation to subject having a tumor in an amount effective to treat the tumor, wherein: the wild type counterpart of the mutant bacterium is virulent against non-cancer cells and/or non-cancer tissues, the virulence of the mutant bacterium against non-cancer cells and/or non-cancer tissues is substantially reduced compared to the virulence of the wild type counterpart bacterium against non-cancer cells and/or non-cancer tissues, and PATENT VIV-1002-PC

the virulence of the mutant bacterium against cancer cells and/or cancer tissues is not substantially reduced compared to the virulence of the wild type counterpart bacterium against cancer cells and/or cancer tissues.

B2. The method of embodiment B1 , wherein the mutant bacterium is administered orally.

B3. The method of embodiments B1 and B2, wherein the genetic mutation comprises two or more genetic mutations.

B4. The method of any one of embodiments B1 to B3, wherein the genetic mutation modulates an activity selected from the group consisting of: a secretion system activity; bacterial type III secretion system activity; a bacterial transcriptional regulator activity; a magnesium transport activity; an amino acid ligase activity; a D-alanine-D-alanine ligase activity; a protease activity; a serine protease activity; an oxidase activity; a cytochrome activity; an ubiquinol oxidase activity; a structural protein activity; a polymerase activity; an O-antigen polymerase activity; a reductase activity; a CDP-6-deoxy-delta3,4-glucose reductase activity; a pyrophosphorylase activity; a dTDP- glucose pyrophosphorylase activity; a sugar synthetase activity; a TDP-rhamnose synthetase activity; a sugar transferase activity; a glucose or galactose sugar transferase activity, UDP-D- glucose:(galactosyl)lipopolysaccharide glucosyltransferase activity, UDP-D- galactose:(glucosyl)lipopolysacchahde-alpha-1 ,3-D-galactosyltransferase activity; an oxidase activity; a monoamine oxidase activity; an activity that suppresses mutants of outer membrane protein assembly; a suppressor of porin (ompF) assembly mutant activity; a hydrolase activity; acetyl-CoA hydrolase activity; a phosphatase activity; phosphohistidine phosphatase activity; a transcriptional repressor activity; a glucitol operon transcriptional repressor activity; a protein synthesis chain elongation activity; a protein synthesis chain elongation factor EF-Tu activity; a potassium uptake activity; a potassium transport activity; a chemotaxis activity; methyl-accepting chemotaxis protein (MCP) activity; an exporter activity; an ABC-type bacteriocin/antibiotic exporter activity; a dehydrogenase activity; succinate dehydrogenase activity; a redox factor activity; a thioredoxin 1 activity; a polysaccharide chain length modulator activity; an enterobacterium common antigen (ECA) polysaccharide chain length modulation activity); and a Hes-B like domain activity.

B5. The method of any one of embodiments B1 to B4, wherein the genetic mutation comprises an alteration to a gene selected from the group consisting of: ddlB gene, htrA gene, cyoA gene, sdhA PATENT VIV-1002-PC

gene, sifA gene, phoP gene, rfc gene, sufA gene, ssrA gene, ssaB gene, ssaC gene, ssaD gene, sseB gene, sscA gene, sseC gene, sseD gene, sseE gene, ssaJ gene, ssaK gene, ssaL gene, ssaM gene, ssaV gene, ssaN gene, ssaP gene, ssaQ gene, yscR gene, ssaT gene, yebC gene, rfbl gene, rfbA gene, rfbD gene, asmA gene, sixA gene, srlR gene, yhdP gene, tufA gene, rfaK gene, rfaJ gene, rfal gene, rfaB gene, mgtC gene, trxA gene, wzzE gene, ubiB gene, trkH gene, purH gene, STM1410 gene, STM0278 gene, STM4262 gene, STM4258 gene, STM3118 gene, STM3119 gene, STM3120 gene, STM3121 gene, a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes.

B6. The method of any one of embodiments B1 to B5, wherein the mutant bacterium is a mutant pathogenic bacterium.

B7. The method of embodiment B6, wherein the mutant bacterium is a mutant enteric bacterium.

B8. The method of embodiment B6, wherein the mutant bacterium is a mutant Salmonella bacterium.

B9. The method of embodiment B8, wherein the Salmonella bacterium is S. typhimurium.

B10. The method of embodiment B9, wherein the S. typhimurium is strain 14028.

C1. A high throughput method to identify a bacterial strain that will selectively infect tumor tissue in comparison to normal tissue, which method comprises: (a) providing an input library of bacteria that are mutants of a wild type strain:

(b) administering the library to tumor-bearing subjects and to normal subjects;

(c) recovering DNA from bacteria that have survived in tumor tissue of the tumor-bearing subject and that have survived in the tissues of the normal subject;

(d) analyzing the DNA obtained in (c) by microarray analysis and/or sequencing analysis to determine mutations in genes and/or associated regulatory elements of bacteria that preferentially survive in tumor tissue as compared to normal tissue.

C2. The method of embodiment C1 , wherein the DNA obtained in (c) is analyzed against a panel containing open reading frames of wild type bacterial genes. PATENT VIV-1002-PC

C3. The method of embodiment C1 or C2, wherein the DNA obtained in (c) is analyzed by microarray analysis.

C4. The method of any one of embodiments C1 to C3, wherein the DNA obtained in (c) is analyzed by sequencing analysis.

C5. A bacterial mutant selective for tumor tissue identified by the method of any one of embodiments C1 to C4.

C6. A method to obtain an attenuated strain of bacteria, which method comprises administering a library of mutant bacteria to a multiplicity of subjects and identifying a mutant strain that is present in the tissues of a subject having a predetermined survival time.

C7. The method of embodiment C6, wherein the mutant bacteria are prepared by a method of any one of embodiments C1 to C5.

C8. An attenuated strain identified by the method of embodiment C6.

D1. A library of mutant bacteria obtainable by transfecting a bacterial culture with transposons fused to an expression system for a selectable marker comprising a T7 promoter; wherein said fused expression system results in disruption of genes in transfected bacteria.

5,5 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0206 004 -013 -109 -022 -079 -0660031 -048 -04#####0128 -074 -0870099 -0490006 029 -07 023 -027 -01 STM0207 -00057 -031 -141 -081 -00900380084 -094 -085 -05 -051 -046 -032 -060169 162 04 1790489 055 STM0208 -006 -008 12 -039 -021 04660344 -080 O2Q2JΪ] -039 018 STM0209

-048 -099 -035 -090531 -071 -097 -11 -03 -14 002 -05 STM0210 -02 -035 04830678 -0190447 -00503660049 -064 -022 -0470836 -0490251 -051 -11 -04 011 -115 -05 STM0211 075 -018 -034 -137 -059 -023 -059 -105 -059 -119 -098 -05705381107 0381114 196 128 2280864 1 STM0212 066 -043 04860532 -024 -016 -06301750136 -0630496 -022 -1021403| -184| -013 04 -05 -15 -01i[~^*?5] STM0213 063 -037 01340864 11691043043305271235 -096 -052 -033 -00734840171 107 017 -01 051 -072 -03 STM0214 0420486 -044 -088 -026 -004 -057 -126 -009 ##### 0040156053200260321 1105 227 121 1970729 108 STM0215 050356 0788 -082 -0730541 -0760248 -054 ##### -068 -07600870604 -039 -009 087 026 154 -098 -04 STM0216 0650262 -016 -177 -0410085 -024 -022 -032 ##### -046 -0460966 -01206590635 153045 206 -038 039 STM0217 0080119 -089 -157 -0380199 -023 -116 -058 mtMtt 00101860002049201030521 232 13 2121036 119 STM0218 0880166 0158 -138 -0720344 -065 -086 -029 -036 -012 -0280347028902140917 237 105 191 1035 073 STM0219 0290262 -057 -112 -07902490721 -05 -069 -06 -032 -022019501620521 0599 22 07 17 118 068 STM0220 040442 -037 -13604270304 -0450137 -101 -0250801 0296060204080481 1145 208 091 2030643 09 STM0221 1140335 -031 -099 -0040706 -032 -117 -102 -015 -024 -047077206630299 043 203 113 201 0798 096 STM0222 -04 012 1741 -051 0721 02460002 -104 -0651468 -1180835 0050563 072 04 162 2 4742112 078 STM0223 -00111 -01 -108 -062 -031 -011 -052 -06 IUtMU -049 -0770719 -03203981055 193099 2420981 026 STM0224 0590192 -04iQiJ>i] -0950057 -022 -05 -019 -013 -030299064802170301 121 229 116 252 1103 088 STM0225 0380436 -025 -116 -132 -015 -06 -126JJJ56J -050288014906540227 -0060289 21 063 1780317 064 STM0226 0240225 -047 -118 -0060049 -05 -132 -074 -0170101 -0390168 -00712360904 211 089 192 1106 076 STM0227 0640193 0201 -093 -041 -0850237 -098 -059##### -025 -03504250537 -0360868 298 116 250593 041 STM0228 071 0468 -053 -037 -021 0073 -016 -035 -08 -049 -024 -0370075080510041318 197 096 248 1152 083 STM0229 066 088 0298 -065 -026 -05 03 -075 -061 -046 -087 -001 0724023701491179 247 13 2481542 11 STM0230 0520104 -033pπisϊ1 -11303860307 -075 017 «#### -06904130854 -03800850849 17 143 209 082 093 STM0231 04 -024 -042 -121 -0560392 -052 -079 -038 -091 -05 -0561101 058906240652 24 126 2730944 08 STM0232 090297 -014 -07602970577 -066 -077 -041 0013 -049 -033 07 -01 0581407 209 112 151 0709 109 STM0233 -05 -011 0818 -014000907980014 10990008 -043 -11419130303 -02201540127 -11 -04~~~^""~~] 2814 028 STM0234 036 -002 11640184 -003 045 -01204790168 ##### 04180102 053 -051 -0250141 057 056 07 -068 015 STM0235 031 1057 07520646 -0380772065402420745 -0290158 -027 1789 -074 19070037 -07 209 -061719 201 STM0236 0470223 -031 -109 -101 -057 -05 -04701770851 0321 06750839 272 16 2060699 128 STM0237 03 -094 -145 -055

12e[-1jj7^" -0430182 -0140474 -061 -051 037 054 033 091 -05 -0 STM0238 0550328 -039 [T68] -051 0825 -011 -055 -099 106 -0260235 -008066811130966 247 13 114 091 112 STM0239 0870171 01 -079 -0790318 -104 043 -075 -077 -056 -074 -009044504830483 186 115 167 -013 092 STM0240 0920159 -0870051 -023 -048 -0270899 -086 -079 -111 -044 -019 -057 -091 -028 072 -02 178 -007 001 STM0242 084 008 -001 -102 -030131 -067 -0.2 -007 -031 -011 -0460516022501890785 222 158 1750534 138 STM0243 111 046 1041 072302220799010308621339 -021 D821 164104870019 -045 -022 02 087 094 -028 -03 STM0244 1370823 167912450343 0901470835 0430353 -1191357 -056 -001 0386 -1 -02 013 0073818 -01 STM0245 -0 -02 -0380545 -052 -106 -016 -141 02790214[-1JeJ -015 -114 -04 -014 -092 -1 027 -122942 -12 STM0246 0570245 01880263 -024 -066 -019 -041 0571 -014 -058 -029 -0570274 -042 -08 004 -0δ[ -18J2062 -05 STM0247 009 -025 -018 -084 -132 -092 -004 -0 δ[7ffl} -003 -053 020206 -0760057 -08 022 -05 -01 -066 -02 STM0248 0790182 -102 -124 -071 -021 0274 -118 -046 ##### -033 -0320324048606050532 157 095 2 111 089 STM0255 -O 20167 05170152 -01400130264 13481161 -112 -071 -O814570399 O0390818 121 07 1230283 021 STM0256 038 -044 0248 -047 -071 0236 -0560678 -14 -001 -106 -096 -016 -043 -039 -025 12046 0760456 029 STM0257 -031005 -121 06570238 -031 -007 -041 0989 -04409950711 0264 -13 -003 -073 -12 -04PTe] 2241 -02 STM0258 051 -008 0161 -117 -07 -061 -073 -074 -072 -084 -074 -026 039 -04 -0030425 186 116 2 1108 093 STM0259 -07 -001 -13203580015 -042 -0270252 067 ##### 06330249 -12θj -1731 -084 -106 -07 011 047 -089 -08 STM0260 -08 -031 -037 -031 05180443 -0090051 0609 -057[Tκ] -106 -079 -038 053 -089 -07 -05 -061902 043 STM0261 0610429 1024 -0770081 00470181 -011 -021 ##### -012 -042 -069 -078 -090237 026 -06 037 -007 -03 STM0262 079 -037 -083 -0170351 -027 -166 -174 .041 -044 -128 -07 -015 -01 0006 -004 056 02 1330138 063 STM0263 0940443 0419 -093 -06402030421 -098 -094 -112 -044 -0570254 -01702131264 256 126 1660498 127 TABLE 1 - Raw Microarray Fitness Data tor tnc jinee red Salmonella

STM0266 007 0493 -002 -011 0624 -006 0242 0842 1276 -079 1207 0931 06 048 0686 0173 004 109 115 0947 042

STM0267 049 0287 0228 -071 -057 -032 -066 -04 -034 -067 -137 0208 -004 0117 -065 -055 -01 -01 031 -061 049

STM0268 -041 -103 -013 -068 -035 -01 -06 -095 -142 0184 -14 -015 -039 0404

STM0269 -01 -04 -026 -179 -151 -029 -019 -089 -039 2093 0356 -112 -045 -032 0005

STM0270 -09 -061 ■057 -095 -083 -0 056 0385 -143 0094 -03 -041 -038 -085 -012 -006 016 -07 -06 -085 -05

STM0271 -11 -025 -065 -123 -046 -069 -003 0027 -125 0316 1 -064 -148 -017 -081 -018 -04 -05 -07 -059 -04

STM0272 -14 -109 -119 -104 -164 -145 -134 -092 -139 -19 -091 -165 -164 -193 -069 -151 -11 -03 061 -018 -02

STM0273 027 -081 -156 -14 ■069 -075 -022 0084 0623 #####0159 -132 -104 Jl⁵I -034 -094 -03 -07 -1 -125 -03

STM0274 -0 -032 -078 -103 -139 0035 -119 -062 -11 -047 -076 -049 -053 -029 1028 -002 044 004 073 0678 076

STM0274A -03 0023 -065 -103 0062 -039 -03 -028 -137 -096 -068 -077 0189 0012 •045 0524 077 03 076 0326 046

STM0275S -12 -084 -14 -041 -019 -045 -074 -112 -086 -056 -089 ±∞L -129 -142 -147 -115 -14 -O -13 -062 -12

STM0277 -19 -115 -172 -047 -001 -012 -105 -203 -Z4 -064[-Z46 -113 -032 -042 -139 -112 -14 -12 -12 -252 -12

STM0278 j^2 -065 -19 -121 -009 -053 -152 -2.22 -3.21 -059 -056 -109 Mutual -05 -062 -122 -07 -09 01 -082 -04

STM0279 -13 -057 -061 -116 -057 -114 -051 -082 -146 0123 -147 -126 LdJL -077 -091 -089 -12 -11 -1 -091 -09

STM0280 -01 -067 -176 037 -057 -079 -057 -071 -138 -068 -111 -136 -079 -088 -053 -126 -08 -07 027 0473 -0

STM0281 019 -001 -079 -146 -093 0659 003

STM0282 -02 0219 -023 0219 0372 -008 039

STM0283 -14 -065 -067 -097 -023 -04 -11

STM0284 -1 β -16 -088 -057 -025 -08 -12

STM0285 -12 -146 -075 -117 -053 -12

STM0286 -17 0349 -021 0822 0929 009 11

STM0287 -2 -088 -014 -001 0367 011 037

STM0288 -17 -052 -005 0083 -009 0187 -06

STM0289 029 052 -066 -145 -073 -045 028

STM0290 -04 -06 -029 -117 -021 0572

029

STM0291 -15 •039 -068 -097 0065 0002 -065 -005 0176 tltlitttll Λ9.1 -121 0532 -141 -008 -075 013 114 051 -11 -02

STM0292 -1 -08 -081 -117 -08 -025 -074 0141 -156 -079 -2.39 -1J57 -005 0395 -071 -102 -08 029 -11 0166 -07

STM0293 065 -015 -031 -106 -079 0241 -05 -127 -088 ##### 0739 -027 0368 0392 0055 0281 125 05 15 054 013

STM0294 066 0406 -009 -147 -09 0253 -043 -126 -118 0126 -101 -052 0513 -023 0287 0802 202 113 147 0494 038

STM029411 082 0217 0129 -137 -023 0402 -001 -029 -043 -066 -032 -058 -024 -026 -053 -002 118 079 15 0911 -0

STM0295 -02 -005 -1 -117 -086 0752 -043 -092 -079 -099 -08 -065 0259 -022 -003 0555 239 073 106 -021 058

STM0297 048 0477 -018 -089 -006 013 0267 -092 1149 -073 0163 -073 0039 0108 0337 085 03 146 -01 -01

STM0299 -07 -052 -068 0134 -006 0099 -029 -058 -082 -052 -053 -066 047 1618 -041 0384 -1 -0 -1 0791 -03

STM0300 -09 -023 0441 -014 0317 044 -059 -052 -095 ##### D 814 2224 1304 091 043 GiS₅] -11 -05 13 -111 -05

STM0301 -04 2937 0095 -011 371 0028 2835 0469 016 -01 -023 -021 -099 1145 0457 -001 -07 039 -12 -009 068

STM0302 049 -109 -004 -061 0201 0855 0404 -024 -172 -04 0084 -1 -053 146 -061 -081 -05 135 -1 -122 -11

STM0303 -0 0027 0404 -002 -017 -033 0219 0054 0348 0092 -116 011 -097 -086 -056 -007 -02 006 -37 -22 -08

STM0304 -06 -076 -066 0531 0227 0282 -062 -121 -116 -026 -052 -014 -008 0179 1334 -04 -14 -01 -13 -094 108

STM0305 037 0465 0125 -153 -019 0046 -071 -056 -098##### -016 -03 0287 -011 0252 0997 198 096 172 086 026

STM0306 -0 -022 -019 0932 0272 0264 -028 -066 -01 0284 -049 -006 1087 0799 -02 0739 -03 021 ■06 -037 002

STM0307 -07 -05 -13 -054 -054 0219 -017 -03 -083 -166 -IjB -077 0216 -052 -054 -074 -03 -02 -04 -062 -06

STM0308 003 -039 -077 -112 -052 -069 0241 -095 -005 -076 -063 2166 -082 -077 1856 -008 029 -05 011 -104 086

STM0309 05 -003 0741 0782 0009 -017 0234 -028 -025 0423 0727 1011 -109 0528 0671 -038 079 011 -16 0495 037

STM0310 085 0733 0546 -093 -109 0331 -013 -107 -016 -03 -004 -044 0307 0654 0269 0652 24 076 198 0803 072

STM0311 067 0664 1591 1491 0107 0648 -049 0853 1322 053[ Tee] 0126 1666 -104 -065 -155 -13 003 -06 -081 -02

STM0312 041 0707 0125 -098 -036 -03 0054 -086 -038##### -045 -053 0201 01 008 0877 249 149 241 0251 0,76

STM0313 -01 0012 -001 0613 0279 0525 -041 -08 0389 -078 -085 -053 -053 0352 0253 -001 -07 -07 -04 -075 031

STM0316 012 0393 -065 -153| -042 -015 0386 1033 0055 1155 -08 -048 1165 -034 -007 044 112 056 077 0852 038

STM0317 066 0411 0177 0403 032 -036 0366 -011 0362 -023 -056 -108 -058 -011 -129 -057 -1 -<M| -19; 1003 -11

STM0318 036 0164 -022 -173 -095 -022 -041 -037 -02 -092 -04 -047 013 -009 0335 0132 093 -0 211 0287 004

STM0319 027 -003 1565 -114 -003 0528 -03 0569 0467 -073 -008 0261 0431 -002 -029 0241 106 093 126 0138 061 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0321 1620367 1455111503820453 -008 12810690108 -048 -086 -0290465 -097 -006 05

-143 -03

STM0322 044 -007 -034 -113 -0250425 -064 -038 -051 -04 -067 -0180209 01 03580685 143 07 1870547 061

STM0325 -07 -033 0342 -075 -020517 -0460429 -064 -058 -012 -042009203470481 -044 068 -05 -12 -111 -03

STM0327 -08 -126 -086 -066 -061

-0561753 -0871313 -101 -04 -041 -115 161 066 097 -092 -07

STM032ΘS -07 -017 -04602760224 -014 -024 -067 -033 -097 -076 -07 -078 -041 -07 -15 -05[^"Te] -073 -02

STM0329 060242 -0060424 ##########0397 -0170029019708120036 ############### -074 324 055 -05 -009 -02

STM0330 0160277 05771156017404430416131610340936 -0641297 -01607940099 -066 -03029| -15; 0976 073

STM0331 0320422 1020419 -0260171 -035 -042 -079092104560845 -0434691 -008 014 234 073 0740637 -01

STM0332 -01 0688 04880795 015 -0390571 0468 -0150825 -1580761 0244 -088 -123 -075 311 -04 -19 -147 -12

STM0333 -03 -048 -00504780135 -0540042 -037001300140333 -040424 -0150406 -062 -1 003 -191446 -03

STM0334 -04 -016 -013 -015 -0520046 -067 -081 -02 -0020124 -06102460201 -025 -083 014005 022 -064 -05

STM0335 -02 -007 -059 -134 -03 -015 -044 -002 -027 -091 0591 -0440449 -021 03580458 178004 146 -005 065

STM0336 0850521 -004059805260443 -00601330908 036 -007 -0050027 -018 -0463109 005 -03 -020347 05

STM0337 0370686 068506870427 -0440831 -002065211350288 093 -043 -079 -0450226 026021 312 086 -02

STM0338 -080268 05330454 -035 -072 -038 -025 -0280643 -001 0377 -131027201460071 285 -05 -02 143 02

STM0339 -01 -076 -023035301640216 -0300940466 -08212721178 -00309640545 -003 -11 -04[ -23|θO56 -01

STM0340 0330382 06706370801 049 -001 -024 -071 -007 -117 -008 -084 -051 -1370069 -09 -04 -151311 -11

STM0341 -13 -109 -0405040072 -023 -091 -076| -178]##### 09 -039 -088 -084 -109 -072QTs] -1

-08

STM0342 -14 -045 -087 -031 -012 -005 -06 -057 -129 -017 -12 -078 -0670607 -061 -065 -14 -12 012 -052 -11

STM0343 -00087 0371 04140153043700160261 -008 -052 -0190298 -061 -015 -0480285 -1 046 19 -039 -06

STM0344 -05 -0140014045504460066 -0130005 031 0386 -11602390497 -119 -037 -061 -14 -08 -2 -081 -02

STM0345 -06 -053 -023 009 -039 -012 -054 -088 -118 -051 1213 -081 -057 -101 0419 -048 -15 -08 -12 -085 003

STM0346 -11 -06 -030405 -0820253 -111 -071

-106 -101 -059 -057 -005 014 -05 067 -082 -07

STM0347 -05 -054 -074 -016 -021 -009 -041 -11 -0731565 -109 -099 -0670025 -035 -05 -06 -09 -05 -118 -03

STM0348 0450021 -018 -10605320305 -028 -076 -092 -041 -077 -0620314 -03603490203 249 12 3040072 103

STM0349 0740085 -055F₁IJTJ -0920105 -015 -044 -004 -091 -004 -0880138035400890524 148 071 1890118 1

STM0350 S -01 1118 184 -128 -1471416 -047 1741 -03031521940511 0392016305540098 045289 364 -042 065

STM0351 -11 104 0392038802250701 0596044703660196 243 -0550085 -1370617 -008 008086 011 -055 094

STM0352 S 0550173 0373 -0130596 -021 022 -001 -02 -051 1316 -009 -055 -02800940195 054 037 061 1814 081

STM0353 011 0213 -046 -067 -0460145 -048 -125 -056 -066 -027 001 032 105907870996 199 092 2161224 07

STM0354 071 0521 03S3[ -196J -032 -005 -035 -036 -089 -04 -06 -0061857041402730984 203 136 151 0606 063

STM0355 0720138 -026 -1 -075 -050153 -067 -025 ##### -029 -0530371 0096 -0020751 269097 1750665 093

STM0356 033 032 -0130463 -0350179058301320474 -013 -00500430554 -0381558 -022 104 052 0520044 22

STM0357 -020224 -04403790092 -04604970447 038 -035 -12 071 0475 -0790744 -018 04902if-37] -027 013

STM0358S 0120025 0201 088029305530421 -0360164

-044 -01 -003 -021 0836 -01 -05 -07 -072 -01

STM0359 042 052 -076 -148 -108 -001 -047 -072 -112 -054 -021 -0150087035805450885 195 147 153 028 083

STM0360 0630192 02880597 -054 -025031504450699 09803460354 -023 -02 -041 0072 -02 012 -11 -003 -04

STM0361 0790615 -0070225 ########## 0347097200230537 -0170064 ############### 004 08029 -0 -028 -02

STM0362 0970591 -015 -1120136034403051156161902660324 -00100250388 -0510706 142046 087 028 049

STM0363 1420376 -005 -06 -046 -0120145 0260736 -032 -123 -012 -077 -04 -099 -017 -06 -05 023 -02 -06

STM0364 0430816 021403870513 0160498 -025 096 -040481 15040138 -01507560768 024 -OSI 103

STM0365 0520138 1075131805880493 -011 07940932 -036050811981166054402832177 112

-129 034

STM0366 0830134 -049 -124 -0680447 -03 -101 -078 -095 -093 -079 -006 -00207220622 239 14 1830144 083

STM0367 0080264 -02 -07 -1370124 -031 -01 -142 ##### 0128 -085 -01901790332 -036 102 013 151 0357 088

STM0368 021 0488 -028 -05 -147 -019 049 -04408180727 -0720001 -027 -046 -020059 128 059 1081583 009

STM0369 -0 -028 -035 -018 019 -082 -092 -04θ[-1J>6j0359 -055 -0460046 -132 -0740208 -0 -03 -020937 002

STM0370 052 -022 -04 -055 -108 -0570039 -042 -031 -053 -113 -07013800170168 -084 028 082 072 -041 -01

STM0371 040264 005903850044 -OOβ 020201761104 ##### -02503590154 -046 -001

-06 -03

STM0372 042 -053 0299 -127 -062 -041 0181 -013 -049 -0370669 -0030352005305530317 123 061 1690325 09

STM0373 0140088 1354042804651227 025 113603132.341 3591 04280405 -052 -013 -01 008058 -030357 -02

STM0374 0 -017 -0290326 0230161 0429 -0040749 -062 -134 -00502732237 -058 -089f-17i -03^26" -04 -15 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0376 025 -048 -0120654 -046 -031 -031 -0307310658 -03 -001 -061 -006 -02 -034 -06082[ -1 β] 171 005

STM0377 034 0033 071501860367 -067 -025 -0750612 -022 -016 -0030522120305130553 099076 089 -0 048

STM0378 025 0424 -0311 -156] -0360242 -075 -107 -106 -109 -076 -0280145000602710898 192131 153 054 -0

STM0379 018 -06 -078 -115 -024 -052 -028 -05204420367 -103 -045 -108 -0790118 -005 012 -04 -03 -132 -01

STM0380 071 0089 -042 -033 -051 -023 -03500550575 -057 -074 -060526021206060946 162116 2020918 082

STM0381 033 0246 -032 -074 -036 -0190312 -0380369 -064 -046 -0240431045401840693 163053 1240302 079

STM0382 086 0912 -051 -105 -04305710007 -133 -098 -036 -048 -06411051097 -0360639 246096 1840366 041

STM0383 089 3E-O4 119116204330566017312071158 ##### -07 -0460208 -00312960367 -13 .0βQ24] -1.29 132

STM0384 083 0003 0332 -112 -067 -016 -0410536 -058 ##### -073 1530577011302370644 192079 1971279 039

STM0385 099 0014 ■036 -076 -025 -001 -096 -091 -113 -02 -085 -02804870423 -0010746 181 088 194 071 078

STM0386 112 -003 009 -093 -001 -007 -059 -1140991 -054 -089 -04904640193 -0060534 197132 23 054 063

STM0387 031 0552 -019 -077 -010182 -021 -062 -026 -039 -03 -0360913068307480639 186096 1780193 013

STM0388 126 0967 0767 -064 -0470125 -013 -05100681152 1250127 -004 -00422631348 199071 129 106 162

STM0389 -011 -025 -0580282039105020245 113037 1020351 -01

STM0390

-11β[-2_55J

-14 -06 -147[-1_54__-1 js] -05 -O8p21 -∑] -09

STM0391 -02 035 -081 1060868 -061001 -08102990164 -03601530555 -088 -033 -038 032009 156 -011 -02

STM0392 -01 0172 -03209680883 -0440595 -07403760257 -081 -044 015 -017 -014 -023 048087 1240904 025

STM0393 061 0477 -02 -116 -014 0450025 -034 -014 ##### -05446030316058515990443 142079 1861084 103

STM0394 -03 -018 -027 -010413 -088 -069 -112 -08902532715 -01 -1020303 -0690982 334 -02 0340184 -04

STM0395 114 -004 -053 -064 073 -075 -034 -1349E-04 ##### -1281772 -Oβδf-iw] -043 -101 -02059 -0 -023 007

STM039B 047 0039 -053 -0_6_ -09 024 -022 -08 -086 -067 -061 -0550175036303810638 151 071 1860173 141

STM0397 06 0287 -062fTi68J -1 -01 -018 -096 -051 -087 -063 0070796036706970335 193079 1490875 091

STM0397 066 -035 -05 -104 -038 -0090407 -118 -023 -038 -075 -0430754026905131114 191 137 1720934 063

STM0398 048 0132 -049 -0180.227 -099 -02 -023 -107 ##### -064 -032 14 -027 -1181099 -02 -08 -07 -085 02

STM0399 034 -008 -0270451 -079 -008 -092 -014 -05 -013 -078 -033 006 -055 -0441042 077 112 0750011 042

STM0400 032 -005 -053 -02104790601 -016 -O67[TM3##### -010862 -011 052 087024 1320253 013

STM0401 -04 -033 -001 -063 -081 -012 -03105990832 -12300850233

-066 -022 051 0

STM0402 -01 0095 -0 0110099 -03 -104 -086 -102 -043 -087 -029 -061 -077 -099 -011 -11

STM0403 007 0232 001801750153022402160237 006 -057 042 -013 -034 -03 -068 -022 -08 -01 -072243 -08

STM0404 -02 0047 •067 -074 -0470175 -012 -067 -094H«t -06 -078 034 -0540007 -039 075007 1720737 1

STM0405 011 0259 0195 -1210.218 -0280291 1232 -101 [-193] -132 -092 -06 -059 -0480195 006 -07 055 -039 041

STM0406 087 038 -053[T89l -028 -072 -017 -121 -025 -106 -06 -0460224 -018 -050619 192091 2270394 04

STM0407 051 0243 -044 101 -0890085 -022 142 -044 -06 -0^1 -0410917028105460972 222 09 Z370706 091

STM04O8 -01 -033 0023 -0180321 -032010401080697 -084L-2JI8_-203] -132 -136[^19 ~3\ 035081βj~5V]

STM0409 029 01 -057 -109 -0050453 -002 -00501220129

-0060289 1250682021288 -01

STM0410 002 0254 -06 -115 -0850058 -025 -073 -038 -043 -039 -04607860228 -010765191072 1830789062

STM0411 038 0192 -⁰⁵⁴LiZ^ -03805520069 -011 -031 -057 -045 -0693448016202570531 117088 2140188041

STM0413 07 -04 -137 -123 -112 -096 -085 -073 -0S3##### -066[TeIs] -068 -137 -0430026 -04 -04 -01 -033004

STMO414 013 0477 -026 -014 -0380146 -028 -096 -051 MHtM -019 -058 -018 -0740055 -033033034 139 069 08

STM0415 032 0703 -O 01 -140089 056 -O 79 -144 -117 -096 -014 -0590225023309721445209074 1740869 05

STM0416 075 0354 -01 -184 -020302 -059 -071 -062 -0370081010708490441 -0071097 235048 Z460896 067

STM0417 059 0242 -022 -1^*85 -0540076 -055 -038 -074 -084 -07 -0 -0140058 -0021039 168124 240637 077

STM0418 067 039 -022 -057 -06706581E-04 -046 -087 -092 -032 -0720119012410951167 259 104 190759 108

STM0419 004 -017 -017 -11902590136 -079 -084 -102 mm -082 -0510279064300010601 243138 1450597 058

STM0419 07 0232 -104 -125 -0380446 -034 -076 -073 -146 -123 -0090318014602860542 157 108 184 062 053

STM0420 -01 0492 -045Ui67] -058 -0460063 -107 -0.21 -0490205 -018 08305610536 108 1681092.230658031

STM0421 066 0675 006 -128 tmmtmm 0321 035 -138 -1142759 -051 mmmmtmmoββ2 162113 2081202 138

STM0422 099 0383 -017 -101 -050374 -015 -076 -064 -121 -055 -0110329003804960913 169089 1930985077

STM0423 076 0343 -0970091 -063 -119 -077 -03 -044 -007025402630672 105 18109 1981108 08

STM0424 073 0222 -046 -148 -093 -0150047 -106 -066 -105 -044 -008 0270614 -0210402 1880862260939094

STM0425 -1 -089! -157 -178¹ 042 -0920754 -075 -094#S### -03 -135 -093 -044 -1410079 086 -11 -05 -116 -1 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0427 046 015 -016 -09 -0320021 -01Θ -095 -051##### -0 -049 068 -00307380481 217 106 194 -019 051

STM0428 074 1230288 -069120507021938100701230095091800220276 -03802570205 113 103 1970244 081

STM0429 04 -010179 -138 -05308290208055808020639 -068 -054 -038 -02503780602 152031 1742228 112

STM0430 -02 -018 -023 041 -068 -079 -041 -006| -16s]θ266 -137[-193| 003 -028 -053 -138 -04 -1 -13[ -1_97J -05

STM0431 009110401180134 -018 -0240267 -028 -031 -049 -0870263 -063 -044 -0640133 -05 -01 -06 -116 001

STM0432 076 -039 -005 -124 -072 -0030066 -028 -0630048 -072 -0460432 -015 -0190481 112 03 1960501 065

STM0433 -01 0241 -01 -054 -0640107 -028 013 -028 -015 -014 -019 -056008506320094 127037 118 -023 069

STM0434 -11 -0150395 -007 -039 003 -007 -0180495 -001031708110019 -047 -0390515 -120 OafTisj 042 003

STM0435 111 -0150099 -079 -0070J)13 -013 -0340434##### -026 -087024903360043 -013 115048 160709 06

STM0436 S -06 -061 -002 -114 -054^1651 -04S -074 -0510151 -03 -0041083 -147 -1470373 -14 -12 045 -027 -14

STM0437 -09 -087 -043 -0030091 -046 -06 -02 -097 -081 -067 -047 -109 -023 -08508551 -2.1 -11 -32 -2.53) -11

STMO437 -09 -101 -04500890274 -025 -064 -029 -094 -094 -034 -0621019 -22 -11 -3 -274 -11

STM0438 -09 -028 -007590746 -0382399 -032 -012

-0590972 -091 -059 -01 -07 308 -017 -14

STM0439 08106210786 -094 -015037708610602115603990839049603341027 0220639 126 119 1321067 111

STM0440 05908440403 -129 -035 -031 -032 -081 -049 -04 -031 -024 04100120478 101 185 149 1561048 039

STM0441 0920265 -024 -138 -0420333 -017 -14 -07 -031 -046 -1030122065602640728 126077 1670539 044

STM0442 -08 -037 -149 -122 -11 -129 -142[^~^2^~4β| -147 ##### 041102070432 -024 -068 -028 019 -05 -0 -064 033

STM0443 -°⁷ -11ifTτϊ| -204] -019 -044 -0608960051 -01 041 -01 -104 075

STM0444 0130216 -051

-021 -032 -027067804431172 -0091013 -0040547 023 -0141334 071 039 0750118 074

STM0445 -12 -029 -1310286 -025 -011 -015 093 -072 -062 -0480401 -03 -061 -0430877 123006 -07 -115 -01

STM0446 089 -0450086 -057 -112 -084 -080038011404270927 214089 1470665 098

STM0447 -11

-023 -073 -067 -121 -137 -057 -128 -132[-209J -145 -1 -13 -12J___-r7J -15

STM0448 043 -029 -037 -148 -032 -032 -03 -108 -069 -016 -069 -007009404650345 073 244 128 1790587 061

STM0449 13605530072pl83] -1150405 -007 -046 -064 -093 -026 -0130085085909391067 206092 1761207 081

STM0450 1050436015702390667 -069 -O 44 -14 -145 ##### -128 -09602130908 -0120236 134041 1280035 005

STM0450 084 057 -0130366 -088 -011 -043^^6] -142 -031 -074 -064015506370032 -035 137049 1030485 08

STM0451 -070217 -066 -13 -032 -007 -085^59J -041 -013 -0310102 -0040764 -0490098 118 138 08 -039 047

STM0452 101 -027[-183]i084 -061 -0330046 -063 -04300711032 -060205 -02804270642 113 04 -01616 031

STM0453 056 0890016 -141 -0690324 -081 -148 -059 -093 -001 -038 015087402281165 195 17 2150852 08

STM0454 122 -013009i[^72]θ331 -0350048 -099 -025 -06 -058 -0170594048400430951 165104 1960357 076

STM0455 093 -050348 -083 -02 -025 -049 -1060173 -054 -043 -0531383 -01 12530955 127099 2021372 124

STM0456 0430012 -0180477 -0390233039211180577 ##### -10202840263 -0121336 -012 -01 052 037 -106 126

STM0457 0720053 -026 -116 -0140111 -0230507 -03f[ -029 -076 -0550317003705980584 205077 2.180755 075

STM0458 006 -027 -009 -0170565 -01 003 026^1^0454 -118 -0693309 -1012641 087 001 132 -05 -061 286

STM0459 21 1006285708140779150803491257160608111161 17991039 -1 34230212 012027 -01176 308

STM0460 07802151583 -03105040679 -0140021 -036 mm -00415910007072319270297 173064 2530333 125

STM0461 038 -007 -021 [TK) -05302860267 -0881402 039 -050172 -0310267 -0250741 109 104 1551545 03

STM0462 0680799 -007 -136 -10600610208 -1010317 ##### -082 -0710117079402650632 209147 1771002 1

STM0463 153013507031199040609230501 16190159 ##### 0650033 -022 -11409522165 167 07[_-V7J -091 094

STM0464 -01 -04607990199 -003 -05101260375 -038 -03204952437 -01 -0090669 -017 -1 -05 -07 -076 045

STM0465 079 0070017 -0610216 -0180186 -0130818 ttttmtt -094 -043 -028 -105 -136 -082 -02 -01 089 -115 -05

STM0466 0040259 -006 -01601450163 1001 -061 -094 -069 -006 020545 -026 068051 098 -026 051

STM0468 095 037 -006027703970486

0960201 D 971 12540966022320460642 164 123 180422 114

STM0469 09 02 -002 [T77J -0590526 -13803913937 -034 027042204040862 147096 165 041 083

STM0470 098 043 015 -116 -0560555 -0320218 -072 -101 -063 -055071201470371 071 208078 201 012 068

STM0471 0140114 -027 -011 -008 -053 -044 -0160265 -0231619 -07501560701 -067 -043 -08 -09 -01 -091 -08

STMO472 04201760259 -03404620254 -056 -047 -0510128 -001 -1028902110808 -01 004 -01 060317 104

STM0473 -03 -0381026072604150841 0104970398 -019^! ^I 55_J -146 -057 -093 -1130315 -13 -13 -13^-157_^-17]

STM0474 035 0080474 -086 -0250537 -036 -0760265 UIItIIItI 016 -04700580077 -001 -007 047041 1840158 006

STMO475 0750173022707580775 -005 10807441226 -0161831 -0210333 -0910698 -057 006 -05 097 -008 074

STM0475 05602870401 0650679 047 131 100911030021 1765 -0340239 -107 047 -057 018 -02 034 -028 063 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0477 -12 -148 -028 -089 -0980043 -033 -081 -029 -05100640134 -0 -043 06 -09 -05 -053J -16I

STM0478 -15 -059 0722 -005 -0870182 -028 -053 -028 -0640604 086 -1

-109 -01 -06 -09 -139¹ .-1θ|

STM0479 -0 0397 -056 -096 -0750321 -049 -0940824 -0960091 -043 -0240145 -0360175 122062 1310985 042

STM0480 12 0646 -034 -116 -0830134 -026 -115 -107 -073 -1 -0090096000507591064 133 112 1730269 065

STM0481 069 ■05 0437 -15 -1230147 -072[Tw] -077 -064 -104 -0860067084704640528 158105 2020435 04

STM0482 05 0117 -025 -121 -076 -024 -027 -125 -08 ##### -098 -077 -0310345 -0260782 142038 1981082 076

STM0483 062 0781 -024 -13 -06 -0070507 -048 -011 -067 -012 -06309950061 0141213 15075 2.15 047 058

STM0484 054 0193 0128 -133 -0930036 -018 -077 -068 -013 -001 -0320387043700861157 264 155 2310529 087

STM0485 074 0463 -014 -128 -055 -0150037 -085 -107 ##### -065 -031 -0220277 -0260613 181 063 2150605 023

STM0486 064 0152 017 -136 -092 -055 -078 [j_5§] -13 -007 -013 -02601660284 -0280601 077 116 1890033 038

STM0487 S > 054 0066 0243 -144 -079 -024 -031 -042 -096 -022 -029 -0470464019806210268 166078 1971106 085

STM0488 034 -054 -107 -13 -09700190121 -076 -057 -082 -076 -0350307005709590823 15117 1391184 093

STM0489 014 -01 -001 -098 -0790262 -042 -013 -1030161 -012 -035 -012 -06 -107 015 069 -02 112 -016 043

STM0490 016 099 -134 -123 -034085301190656 -104 -0770315 -046 -081 -019 -036 -011 041 041 0841455 043

STM0491 -07 -022 0749 -o 92 ttmmmmm o 3650414 -063 -O31 -1480605 mmmmmmm -005 -oi -02 1131905 024

STM0492 056 0124 -033 -048 -067 -04016409371072 ##### -054 -0230057 -0360204 -019 085041 1220226 026

STM0493 -04 1009 1638 0282131608790922090103820463 -05802551909 -077 -016 -006 -03 188 -04 -08 -03

STM0494 082 0961 0517 03030618 -0020269 -1460187 -0100281483084609110568 175 125091 0171494 055

STM0495 033 073 -023 -048 -0530157 -01 -0491255 -077 -101 -0301740631 -010442 17 1 1881963 051

STM0496 -02 -013 -031 036900410062 -005 -019 004##### -014 -095 -133 -093 -075 204 -04 -01 _-03 -085 -09

STM0497 -05 0014 -04106240181 -014 -028 -058 -060858 -058 -017 -071 -037 -0991643 -1 -0i( -26 -Zoji -13

STM0498 059 0666 -074 -007 -033 -0541034 -027 1 -08 -097 -030452 -00809471804 024046 130059 033

STM0499 077 027 -103 -125 -061 -003 -01 -005 -083 -096 -038 -0104590449 -0191311 165 142 1850935 054

STM0500 05 0376 -051 -132 -002 -03400350549 -006 -037 -083 -056 -0170373 -02 -03 04035 162 -008 061

STM0501 -12 036 0268 00760691 -05700810012 -028 Ws/Tw] -001

-109 -031 -08 -01 -05 -034 -06

STM0502 061 -004 02380539022104880467 086 -01 -0761936 -0370025 -034 -051 -003 18 -0i) -19]θ464 -05

STM0503 09 0547 0129 -0151013 -017J^"-152] -004f-T84J 0211297 -0082762 17904050458 01 211 0640553 069

STM0504 104 0732 0086 -118 -0 -003 -07 -008 -0 -1150049 -0390177287902070517 166 115 2140426 -0

STM0505 075 0371 1125 0353 -022 -011 -00308520232 -08610952224 -01 -0210824 -021 -0259 -0 -05 112

STM0506 036 0236 -055 -007 -0280414 -013[ -1641 -104 -009 -0590489 -032 -055 -049 -025 042 09 0990067 -04

STM0507 138 1049 -045 0427 -0050384 -023 -131 -0830324 -015 143 -002 -042 -015 -002 099088 1530538 027

STM0508 121 0839 1558 -056029103580385 0670089 -076 -07501630326 -039pT∞|θ847 071 028 050544 044

STM0509 01 0292 021933450169 -034064706360593

0158 -1 -014 -028 -07016[TTI -12 -05

STM0510 008 -112 -051 -045 -072013407810411 -062 -103D047 -098 -08224690046 -062 019 -0 057 -097 049

STM0511 -01 0264 1117 -013 -1217E-04 0081103 -0590735 -004 -003 -104[ -173J 03520136 -05004 -04 -07 068

STM0512 054 -026 0553 -084 -0660415044811450229 -035 -055 -019 -001 -057 -0050663 151 048 1830258 107

STM0513 004 -042 -141 -071 -047[-156| -016| -307J0104 -011 -008| -2-37 -159| -108 -066 ■038 016 09 -0 -097 -01

STM0514 08 0647 014 -074 -0470905 -014 -027 -01 mm 086103160863 0586 0806 1771 159 143 149 1054 125

STM0515 015 04 -038 -08 -0440141 -062 -058 -045 -013 -111 -0510517 -009 0305 1595 173 097 181 0727 084

STM0516 -03 -029 076 -011 -037085402450911 1065 -0440309 0180085 -123 -088 -041 -11 -06 -05 1465 -02

STM0517 -05 0137 0453 -051 -0530397 -0021114 -0203280393 171 1207 -091 -024 -039 -03 066 -06 0901 013

STM0518 -02 -059 0074 03801980538037603650315 -0260044 -0330966 -047 0707 1232 024 104 -45 0261 07

STM0519 -04 0527 03340299025908240262045302631852059616520081 -046 -076 -046 -02 -06 -29 2177 -07

STM0520 -04 -03 024300430107 -0 -046 -021 -0351319 -0210139 -022 -076 -065 -039(7-16 -04 -3 -124 -09

STM0521 L±βJ -095 -12 -149 -09 -126 -081 -074 [ -23i] -143^^»] -037pT69l -146 -173 0365 -09 -09 -06 -031 -12

STM0522 -03 -042 -006 -01401990225 -011 -048 -02 -049 -011 -031 -024 0123 -135 0537 -14 -08 123 -143 -11

STM0523 009 0219 006700690203 -044 007 -0120309 043[-1_5βj 014 -058 -085 -008 -02 -03 -04

STM0524 048 0274 0596 065 0150497 -0290605008702810779 -035 -043 -071 0081 0034 -07

008

STM0525 071 0519 1115 083074608940526072602881008 -0810426 -056 021 -054 1094 044

STM0526 -0 0021 036907390307 -0180435 -0310342 -015 -048 -011 1466 -007 0566 -071

072

STM0527 039 -076 -062 -058 -018 -073 -008 -075 -055 -018 -066 -043 -06 -078 -035 0636 093 -04 078 063 001 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0529 082 0365 -035 -OJ29 -054 0339 -032 -OJ40109 -019 -023 -005 -009 -031 -0020569 209 125 21 0518 078

STM0530 054 0581 -044 [-164] -04 0107 -097^2*17] 0294 -01 0264 0.29 092 -014 0270741 21 093 2521392 113

STM0531 091 043 0536 -139 -059 0616 -041 -0590554 -057 -059 -02306850205 0061045 25 105 201 1287 062

STM0532 088 -021 -094 -085 -07 -045 -040099 -047 #*«## -0490761 0053 -046 -041 -001 061 012 072 -037 -01

STM0533 026 -018 -018 -073 -01 0169 -0230481 0705 -076 -1130586 -082 -089 -084 -033 038 -01 078 -033 023

STM0534 073 0168 0026 I '-2111 -04 076802940435 -038 -063 -022 -0160123046905840815 2 136 2440953 117

STM0535 064 0243 -031 -083 -061 0069 -006 -077 -036 -062 -082 -02708720327 0220834 228 147 2.230851 073

STM0536 104 0522 -022 -102 0287 002 -033 -095 -104 -101 -098 -01 0157041402431021 191 131 2360927 191

STM0537 072 036 0294 -074 -024 -038046205340391 -0242213 0560504 -0220455 069 154086 1160428 087

STM0538 024 0419 -04 -007 -04 0280641 00290153 -061 -01202140614 -041 0361 0861 112 067 0980316 115

STM0539 04 0575 0874 0494 0492 0829 -06401090009 -008180202641266 -11 06150559 039025 -09 -131 022

STM0540 -1 036 0628 -08 -037 -002 -006 -0303190666231903171722 -053 -038 -019 -13054 -07 -09 -05

STM0541 061 0165 •075 [-173J -074 .004 -041 -121 -032 -056 -036 -0640653 -0420357 1268 194 09 2470414 052

STM0542 032 0636 0086 -048 -073 0401 -13 -143 -1170019 -0370996 -029 -04 -002 -005 072 -01 1380135 055

STM0543 09 0107 0807 0061 -075 0486 -0380109 -097 ##### 0991 03720635 -007 -041 1167 079 036 0230445 002

STM0544 -0 -008 0193 -07 -032 01 -0250252 -131 -00555059403850163 -0270006 069088 1570204 037

STM0545 -02 0849 -005 -063 0261 0781 -007 -078 -048 ##### -0040016 -062006304230776 045037 049 -07 -03

STM0546 089 0625 0159 0864 0102 0472 -018 -01712291193 -0521803 -088 -058 -041 0448 003072 2770944 056

STM0547 024 -016 0311 0089 0394 032 -04703090018β#### -062 1347 -073 -085 -0920304 -03 -03 -03 -116 -06

STM0548 014 0171 1399 -06 -029 0312 -053 -07 -109 ##### 07980231 -01 -037 -0621696 052 127 1150639 -0

STM0549 01 0421 -04 0852 0114 07860253 -004 -017 -011 23130077 -035 -061 -081 -007 068 116 008 -022 -0

STM0560 -06 001 -057 0602 0166 -015 -0350063 -009 -OOβj -21i| -013 121 -005 -082 Q 098f~-T6J 048 j^" -24| -095 -09

STM0551 -04 -023 0058 -131 -009 -026 -073 -103 -114 -031 -008 -073 -053 065 -1 -021 032 -02 0930002 -06

STM0552 -03 -052 0185 0781 0648 0707 -012044404050253pi^"99~| -144 -064 -0751019 009[_-1jj -14 -15 -118 052

STM0554 054 -052 -076 0345 1102 -015 2445 -136 -141 011202250131 0014 152 059 054 -038 -01

STM0557 -01 0265 -073 0378 -013 0139

-040289 -12313260593 -040311 -02 -07 104 QiJj -04

STM0558 -06 0071 -011 0242 0251 -005 -09603031466 -096 -045 -01 ############### -052 -06 -11 -09 -062 -04

STM0559 061 -007 -064 -089 -08 -0220065 -1330318 -093 -072 -01 -0170014 -0150574 212 075 1820503 033

STM0561 -0 0168 0391 0221 0105 05 -0320318PiTrI 0294 -084 -019 -054 1379 -011 -03 06 045 -1 1203 -02

STM0563 058 0149 -005 -104 0275 -0030007 -037 -0460208 -046 -0551036 011 0343 105 215 103 1830848 152

STM0564 -07 -038 -047 0394 -043 -038 -012 -025 -065##### -077 -0630334 -005 -054 -023 086 -01 -08 -022 -07

STM0565 04 0165 0178 -052 0159 0084 -02 -056 -001 -108 -04 -111 0377 -04607280039 013 -01 024 012 082

STM0566 008 0216 0374 -064 -029 0401 -01604660376 -075 -022 -006 -034 -046 0640075 -0 -01 011 0556 043

STM0567 -01 -004 -046 -025 -084 0733 -022 -0660096 019 -04 -015 -1020128 -0390312 -03 -02 089 -078 028

STM0568 026 028 0247 -041 -012 -0080393 -014 -0080396 -059 -063 -05403620916 -011 126 103 1490304 065

STM0569 015 -049 -049 ■039 -061 -0950023 -0340395 -047 -003 -034 -0420021 -074 -075 023047 0490558 -02

STM0570 -05 0421 0666 0065 -013 -026 -0020605780076 -001 0285 -041 -059 -0591188 -1 089 -140523 -01

STM0570 -0 04 0612 0254 0053 0143040403720641 -00101850188 -025 ########## 1808 -11 101 [^"-Tel 0829 039

STM0571 -1 -017 0104 -044 -016 -102065203640689 ##### 1483 -066 -041 -084 -031 -04 -07 02 -1 0253 007

STM0572 -12 0119 -037 -066 -007 -0420378 -01 -015 -044 -0881284 121 0499 -084 -029[Te] -0 βQsLβl J>39 -07

STM0573 -03 0223 -053 -033 0288 02230081 -0080206 -053 -1380406 -083 -032 -0250498 -04 009 -0θ[ -Ijjβj -07

STM0574 036 0373 -065 -084 -036 0179 -031 -046 -052 -039J124 -0091028022201520732 151 11 1460532 123

STM0575 -13 -012 -064 -145 -056 -04500350965 -1J38J -0561 -IJH)J -122 -12 -098 -12 003 -06 -03 -070276 -09

STM0576 04 0971 0041 [ ^87] -083 0316 0040481 065 -0920021 0226 045 -047 -0470835 196 111 21 0261 044

STM0577 111 0222 -003 -124 -071 -004 -003 -112 -046 -09 -092 -0820619021506430847 175 109 227 01 029

STM0578 -09 0278 0369 -149 -064 -084 -0130355 -04 #####'_-1_54J -059 061 -0620063 -022 -02 -06 079 -065 -0

STM0579 013 022 -059 -088 -015 -036 -O 16 001 -074 mm 1391 -0570263 -0130351 0128 083 068 111 0203 071

STM0580 01 0371 -092 -125 0266 -0360034 -069050702164425 095 1276311301370182 087 007 121 0083 03

STM0581 -01 -024 -1 -142 -061 -061 -0380581 1165 -0410408 -1140085 -09 -0470505 -01 -02 0872124 -02

STM0582 079 025 -008 -086 -05 0193 -021 -080393 -041 -016 -076 -026 -053 -0090527 167 122 1850121 081 TABLE 1 - Raw Microarray Fitness Datajor Engineered Salmonella

STM0585 L 4⁹] -1.21 -1.18 -1.28 -0.82 ^■0.52 -1.46 -0.64 ^6* 0.676* -'j.95' '-1.52 0.609 0.471 -0.46 j -¹-² -0.2 -1.2

STM0586 0.29 0.555 -0.42 -0.9 -0.45 0.157 -0.07 -1.01 0.806 0.278 0.013 -0.73 -0.43 -0.69 1.152 0.698 0.98 1.31 1.65 0.52 0.9

STM0587 0.39 0.548 -0.42 -1.84 -0.33 0.451 -0.04 -0.74 -0.66 -0.48 -0.89 0.228 -0.01 0.562 0.915 1.359 2.13 0.78 2.38 0.321 0.63

STM0589 ^', L_ -1 6 J! -1.04 -0.28 -0.18 -0.33 -0.02 -0.24 -0.14 -1.33 -0.8θ> -256 -1.27 -0.86 -0.96 -1.85 -1.7 -0.9 -2.9 0.5 -1.2

STM0590 0.76 0.619 0.153 -0.91 0.022 -0.28 -0.12 -0.87 -0.08 -0.38 -0.18 -0.01 1.134 0.396 -0.02 0.881 2.34 1.59 2.25 1.14 0.19

STM0591 0.65 0.487 -0.24 -1:54 -0.71 -0.41 -0.36 -0.06 -039 -0.36 -0.72 0.115 0.189 -0.19 0.182 0.702 1.86 1 1.49 0.421 0.53

STM0592 0.81 0.542 0.009 -Z24 -1.36 0.188 -0.08 -0.61 -0.97 -0.78 -0.27 0.542 0.003 0.566 1.243 1.79 1.03 2.35 0.819 0.57

STM0592 0.84 0.447 -0.45 -0.97 -0.74 0.738 0.048 -1.3 -0.52 0.016 -0.05 0.424 0.683 0.434 -0.01 0.888 1.96 1.18 2.45 0.358 1.08

STM0593 0.38 0.482 0.128 -0.73 -0.68 0.066 -1.06 -0.04 -1 79 -059 0216 0.19 0.271 -0.24 0.016 0.734 1 53 O RS 1.37 0829 1.31

STM0594 0.06 0.385 -0.71 -0.99 -053 0.161 -0.38 -1.13 -0.13 -0.4 -0.75 -0.44 -002 -0.11 -0.1 0.734 1 49 0.7 1.77 0.69 0.65

STM0595 0.63 0.033 -0.24 -0.81 -053 0.235 -0.06 -0.8 0.036 -0.7 -0.74 -0.49 0.05 0.319 0.73 0.36 1 91 1.24 2.46 0.693 1.27

STM0596 0 18 -0.51 0.183 -1.4 -ZOI -0.46 -0.24 -0.13 -1.06 ##### -0.91 -0.68 -0.38 -03 -0.71 -056 084 -0 1.2 -0.27 0.28

STM0597 0.2 0.458 -1.3 -1 02 -0.42 -0.38 -0.22 -0.37 2 155 -0.23 -1.13 -0.41 3E-04 -0.13 031 0.558 1 27 0.41 2.34 0.163 0.73

STM0598 -0 1 0.553 1.106 -0.49 -1.3 -045 -088 0.517 _-2.23 -0.62 -139 1.728 -0.59 -1.24 0.022 0.944 0.42 0.84 -0 -0.99 -0.2

STM0599 -0.1 0.206 0.627 -0.58 -0.54 -0.07 -0.03 -1.11 0809 mm -1.14 1.217 0.143 0.012 1.251 0.844 -0.3 0.91 1.4 1.137 1.87

STM0600 -0.2 0.168 -0.59 0.019 0.01 -0.2 0.287 -0.48 0.24 -0.5 0.191 -0.73 1.384 -054 0.775 -0.73 0.23 2.03 1.1 -0.11 0.88

STM0601 1.21 0.841 -0.42 -0.7 0.748 -0.14 -0.25 -1.49 -0.57 -1.15 -0.54 -0.45 mmm 0.521 0.133 0.268 1.61 1.48 2.16 0.566 0.72

STM0602 0.4 0.451 -0.85 -0.55 -0.15 -0.48 0.253 -0.76 0.057 -0 1 1 739 0409 -044 -0.67 -078 0428 097 077 0.98 -0.29 074

STM0603 -0.5 0.278 -0.33 0.084 -03 -0.33 0.403 0.553 1.382 -0.5 0.491 -0.07 -1.21 0.389 4.33 -0.19 -0.5 -0.1 -1.4 0.245 0.25

STM0604 -0.2 0.222 -0.38 -0.63 -0.38 -0.93 -0.16 gϊϊ*62 -1.2 -0.09 -1.41 -0.12 -0.09 -0.62 -0.03 -0.4 -0.5 -0.6 -1.21 -0.9

STM0605 -0.3 0.033 -0.35 0.178 0.202 -0.06 0.304 -0.42 0.11 -0.13 -0.94 0.057 -0.15 -0.16 -0.13 0.127 -0.7 *1 -1.8 -0.49 0.15

STM0606 -0.9 -0.54 -0.32 0.548 0.055 0.91 -0.06 -0.59 -0.72 1 17 -0.81 1.16 -0.46 -0.67 -0.65 0.333 -1.1 -0.1 0.37 0.566 -0.5

STM0607 -0.4 -0.3 0.073 -0.97 -0.28 -0.41 -0.4 0.525 1.365 mmm -0.34 0.028 -0.43 0.968 0.891 0.128 0.34 -0.1 1.01 -0.54 0.61

STM0608 0.72 0.132 0.174 -1.12 -1.06 0.435 -0.39 -1.12 -1.04 mmm -0 •0.56 0.689 -0.09 -0.05 0.452 2.23 1.68 1.93 0.901 1.27

STM0609 -02 0.646 -0 17 -1.3 -0.53 -0.13 -0.41 059 -0 16 ##### -0.36 -0.56 0.502 0.767 -0.1 0.815 1.86 1.2 2.1 0.645 1.3

STM0610 -0.4 -009 -0.09 -001 0.284 0.322 0.03 -0.07 -0.1 -0.8 -0.55 0.601 -0.38 -0 -0.96 -0.45 3.32 0.23 -0.3 0.425 -1.1

STM0611 0.1 0.016 0.044 0.17 -0.18 0.436 0.453 0.777 0.784 -0.41 -0.3 -0.4 -0.65 0.126 -0.55 -0.42 1.24 1.04 0.51 0.362 -0.4

STM0612 088 0.535 -0.14 -1 16 O fW 0.614 0.075 -0.83 -0.03 0.405 0.024 -0.33 0.44 -0.71 0.107 -0.18 n <rc 057 1.8 0.064 0.67

STM0613 -1.3 -0.5 0.983 -0.44 -0.12 0.035 0.211 -1.3 -0.78 1.863 -0.15 -0.59 -0.96 -0.01 0.097 3.52 1.23 -1.9 -1.99J -0.3

STM0614 -0.9 -0.35 0.502 -0.39 0432 0.04 0.001 2.337 0.093 -0.52 -0.19 -1.21 -1.12 -1.45 -1.02 ^"-T.7- -1.1 -1.3] -1.85 -2

STM0615 -0.1 0.368 -1.04 0.425 -0.14 -0.47 -0.32 -224 -0.7 -039 -0.83 -0.07 1 729 -1.4 -03 -1.3 -2.47J 1.17

STM0616 0.92 0.758 -005 -0.67 -0.38 0.192 0.764 0.031 -0.16 mmm -0.74 -006 1.14 1.269 0.034 0.854 1.84 0.69 1.75 0.603 1 09

STM0617 0.32 0.277 0.492 0.017 0.754 -0.8 0.113 -0.6 -1 01 -0.55 -0.04 -0.29 0.011 0.189 0.179 0.468 0.54 1.29 0.17 -0.88 0.08

STM0618 -0.2 -0.66 -0.05 0.473 -0.11 0.277 -0.07 0.939 -0.27 0.82 -1 -0.66 1.832 0.397 -0.31 -0 0.56 0.12 .__!_??] 0.39

STM0619 -0.2 0.675 0.005 -0.53 0.249 0.302 0.506 0.087 -035 0747 0053 -028 0043 0 118 0 186 -075 038 -0 1 -1 8¹ -082 0 17

STM0620 0.44 0.526 -1.01 -1 35 -039 06 -0.83 -1 -033 -0.6 -0.23 0.449 -0.04 0.275 0.086 1.14 1.99 0.6 2.09 0.98 1.2

STM0621 1.08 0.275 1.586 0584 -0.49 -0.13 -0.03 -0.13 -0.52 0.694 -1.14 -0.68 1.064 -0.68 0.75 1.852 -0.6 ■0.5 -0 -0.21 0.92

STM0622 -1.4 0.068 0.408 0.154 0.86 -0.22 1.077 1.548 -0.48 0.607 -3I44 -1.24 -051 0.169 -0.4 -0.2 -0.₉[ -^'•Tβϊj -1.3

STM0623 0.67 0.362 -0.46 -1.49 -0.19 0.242 0.05 -0.81 -1.05 -0.41 -0.6 0.027 0.558 -0.16 0.461 1.87 1.02 2.05 0.416 0.47

STM0624 0.14 0.418 -0.65 0.691 0.282 -0.19 0.217 -046 -148 1.257 -0.42 1.871 2.021 -0.73 -061 -036 -0.3 032 -1 -073 -0.6

STM0625 0.02 0.384 -1.21 -1.11 -0.45 -0.62 [-1.87 -1.88 -2.46 -0.68 -0.29 -0.96 -0.62 -0.67 -0.7 -0.33 0.19 -0.5 0.67 -0.25 -0.1

STM0626 -0.9 -0.76 -0.2 0.217 -0.14 -022 -003 0.364 -0.37 0.289 4.11 -1.45 -0.55 -1.36 -0.32 -1.2 0.1 -0.1 -1.9 -1.01 -0.3

STM0627 -1 -0.45 0.078 0.209 0.003 -0.26 0.243 -0.03 -0.06 0.008 0.145 1.268 -0.31 -0.14 -1.13 0.121 0.99 -03 -0.7 -0.37 -1.2

STM0628 L -lβ] 0.004 0.661 -0.41 0.445 0472 0432 0.502 -1.1 -0.18 -0.25 -0.94 1.378 -1.09 0.176 -0.85 -0.8 0.5 0.3 -0.69 0.2

STM0629 0.3 0.475 -0.17 -0.93 -0.49 0.439 -0.18 -1.02 -1.25 -1.31 -0.3 -0.5 -0.1 0.23 -0.21 0.941 2.32 0.41 1.77 0.939 0.86

STM0630 0.03 0.008 -0.21 1.591 -0.68 -1.01 -0.35 -0.72 0.002 0.374 tøftjfoj 0.457 -0.46 0.658 1.602 -0.52 -0.4 -0.8 -0.2 0.57 0.62

STM0631 0.25 0.258 0.581 -0.67 0.76 0.598 0.963 0.146 0.176 -0.47 1.556 -0.56 -0.25 -0.38 1 109 -0.04 0.94 1.46 0.58 -0.34 0.4

STM0632 0.78 0.554 -0.85 -1.71 -0.94 0.636 -0.27 -0.55 -1.22 -0.43 -0.31 -0.62 0.074 0.647 0.37 0.839 2.19 1 32 2.39 0.858 1.46

STM0633 -0.6 -0.84 -1.09 0.355 -O -0.66 0.101 -1.36 -0.67 -1.18 1 133 -1.16 -1.2i[^"-i!β9 -0.91 -1.5 -1.1 -0.7[ -1.83J -1.4

STM0634 -0.6 -0.07 -1.05 0.26 -0.23 -0.37 -0.29 -0.75 -0.88 -1.38" i2ro9' -0.85 -1.17 -0.95 -0.85 -0.54 0.45 -1.11 -2.1 ' 1.594 -1.4 STM0637 041 -021 042 _0 153 034 013

STM0639 -11 j -Oβ^β] -12[-1_87J -12

STM064D 076 111 1941007 09

STM0641 066 191 068 220328 108

STM0642 042 224 112 245 121 082

STM0643 -09 -04 -04 094 -13 03

STM0644 004 121 132 1710101 042

STM0645 08 102 1880603 071

STM0646 059 276 037 014

STM0647 042 218 135 2560417 092

STM0648 039 173 151 2350698 1

STMO649 s[ -08 -07pl68J -14

STM0650 -14 21270426 -104 -11 101 -O2[-2δ|θ612 -15

STM0652 -14

-048 -04 -03 ^cT^L^Tω] 018

STM0653 -03 -041 -074 --112244 --003377 0020166 0450309 -006 -152197 -082 -08 -041 1051 -0027 -01 -09 -06

STM0654 -07 -012 0393 --001111 --0055 -011 -002 -039 -056 -0110956 -035 -007 -0460792 -025 -13 -04 -0

056

STM0655 01 0868 -045 --009988 --007755 -022 -02900030391 -065 -019 -030166093716220014 073 -01 139 078 133

STM0656 -02 -001 0028 --003388 --002255 -04200220254 -047 -0310957008202551224 -071 -092 -07 -04 3251353 -06

STM0657 -07 063 0086 00443300442244 020100140368 -031 -05601261109 -02245806310398 -05017 -062718 009

STM0658 033 0157 03980066773300338811 0964069807420625 -11 0150003 -1350575 -017 -088 -12 -08 -2.7L-1J5 -06

STM0658 034 021 02440044666600336644 0884 07107870808 -1020437 -013 -118 043 -019 -079 LLJdJJSJ -09 -38 -186] -04

STM0659 006 -003 03 --002266 --003355 -014021301520166 -062 052029305680397_^0002 -033 -01 008 -03 -069 015

STM0660 059 0804 -0240066999900007777 -022 -079 -0490109 -038 -103 -02 -05 [-24? -0440867 -09 08 -i[^β4] -01

STM0661 025 0097 -01700005555 --002211 -0120046 -0150575 -067 -09 015 -058 -0840082 -033 077009 0030J85 093

STM0662 -01 -019 -013 --001199 --005555 -097

-0240601 -039 -063 -022 -14 -135 -08 -02 245[_-26β] -09

STM0663 082 0426 0083 --1144001144880487 05103850307 -062 -011 -0470309 -00704830519 231 101 1961095 13

STM0664 072 0551 -00300554466 003333 -0320323 -008 -0220424 -125 -0330753QTsJi] 05 -109 -03032 -09 -069 031

STM0665 029 053 0455 --110022 --006688 005 -059 -0530048##### 008 -0170006021106050566 161 051 141769 054

STM0666 06 0347 -007 --112277 --008844 -016 0310208 -014 -059 -039 -03030401420013 049 125 08 1320809 085

STM0667 058 014 -053 --005511 000055 -0150099 -044 -0410133 -009 -0300261394 -005 -013 086044 143 -006 088

STM0668 007 -051 017100331166 --006666 -0240033 -034 -051 -132 -108 -096[-1 _83J -088 -1470874 -06 -03J -17^196] -06

STM0669 -0 039 054500330011003322110121 -024 -O08 -025 -141 -055 -0871657 -051 -0δQi5| -1 -02 -070005 -0

STM0670 -06 -011 -036 --002299 --000044 -079 -026 -092 -062 -0641962 -0430159 -06 -05 -009I -1 β, -03J -36 ^64I -06

STM0671 004 -052 0044 --007733 --002222 02710365 -06 061 ##### -116 -0580851 03 -0231235 103049 1181645 06

STM0672 042 0317 -0210044115500448866 -0160102 -0970597 ##### -001 031 -025 -061 -0020076 -09089 1171363 006

STM0680 066 0159 034711337722 --003399 044601360156048109090875 -118 -00764 -0680653 039 -03 -08 -102 -07

STM0681 003 -026 135600119999 --005511 0782 -0522282 -076 -081 -047 -013 -1480266 -145 -004 002242 -03 -143 -07

STM0682 -02 -038 -O 32 --1111 --002277 -023 -095018101721434 -076 -053 -071 -011 -035 -012 099024 1310177 -01

STM0683 -0 -01 -⁰⁵⁸G ^~TiUδ] --°0⁶6¹1 0298 -039 -094 -057 -0650896 -0070076 002 -0070419 124064 135 08 07

STM0684 008 0317 -06 --113344 --008899 01 037 -135 -061 -085 -063 -0620642029306160601 165 151 1870593 066

STM0685 -07 -059 -068 --006688 --009911 -137 -067 -0270892 -0680347 -032 -0030321 -029 -037 134 -04 131 1237 124

STM0686 029 0189 022 --111100003388 0169 0510165 -026 -015 -03501660582 -0221101 103 219 129 2090857 116

STM0687 01 0535 04150055771100667722 -0090454 -01601121072 -043 -0690303 -039 -0070036 -14 -09 -120605 -01

STM0688 111 0027 0941 --112299 --009933 0438023701140561 -05 -113 -0580087 -007 -086 -092 214039 0123587 -01

STM0689 089 0765 0355 11115500558844 035080307420553 -04500130564 02 -0410771 -018 -0108 [^"Tδ] -0 127

STM0690 044 1229 076500776677 --002288 -022 -04303520662 -0550259 -045 -0530615 -086 -025 -06012 007 -12 -11

STM0691 073 1185 0461 --003311 114411 -0380419 -0830766 -01045513570733018312770759 15 171 3640036 129

STM0692 222 0101 -05311005533 --002244 0912 0850442 061 -068 -068 -0250235022451791966 117093 1740456 533

STM0693 -13 -031 -094 --006655 --003366 -036 -O3β| -17βl -0610515 -0890721 -003 -071 037 -077 -05 -05 -08

STM0694 036 0329 -0200553366 --003399 -088 -026 -139^182_JfSSWS -062 -0072118 -068 069 -009 -12 -09 163 -177*031 TABLE 1 - Raw MicroarrayJ^tness Data for Engineered Salmonella

STM0697 015 -04 0021 -111 -09

016 -041 -0 STM0698 0740479 -052 -08 -075 -002 -008 -05 -034 -065 -112 -0680588 03209761348 248 13 2280797 103 STM0699 012 -039 -028 -035 -058 -0120098 -012 -073 -055 -032 -027 -027 -01 0737 -022 097 059 061 -039 083 STM0700 1140793 0998 -1030511 0686 -039 046 -066 -046 -046 -024 1319 -01613150714 176 164 162216 108 STM0701 -00132 03650201 -033 -103 -003 -021 0312 -021 -040885040628320698 -054 041 057 -14 -133 076 STM0702 092 -002 -042 -079 -07 0121 0446 -055 -036 ##### -06 -054 007 -0130751 0655 148 104 194 147 053 STM0703 0690961 004 -0950159 00570206 -104 -055 -148 -045 -02201962.4950411 0932 209 11 198 038 061 STM0704 0440566 -071 -134 -018 0125 -009 -060591 -115 -051 -011 089902970491 083 237 144 212 -0 096 STM0705 051 0423 0069pTra] -064 -005 -0 -053 -078 -0830215 -011 0433007904060866 221 158 1840986 09 STM0707 019 1055 -O 57 -112 -107 0126 -04 -044 -039 -082 -0601660462054203280423 201 124 251 0792 068 STM0708 0470406 -086 -042 -069 0399 -039 -1280429 -036 -071 03090145 -01303660481 07 009 158 072 064 STM0708 021 05 -049 -057 -055 0141 -009 -093 042 -07 -117 038 -058070500060795 084 009 1460743 015 STM0709 047 076 0006 -107 -03 0231 -004 -059 -042 -098 -035 -03603710613 -0060662093099 1720307 028 STM0710 -06 -0140113 -118 -005 02320111 -003 -108 -04 -1060422 -108 -051 1048 -091 -13 -03 -03 -098 067 STM0711 -080905 -0370464 -O 320254 02 -011 -126 -025 -0460117 -017 -03400340644 043 023 039 -0 026 STM0712 0790649 -103 -126 -07600170052 -076 -031 -097 -013 -0342695030701370329 2 107 2340494 041 STMO713 -⁰³LiIiU -O 3206390015 -035 -09 -117 -103 -0220989 -118 -142061915040124 -05 03δ[ 174 STM0714 -06 -018 1107 -059 -001 0185 -0381617 -0380341 -07

-036 -033 -075 -05 -01 -021511 022 STM0715 -01 0081 -026 -082 -080613 -049 -092 -065##### -066 -0190054 -00900020616 214 18 2970147 096 STM0716 -02 -053 -02610970465039502930013 045##### -111 -009 -011 -002 -068 -026 -1 027 -12 -083 -04 STM0717 -08 -1 041308150253 -0160001 -0570368 -072 -105 -1350156 -057 -108 -046 -06 -05 -07 -114 -05 STM0718 05 -003 -033 106 -022 -076 -08 -064 -0290641 0920206 -053 -0640474 -061 -02 -07 026 -042 073 STM0719 -07 -027 -082 -06700170305 -049 -108 -074 -05 -0771329 -0020091 0111 -024 086 008 043 -042 -0 STM0720 -0 -077 -099 -0280051 0081 -142 J -15β| -143 -056 -078 -0390543 -001 -0070371 126 02 1730331 023 STM0721 014 -02 -017 -092 -0740255 -005 -072 -03 -084 -116 -03 -0050731 037 1044 158 107 2020942 094 STM0722 -02 -044 -078 -00502430124 -053 -055 -079 -04 -037 -025 -0314530071 0021 009 -05 02 -093 -06 STM0723 021 -056 -086 -143 -017 -054 -1081 -174^kj166| -085 -032 -011 21720367 -03 -006 121 101 1530471 078 STM0724 026 -019 -027HiIi] -084 0427 -082 -11 -086 -066 -062 -0980419 05502280156 165 122 2010202 136 STM0725 0640309 -001 L-IJHJJ -057 0021 -049 -121 -064 ##### 0411 -01414480122 -0031012 174 19 2390486 106 STM0726 -00155 -036 -111 -031 -0130122 -141 -018 -072 -094 -03206280608 0550959 202 135 1980494 034 STM0727 -07 -030894 -032 -051 0414 -0290107[T52]#####10031042 -043 -103 -091 0235 008 -08) -26 2915 -13 STM0728 -00386040205480274 012204560611 0211 -0180656 -0240273021600650088 -12 173 -19 1936 -05 STM0729 085 0920406 -022 -038 0169 -0560279 -079 -0180656 -087 -0021023 -051 0664 128058 121 0445 017 STM0730 021 0331 -039 -088 -053 0065 -087L~£7] -1 Umtm -O770131 0128 00400650382 134 092 161 0711 051 STM0731 -05 -1240009 -I55I -045 0182 -019 -083 -111 -031214100590029 -018 -0380529 056083 054 -011 -02 STM0732 037 -038 -11 -177I -119 -063|-157 -224 -169J -137 -075 -105 -0140128 -014 -016 17 065 123 025 01 STM0733 051 0348 -006 -163J -103 0899 -101 -024 -125 -086 -061 -0770245 -007 -0020078 214 121 1670608 151 STM0734 -06 -084 -131 [ -162 -153J -069] -Z35 -37~'-2-i] -02 -029 -030044 -0191845 -039 063 022 072 -025 178 STM0735 054 -0 •002 -12 -055 -039 -077 -1220589 -061 -058 -0920306 -004 -0480612 226 073 1590065 039 STM0736 0650381 -017 -077 -045 02730134 -109 -053 -052 -021 -026098606361084 1064 198 118 1871204 044 STM0737 01 0221 -033 -128 -09 0036 -054 -142 -059 mm -039 -0270.204041403760517 21 068 149 107 046 STM0738 -01 -133 -131 Qϊliεi] -145 -089 -129 ^r-25β.^N-172| -091 -135^1 S2| -12 0950524 -052 -0 112 005 -138 006 STM0739 -06 -084 -099 -113 -067 -118 -139 -173 -196)0063 -065 -085 -103 -048 -097 -027 041 -03 064 -066 -07 STM0740 0340308 -073 -111 -07 002 -042[-156) -088 -033 -056 -0690726017505390935 176 091 1620878 076 STM0741 0660417 -007 -128 -093 -028 -012 -044 -089 -09 -02 -0730107 0120365 075 157 038 1530092 042 STM0742 0407280499 -1018E-04 0479 -01 -09 -067 -086 -053L-152I -0090271 1251097 215 043 1350084 -03 STM0743 -02 002 -046 -144 -051 0411 -027 -146 -1220049 -074 -1120225 -02 -021 024 071 -01 158 -009 -02 STM0744 0590684 -052F-179¹ -029 -0330171 03030782 -123 -036 -031 0902003911861207 204 118 1740473 069 STM0745 0160148 -⁰⁴²LiLJTJ -°⁷⁶ 0062 -003 -08 -009 -065 -042 -047037703670761 0437 221 047 2131166 104 STM0746 0480618 -049 -122 -043 0498 -004 -088 -069 -069 -083 -0.20699001503391195 177 134 2681103 056 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0749 0610677 -076 -125 -0820269 -056 -123 -093 -049 -066 -0570451 -021 -0230677 245099 2030356 147

STM0750 01 1025 1229 -0740042136900341262,feT'85J -011265423590231058502880229 011 033 1231645 076

STM0756 0420304 -0120449 -014 -07 -036 -0081141 1165061505081561 -0770162 -028 -02 -01 -07 -063 033

STM0757 -020208 -002 -0 -031016602280354 -0820058 -048 -053 -068 -061 -092 -104 -01 025 215 -075 -09

STM0758 -02 019 -021 -034028902560061 -069 -071 -019 -049 -14 -103 -008 -028 -045 -11 036 -09 -051 -08

STM0759 0190742 -002 -06105340526 -033 -101 -001 -046 -0360038 -036 -0370645 -019 -01 169 083 -092 058

STM0760 _jO4 -027 -115 -081 -059 -046 -017 -134[^~T73jfl#### -039 -08807930283 -0040543 092 -03 1 1 -013 004

STM0761 -15i -059 -03 00601970206 -044 -025 -13 -049113300360099 055

STM0762 -14 -034 -081 -02 001 -051 -0_15_-0!»_-1390031

-0 θs[

-1 sϊ\ -063 -06

STM0763 s 045 -014 -023 -143 -057 -037[-1J3 _I!73_-1j98' -113 -059 -0670504 -003 -0170749 146037 1650013 042

STM0764 -040078 -056 -1360094 -027 -093 -05 -089 -116 -114 -046 -087 -062 -018 037 084 -0 128 -06 016

STM0765 _-1 -088 _-14 -061 -0450014[Tw] -084 -084 -059 -051 -086 014 -05 048 -107 -08

STM0765 f-ie] -111 -17| 002 -02 -042 -143

-1 -124 -044 -054HiSeI -0? -1 -01 -112 -05

STM0766 -010124 0252 -142 -007049704290386 -091 -113 -054 -0460592010502940332 135052 1410194 103

STM0769 0660389 -039 -138 -007 -026 -011 -063 -0311111111111 -03 -0620538022604681094 219 149 2.110977 053

STM0770 0630326 -031 -10900530101 009 -025 -009 -0590208 01 -002049701410632 175097 1760337 027

STM0771 -06 -026 -009 -1010171 0280609 -086 -13 -103 -07 -117[Tκ| -069 -052 -05β[_-1_9) -O β[j2jjj -124 -07

STM0772 0910042 -051 [JTMJ -071 -011 -026 -1050237 -125 -054 -055014300850067 021 134071 1830611 068

STM0773 044 -037 -110282 -044 -035 -029 -069 -08827881391 -0140662 -086 -018 023 -06 -02 104 071 06

STM0774 015 -083 0695093712440156157308731081 -06508520205_^0415 -08320980083 -02127 054 -045 186

STM0775 -11 -115 -032 -069[_j1J>2] -137 -021 -103 -063 -112 -04 -074 j-251) -095 -133 -135 -1 -13 -130971 -14

STM0776 021 -017 0253 -086 -059 -009 -0290106 -01 ##### -087 -02502460152 -030605 143055 1110624 049

STM0777 -11 -08 070639 -0480699 -0870167[Trø] -02912120691 -06 -0750705 -035 -09 06 -02 047 016

STM0778 -05 -0 0087 -051008201530041 -023 -0741082 002 -088 -0380018 -065 -012 -07251 -07 -082 -02

STM0779 0310368 -021 -1 -031 -011 -055 -08 -12 -048 -103 -111 -049016900480597 086021 1590093 059

STM0780 090075 -086 -093 -023 -017 -039 -061 -1 -086 0381 -0460886 2049 1890177 068

STM07Θ1 Gill⁰⁰⁹⁴ -093 -0710226 -002 -086 -058 -0491193

-021 -089 -1 ttQTβ] -Qi] -19 -197] -11

STM0782 -02 -082 -0780024 036 -0350574 -035 -016 -067 -0781138 -102 -00515 -07 -07 -04 -0 -081 002

STM0783 -07 -009 -0460082 -004 -022 ##### -06 -072 -053 -163 -087 -061 -0 -07[_-27j -07 -06

STM0784 -03 -09 -039 -116 -09 -069 -148 -1090113 zlZή -043 -086 -06053 -12 -012 -05

STM0785 083

-0201610822 -032 -062 -03102830003 -0580859 084 113098 1480517 092

STM0786 0690643 0672 -08402490473 -067 -016 032 -1060221 -019 -027 -0510269 -032 046 -02 1541726 101

STM0787 040314 -028 1120453 -0290225 -0150232 -0795E-040015036204070371 -062 26075 -041145 058

STM0788 0440228 -052 -084 -00900880038 -044 -08 -072 -058 0120383 -00409950312 268086 155 -015 117

STM0789 0260456 0429 -099 -13805040011 -092 -055 -064 -0250002 -0120113 0090361 233 131 1670819 069

STM0791 -01 -005 -048 -03 -0150222 -006 -043 -0290582 -034 -095 -066 -0480052 -006 -04025 071 -018 156

STM0792 060471 -014 -032 -0420561 -013 -043 -061 mm -058 -077051707630081 013 217 08 1690561 023

STM0793 0870018 -064 -112 -099 -002 -021708 -102 -019 -027 -01100690269 -0110447 181 071 1610133 039

STM0794 -09 -004 -0810006 -102 -075019500740361 -105 -06 -079 -099 -1350848 -006 -08 -O3[j2j] -035 064

STM0795 -080335 0046 -003 -062 -024 -01 1173 -039 ##### 14280487 -035 -03507210355 015082 087 -049 082

STM0796 -030472 -003 -092 -029 -049 -001 -146 -087 -0290394 -0560564 -0070188 -015 157092 153 026 033

STM0797 02 005 -089[-164J -0970123 -016 -14 -111 -005 -055 -O220132072610160379 211 16 1760069 068

STM0798 -1 -083 -039 -036 -0810396 -060213 -08 -063 -06708060031 -036 -0360576 096 -01 1640835 125

STM08Q0 -09 -038 -013 -02901550259 -013 -021 -016 -017 -075 -0.230091 -004 -067 -002 -11 016|_-1_β] -038 -08

STM0801 -00754 -009^-177] 0338 -095 -003 111 -133 ##### -0870175 -0431142 -0980093 -0006 08 -02 003

STM0802 0860537 -011 -037 -025 -0390085 -011 -064 -032 -081 -0010737069505370629 172042 2.240185 049

STM0803 0670359 -068 -042 -0330441 -038 -011 -078 ##### 0037 -049 066 -028 0710944 265 113 2120381 098

STM0804 0830355 -032 -096 -0430123 -01 -109 -031 -037 -052 -033 031 -033 -0090269 146 12 2020737 089

STM0805 0180084 0152 -096 -011 -024 -022 -0970367##### -069 -1040422 -011 -0160173 106089 092 -08 -01

STM0806 -O 0534 -09 -12 -0310514 -009 -07 -047 -097 -086 -0931379 -13 -112 -073 022036 044 -117 -04 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0809 -01 -093 -086 -041 -091 -081 -087 -15 -1190915 -084 -101 -035 -119 -057 -06 013 -06 005 -086 -04

STM0810 -1 -076 -099 -06 -038 -112 -071 -128 -126##### -146 -064 -143 -101 [^58] 0045[Ts] -1 ] -27 -244[ -15

STM0811 017 -008 -024 -106 0209 0042 -007 -003 -045 -05 -02903410274096105610418 167069 1730313 08

STM0812 -01 -006 -011 -073 -012 -022026200580991 #####J_-2_3Sl] -082 -049 -031 -0631446 -03 -08 388^-1j64] -06

STM0813 043 0246 0667 0642 0514 113102220546 -0340138194305090084008200190971 03057 -090865 093

STM0814 082 0337 -069 -139 -043 030232 -093 -062 ##### 0125 -0310126039107830993 24177 221 065 076

STM0815 078 0208 -086 -081 -073 -0370176 -081 -073 -082 -037 -1160095 -031 -010407 102 105 251 0318 11

STM0816 -03 0657 0319 -056 -006 -042 -011 -083 009 -05 -138 -0370435 -0750208 -014 035 -06 002 -001 -02

STM0817 -04 0306 f-1_73 { -127 0337 -0290384 -067 -022 -066 -098 -0821787[TT₄] -062 -148 JH3 -04 184 -054 -03

STM0818 -06 0388 0017 -047 -037 -1140358 -0150306 -0082344 -04 -0990283 -04 -056[ -19] -04 -2.8 -2.78I -05

STM0819 -03 -018 -046 -029 -032 -02501810207 -006 -0780681 -1180061 01403282838 014 -13 -09 -012 044

STM0820 -06 -034 -146 -083 -084 -166[ -037107503810069 -054017β| -20β| -089 -048 -049 -09 -08 -14 -097 -1

STM0821 039 -039 -049 0119 -028 -0010358 [vTsβ] 0097 -0251021 -0610811 -0630245 -104 038 -0 019 -011 -04

STM0822 -11 -097 -014 GΪ₆₈J 0882 -086 -0020771051500090176 -098 -058 -093 05 032 -02 -08 304 267 -02

STM0823 -01 -012 0234 0366 -094 -01308350488 -115 -018 -111 -0970578045906460473 143026 1090027 -04

STM0825 043 0235 0151 ΪΞE -047 0513 -012 -084 -016 ##### 0099 -0160441051906730682 128091 1630547 075

STM0826 036 -014 -123 0426 0455 00870409 -0250626 -017 052 -056 -057 -097 -0570753 159 -03 -032489 -01

STM0827 -01 -001 008 -055 -012 004507210407 -014 -0080282 -043 -042 -0590249 001 -09009 277 -012 025

STM0828 -04 0123 0496 0163 -056 -02303910432 -045 -0750545 -0360314 -02100430042 -09 184 -08 128 007

STM0829 015 -026 •045 -048 -005 -0630347 -0060302 -081 -038 -095 -109 006 -0220691 -01 057 -020777 072

STM0830 048 -042 -141 0868 0373 -0720508 -0980057 ##### -149 -0350806 -0961386 -008[TU -03J -27] 1686 09

STM0831 002 0069 -108 146 -077 -026 -O33LJ65J -049 002 -006 -0480317 -018 -031 -004 049062 124 -02 023

STM0832 035 -055 -012 0079 -062 -045 -0581023 -10501610395158609521508 0870637 -02 05 -03 -005 046

STM0833 093 0329 0137 -129 -024 -025 -034 -0490654 -012 -0690004 -012 -041 -051 113 18 01 1110753 032

STM0834 03 0258 -015 0364 0045 0076044913660697 ##### 1630235 -07[-JUTII 181 -077 -11 -06 -07 -065 089

STM0835 044 0566 -058 0685 -016 -0390701 -0250546 -076 -068 2132368 -10300871071 -04 -01 1680477 -05

STM0836 029 0096 0875 -073 -094 -05 -0310343 -095##### 19390348 -095 -096 -103 -014 -08 -0 -05 -066 -06

STM0837 103 0062 1571 1072 0345 11040804 20710250239 -016 -061 -12409551187 -012 003 -07 -110889 055

STM0838 019 0211 0148 -121 -03 -0530474 0581145 -042 -0270584075903090064 -007 081 098 024 -022 027

STM0839 -05 -053 -012 1 06620484 -054 -057 -0850502 -095 -029 014 -0760043 -06 1 -05 Qz4J -011 022

STM0840 -03 -029 0298 -003 -017 063 -0060009 -047 082 -07206851128 -017 -039

079 -1 -054 -08

STM0841 047 0358 -012 -125 -0730681 -026 -103 059 -076 -056 -038 -003 -03 -011 1801 192 143 236 055 074

STM0842 002 -002 0485 -121 02650081 -04503120291 06462594 -0192432 -079 -091 -046 -0029 -05 -076 -09

STM0843 07 0211 1041 -086 00190673027403T40344 -0050223 -011 -0 -016 0260391 044 -0 1350041 051

STM0844 099 0223 0532 091 -0320515029203450933 -06 -0 β 065T 0042 -012 -0060236 002049 _:?^~-7Ji] 024

STM0845 -03 -002 -113 -023 106606160319 -045[T(STj -0T5081205192248 -016009404T5 0T5023 -0801TT 036

STM0846 011 017 -036 I -ΪMBI -079 -051 -033 -1 -077 mm -03 -0540214023806020966 15T 085 1780291 154

STM0847 029 0381 0301 -142 0122 -02103891155[TS) -0T1 -0371403 -015049505680156 122066 1610641 059

STM0848 169 1141 1079 0541 00Θ1 14909850718172504210121 -00803480552 -0480786 045 113 0520255 -03

STM0849 098 0249 -009 0591 -04 -0440439 0410014 154207608781316013304610526 -12065 -12 -028 045

STM0850 002 -034 -034 0224 -054 -0650044 -0020527 -046 [TTO] -11 [-1_9iJ -02502510646 -07 -09 -130624 -05

STM0851 -03 -008 0017 0795 -0170194036609061327 -04 -121 -08 -052 -02 -0231572 006 -05 -041707 -02

STM0852 056 0336 0124 0247 -019 -0720394 -006 055##### -0340541 -109 -083 -0580702 029 -04 -121166 025

STM0853 069 0171 0201 -095 -029 -004 -073 -109 -135 ##### -045 -00507940636 -0470595 124 015 1440343 -0

STM0854 -05 -051 0431 -133 -077 -004 -06 -153 -193 1232 -1 -017 -0530204 -01 -023 059 -02 088 -003 059

STM0855 -135 -13 -051 -005 -064 -145,-198 -2.38jfl##*# -1711 -056 -069 -097 -101 -118 008 -12 003 -135 -03

STM0856 013 -053 0081 0009 -099 0333 -08 -103 -068 -094 -095 -13901950404 009 -048 -11 -01 083 -024 032

STM0857 -06 -084 -064 0309 -007 0221 -066 -034 -104 -053 013 -08 -005 -022 -078 -069 -11 -1 -42 -18j -09

STM0858 -06 -087 0674 -01 -005 0502 -035068102540209 -0840176 -023 -042 -0940505 062 -04 -38I-086 -13

STM0859 -05 -055 -044 0201 0209 0151 -047 -088 -1420239 -09 -037 -058 -038 -037 -061 -02 -06 -31 !θ 758 -05 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0863 0310020086 109300340639 -00302931231 -08 -104 -0280422 -033 -036 -08 -07 -02 144 -075 -06

STM0864 1130254 -009 -0460397 -039 -025 -1050388 -1250124 -068 017 -01904490346 207 09 150752 058

STM0865 090599 -1130195 011 -112 -004 -008 -122 -042 -11703730608 -07 -148 -047 -11

-14

STM0866 05607451538 01140105105108131521 -035 -051 -0521378 1470525 -017 -022 _v -1 064 -04 -12 -01

STM0867 03604361019 -01805560529 -002 -0 11401220425 -0190495 02 -0040476 049 133 055 -038 -01

STM0868 06804280305 0092040205260377052209810469 -077 -0070075006902760895 [~T^ 005 564 -112 011

STM0869 -0406071554 -087 -08054905710707 -11 111801280284 109 -09408650715 127013 2540946 164

STM0870 06802980401 0183062504390138 -012043214710441 -011 -0050194 -0440429 013 -02 -030395 -01

STM0871 0040189 -024 -0090025 -06 -042 -061 -042 -026 -0720948 -009 -026 -127 -116(~T§ -09 -06 -121 -14

STM0872 0290436 -015 -148 027 -021 -021 -049 -031 -047 -006 -01710260335 -0030317 127 116 1370225 011

STM0873 16709331996 -077 -0410231038306980727 -031 -07912030306 -056 -030068 086077 1240083 -01

STMO874 096001820070863 -011 1416 068105213441624 -09202110181 -103 -012 -122 -0 -12 -06 -087 -01

STM0875 1380106 -038 -0790017008311370205 -061 -041 -01 -071 -0010683 0090644 246 139 1740587 098

STM0876 05 -0080042 -143 -0610512 -056 -127 -044 -09 -027 -0340236022202360756 169092 112 087 112

STM0877 03703190176 ■03 -020777 -013 -101 -016 -053 -014 -0030781028300150941 162073 2190583 084

STM0878 07 -078 042 0077 -1130218 -067044811630008 -0610332023151570462 -072 033 -01 -I]TU] 018

STM0879 019 -042 -02 -0810773 0270286 -029 -009 -064 -079 -025 -01 -00903160317 103076 05 -016 018

STM0880 -02 -0220585 0316 05905440684067611310791 -069 -009 -006 -0640476 -008 033 134 -11 -051 006

STM0881 -040047 015 -13400260289 -02 -0 θ[-1 sjj -089 -035 -0.201950242 -0280019 049004 061 -046 -03

STM0882 080197 029 07890681 -0140506 -048 -078 ##### 1142091 03106870601 1309 003095 -04 1583 086

STM0884 -09 -05 -0620165 -001 -03 -019 -087 -06##### -068 -05 -0630095 -063 -071 -15 -02^32] -106 -09

STM0885 -07 -009 -023 -0640047 -009 -012 -05 -012 -023 -1120012 -01 -06801110495 022017 -03 -122 067

STM0886 016 -006 -027 0075 -053 -00144 -012 -047 ##### -047 -0170097023605150759 -0 -01 -022242 044

STM0887 12401280138 129 -0681011 -037 -109 -063 -07 -056126708870812 -0151221 -03053 068 -033 -01

STM0887 103 -001 -004 1327 -0280578 -053 -117 -058 -047 -066 110549029200951163 -01 031 014 034 034

STM0888 -05 0120323 -073 -086 -0590171 -0250171 -03106590081 015 04 -080588 199

STM0889 -08 -0040656 -099 -096 -071 -0250642 -038 -0430539 -001

-07 -04 [^7] -121 059

STM0890 -0200760934 0323 -0260152 -0210198 -027 -02110541219 -057 -0010125 -02 -04 -04 -00205 06

STM0891 07408060306 -02505370707 -0030091080503090736 -0160321 -00902510799 09016 0960403 05

STM0892 09405660176 -0120413092909010631 081 -068 -071054806460345 -0230568 137052 060487 02

STM0893 0660722 -034 -115 -015 -01 -084 -096 -036 -026 -038 -0071116002101730906 23 198 172 002 057

STM0894 0760503 -008 -14 -0690466 -021 -087 -06 -074 -049 -078 -0150518 -0191117 22 108 2130249 071

STM0895 08608760103 -131 -09 -046 -019 -11 -0.25 -1 -016 -10605760597 -0140939 314052 2550052 -0

STM08951ι 1120168 -023 -12 -072 -006 -016 -133 -077##### -093 -040511 -00706130961 19 101 168 -017 04

STM0896 1290986 -O 57 ₄^77] -024 -0380208 -019 -05 -064 -057 -081 -008047600681014 131 133 Z061059 025

STM0897 063 -003 -009 -13 -082 -031 -077 -132 -095 -115 -094 -084 061 -01 -0420928 204 103 2410515 041

STM0898 0680477 -024 -166 -042 -0730083 -11 -085 ##### -085 0050644029504020546 244 13 180199 097

STM0898A 10204510078 *-194: -0760125 -074 -107 -053 -066 -034 -0080173 -008 -0021367 201 111 1820506 126

STM0899 0830819 -008 -0140028 -026 -065 -033 -037 -063 -020649019400940452 229 127 208 -031 051

STM0900 070211 -03 -05101590215 -115 -02 -089 -086 -0260355138801160544 193057 24 04 041

STM0901 025 033 -062 -114 030404 -007 -056 #####0021 02303820827 -1090909 222 153 2.370952 091

STM0902 093 039 -034 -131 -0140365 -087 -111 -095 -06 -00505390509 -0170422 19 123 1890826 097

STM0903 1020764 -04 0138 -029 -089 -068##### -02 -0330161059202110644 181 168 181061 015

STM0904 035 -01 -028 0154 -085 -118 -07 -105 -052017603080196 -0160226 255 19 1840406 051

STM0905 -01 0340056 0496 -003 -109 -044##### -06502110102085600760707 169 177 1870132 019

STM0906 0140487 -O 16 0543 -033 -119 -101 -076 -008 -0210222022505431215 23 157 Z020686 069

STM0907 05804980173 02110063 0581503 -0660328 -0230534128300731271 135 172 1150181 097

STM0908 016 -029 -041 -058 -064 -015 -031 ##### 11990128 -077 -014 041 -013 -02047 002 -071 057

STM0909 061 035 -049 -0240101 -1180549##### -037 -0890113017902140939 197058 1670891 108

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0913 104 -009 ^44^f§|] -06 -056 -017 -047 -042##### -035 -093 -007000514310886 2 118 190947 085 STM0914 -020736 -019 -142 -095 00650334 -104 -024 -084 -1 -014 018050107440702 215 166 2590557 084 STMO915 0066770033889900003366^L--11JJ8] -026 -0030008 -076 -075 ##### -02 0380352015102671044 194 123 2250573 074

STM0916 0340534 -O 71 -099 -13 -004 -092 -07 -0 -101 -034 -039 -003 03705280111 136 06 1240284 -0 STM09161106704410185 -11 -062 01340356 -135 -102 -037 -028 -0280082018701091009 178 111 2260449052

STM0917 -140213 -027 -1120497 -08514440164 -08 -0451471 -0520978 -028 -069 -066 064 -11 -24 -221 -i^"ιs1

STM0918 044 041 -052^^ -067 0402 -043 -007 -061 -0720091 -01306880556 -0120339 231 129 1460373 034

STMO919 04902830084 -135 -065 0031 -031 -111 -0 -055 -073 -010534004802010331 233 116 191 0541 074

STM0920 067 044 -O 15 -128 -142 0473 -009 -035 -018 -094 -035 -088 -001028310541428 182058 2650434 12

STM0921 05 -011 -066 -1 -038 -0040358 -078 -079 -117 -015 -0690382012905510526 19 186 1280535 029

STM0922 024 001 -05 -051 -029 -052 -02 -068 -059 -044 -028 -0390348 -032 0050919 005 -01 057 -014 -01

STM0923 04702270162 -073 -004 -015 -011 -09 -073 -029 -00801010279 -0203580998 03011 1280228 053

STM0925S 0350146 -047 -0720112 -0120138 -0030116 #####0391 -071 -017 02501110252 14061 131 -016 061

STM0927 -040313 -017 -008 022 -041 -007 -089 -094##### -042 -064 -031 -035 -017 -063 -07 -07 -05 -132 02

STM0928 0640678 -06 -081 -03 -0180312 -105 -062 -0770011 -0607160649 -031 1131 219 136 1531295 066

STM0929 055 035 OOO7Q2IT] -116 -014 -045 -06 -13 -081 -017 -071 -010572 -0290916 213 144 2110916 07

STM0930 -1 [__-£β] 0295 -132 -06 -099 -0660406 -1322072 -146 -049 -06 -136 -1080398 -02 -06 -03[;152J -12

STM0931 0880141 005 -133 -01 032307070626 -0760838 -056 -0880421 -04400050789 128 136 172 -008 057

STM0931 021 0472 -026 -093 -018 020107161623 -092 133 -001 -048 -007 -03603831169 144 081 370234 058

STM0932 -03 -036 -00303590087 -0040626 0750594 -042 -003 -098 -106 -063 -068 -042 035

-081 -02

STM0933 0240156 -047 -062 -117 0665 -013 -105 -042 -062 -088 -0070311097108270695 19 108 2311032099

STM0934 0551053 -035 -141 -039 0522 -014 058 -029##### -061 -017 04 03506160818 163 16229 002 06

STM0934 01604180222 -0470173 00150376076504851695 -0570081032807320424 103 093 115 142 -006025

STM0935 -0 08303940062 -038 0421 -0206220107 -0222387 -10303450191 -069 -052 243 -02 03 071 025

STM0936 07 -O 32 -031 -104 -074 0608 -061 -031 -036 -095 -09 -04 -024 113 -082 -057 084 034 0832014 -02

STM0937 052034707570385 -033 -09602610109078500320823 06 -141 -116 -0310048 -11 02 05 -001 -03

STM0938 -01 -091 -087 -076 -075 02750123 -0870135001404160417 ##### -09514270645 015002 1150689 197

STM0939 023 062 -0061502 003 -0820911 -121 11851041128705840186 -04807880056 04 -0 3152866 087

STM0940 -01 -0304140624 -002 093 -01804380581 ##### 33480349 -041 12770213 -012 07 -01 205 -065 007

STM0941 0230277023402740263 0265153706740333 -033 -135 -031 -148 -0730529 -037 -02 -02 006 -02 036

STM0942 0360571 -017 -061 0697 048 -006 -11 -073 -067 -066 -0061146038305391092 169068 145 077 071

STM0943 061 0652 -062 -1j43 -06 0611 -073 -103Q?59J -074 -027 -0251185 -0104830833 32 09 210164 096

STM0944 104 1205 -026[^e] -054 -007 -054 -123 -098 -074 -051 -08303430452 -0120746 195 107 Z140753 083

STM0945 043 -006 -016 -113 -019 -0030573 -041 -116 -066 -001 -020232 039 -0050539 178057 1730096 068

STM0947 -040172 -034 0170199 -01200660642 -0210152 -035 -053 -0451168 -015 -03 -04 -03J -28_-1'72] -09

STM0948 -04 -007 -022 -048 -002 021 -007 -111 -035 -092 -05702910079 -0409510707 177033 254 087 055

STM0950 01805380235 -036 071 12830282 0480813 -079 -078 -061 017 -0222465 -082 023003 026 -085_,263

STM0951 031 -008 -029 -029 -021 0150131 fW|βj 0203 #####0238 -058 -073 -00710020051 019012 0740653 144

STM0952 041 0465 -08 -113 -061 00260181 -146 -121 -063 -066 -0170859021805320708 252 109 2030355 028

STM0953 1290207 -009 -074 -091 0187 -068 -002 -083 -091 -022056802960265 0510802 211 154 1920576 116

STM0954 0680099 -O 51 -137 -041 -006 -003 -036 -076 -061 -024 -023 233 109 2670784 117

STM0955 -00207 -O 77 -083 -047 -092 -053 -103 -1280181 -054[-19ij

-06 -05 -040404 -08

STMO956 05903080188 -091 -039 0018020805380091 -101 -023 -046032502820504 1057 192 159 209 1452 069

STM0957 0990063 -052 -094 -008 -009 -032 -105 -061 -061 -098 -00584017409840691 175 093 2110735 091

STM0958 -0 -08 -O 93 -099 -141 -033[ -154 _j238 -262 -089 -083 -057 067 -067 -07 -095 032 -08 099 -026 -02

STM0959 041 00290262 -098 -045 040801110529 -0 -199 -061 -16 -09 -115 -126 -078 -01 -07 -1 -124 -07

STM0960 0090264 -018 -121 -014 -0220168 -03 -071 ##### -0780211 -03 -079 0130072 141 053 1510638 077

STM0961 0370871 0298, -155 _-03_^ 0056 -0780598 -106 -082 -009 -007 J)0£ -005 -0040289 179 123 1170663 061

STM0962 -09 -0740368 -038 -173¹, -055 -0950374 -114 ##### -12 -0481 -172 -2131 -005 -11 -14 -03 -09|^58j -03 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM0968 -00495 03580145 -005 0081 -0230135 -02 -00209550186 -034 -0190233 -017 -03013 070114 052

STM0969 -05 -035 -04 -007 -004 -041 -009 -05501860179 -002 -023 -007 -089 -057 -05 -14

STM0970 -06 -06801760024 -078 -058002100461649 -15 -09

STM0971 040003 -035 0790562 054 04706020868 -05

STM0972 -01 -051071501120233 -056 -03 -001 -069 -148 -092 -074 -103 -114 -084 -135 -09

STM0973 056 -001 -0080315 -105 -068 -00201780534 -029 -05

STM0974 -03 -044 -017 -0520215 -0590092 -055 -037

-130247] -183^-075 -118 -119 j -164^ -1

STM0975 0641554 1260757 047 1012070508930676 ##### 011 -072 -020521 -013 -026 041 -0 -070431 029

STM0976 0601580116 -0670633 0497 -024 1036 -0205050421 002702270348 -0060144 163 145 1290676 046

STM0977 -04 -09806910612 -054 -057 -034 -0340199 -118 -2.68 -121 -224 -1 -024 -041 -08 -OeHzS -065 -05

STM0978 I -26 -235 -279 -267 -351 -2.84 -339 -407 -39 -208 -Z7i| -1 45 -205 -195 -175 _j-IJSj -05 -09 -1 -142 -»|r_-16]

STM0979 -020298 058900610388 02490559 0350435055901790439 -076 -05403920022 -08 -Oif-Z3J 062 -0

STM0980 08903790127 -086 -052 -001 -034 -0750044 -041 -047 -02 -042 -02213280112 131 029 218 049 08

STM0981 1040264 -014 -13 -049 027 -036 -079 -034 -072 -046 -030505027702120982 171 118 230676 03

STM0982 03910080049 -11 -025 -0120446 -043 -078 -1 -12 -011 -0040145 -001 1038 169043 2840724 058

STM0983 0520516 003 -0350322 01930265 -034 -06521331734 -038 -062 -08509650236 -04068 -020947 156

STM0984 0430326 -033 -055 -05 0147 -051 -09 -0170232 003 -019043904040458 099 25 102 221 0829 046

STM0985 0870362 -022 -069 -034 0178019β' _-1θ' -111 -035 -028 023 1630382 -034 05 _^92063 1950444 09

STM0986 0080081030101160086 -051 1084095103540143 -08801931736 -118 -063 091 [_-15j 004 -08 -028 024

STM0987 -05 11610706 -0790927 00651281 0491 1055 -163J 00120804 056 -0910108 -041 115 -03 079 -02 073

STM0988 1020578 -074 -094 -024 0678 -053 -108 -02 ##### -02500250935 -02701780525 108083 2561046 119

STM0989 0860561 -011 -011 024 0787068303351308 #####| -15213955 -0240643 -0220317 122041 0020804 029

STM0990 0940482 -03 -112 -035 05990149 -056 -052 -062 -07500990302025706860619 244 111 244 027 045

STM0991 00807250505 0340412 -015096806830967##### -104 -046 -133 -038 -005 -063 -14 -03 -12J_-1J»J 06

STM0992 071 123 0061034 -016 008701770382 -0330091039313060293 11500051989 101 035 0460165 051

STM0993 0740395 -05 -142 -078 0376 -049 -049 -012 -053 -08 -009 -05405090422 103 141 161 1990708 092

STM0994 0070242 -029 -124 017 03990105 -064 -034 -005 -058 -0550676 03404431171 185 124 2.06 059 07

STM0995 09909410137 0570004 0836040611520792 ##### 328832520096 -01715861272 037 131 -090337 219

STM0996 025 -0220825 -112 -012 0325 -018 -0010526 -0940767 -14 -005 -049 018 002 064 -0 063 -021 -04

STM0997 07404920884 -089 -054 -0410089 -065 -002 -017 -0580101018103780223 -061 01 -02 120389 -01

STM0998 0650082 -029 -142 -043 -037 -014 -096 -08 -034 -05700170137 -00302250975 151 12 150313 006

STM0999 -01 -04800990537 011 -003 -011 05480808 -005[-193| -052 -08 -049 -053 -078 -03 -11 Qijjj -082 -03

STM1000 0790468 -017 -115 -016 0246 -005 -073 -055 -044 -014 -0381028011405110566 219 112 223 123 074

STM1001 -1 -097 -095 -077 -019 -033 -03 -Λ2[-192J 0672 -0690188 -079 043 -086 -084 0018 0360505 06

STM1002 001 -01201250531 013 01670109 -00100080083 -013 -041 0082762 -0360113 -0701i| -3il -027 -05

STM1003 0030038 050725 -01 0546 -0380093 -008016418062333 -0150018 -028 -014 -07 -θL-26jθ542 011

STM1004 1090013 -0470165 -148 -054 0780614 -0140113 -062 -0.27 -02 -067 -0310909 034 03 024 -005 029

STM1005 0830492 -0780674 002 -099 -005 -012 069 -048 ^v -1 -105 -049 -114P-Te] 0572 -07

-086J^"~-1^~7l

STM1006 04706350033 -118 -098 0554 -024 -072 -047 -116 -016018300270138 0420816 173 105 1620959 057

STM1007 001 -0090818 -12 -074 -021 -061 -002 -119 ##### 10540747 113 -089 -017 311 -04 007

STM1008 S 1190845085609480357 0170771 Ojy ^0/190725 -032 -045 -019 -067 -018 -046 -09 -04

STM10101ι -01 -009 -023 -0410132 -042 -126 L -2

88 -2^310528 -019 -0520103 -013 -025 -011 -03 -03 -080004 01

STM1011 13607320139 -009 032 0602004601020071 ##### D 29502440241 084 -0161838 -01 042 -020193 04

STM1018 -010406 -035pT63] -03 -002 -033 -099 -032 -094 -096 -0640657058201550848 215 1 2210372 003

STM1020 0630842 -007 0240475 0268 -001 -03301870044009803140323020106650154 -03 -0 -090988 076

STM10211ι 00302920099 -073 -046 -016 -111 -O 89 -086 ##### -040008 -045 -0190349 -001 117 03 099 -067 072

STM1022 009 -028080910710506 1409 -017 -058 -068 -0591394014800880307 -0820257 -03 -01 [Ti] -125 -05

STM1023 -02 -0410575 007 -025 01170107 -01404260245 -00708651963 -0371346 019 -07007 -050444 066

STM1024 0980395 -022 -124 -021 -048 -049 -039 -015 -031 -028 -0180503011904670638 197032 2090766 082 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1029 014 -0051228 0142 -003 072 -02808220094 -02904040Θ14 -012 -08801470724 -02 049 -01 -06 087

STM1030 -050113| -16 -0580079 -0920037 -09091303550798 1744 -069 -055 -078 -034 -05 -05 0250442 021

STM1031 04510130141 06570457 111 068309130153 ##### D 421 02470001 -053 -013 -058 052 -03 0680702 02

STM1032 04605491448 03260449 -028 -023 -0730731 021 -127 -03303830688 0360555 108 003 0730743 -02

STM1033 -04 -0361295 -123 -088 1121 -06411160348 -028 -082 -005 -053 -0440361 0233 092 -04 8090247 069

STM1034 -09 -1 -099 -035 -018 -079 -02 -0550174 -037 -007 -083 -044 -108 -069 -011 -13 -09 -07 -Z38 -1

STM1035 -11 -091 -109 0124 -026 -058 -038 -0050736 -024 -058 -141 0269 -134 -061

-1 -14 -245 -08

STM1036 160266 1091 1650783 -014 -02 0.28 -0132843 -026 -0 -055 -06902170523 091 -O6Qv6J -121 025

STM1037 -14 -122 -001 -106 -075 -095 -089 -025 -0342164 -0430807 -11 015508232535 -02 -0 -09 -133 15

STM1038 -00068 -012 -089 -073 -008 -048 -0720506 -013 -082 -0220932 0516990616 168 081 2061422 24

STM1039 09708481459 0554 -02 0878 -01402770145 ##### -127 -161104561006 -028 -024 044 09 1044215 -03

STM1040 033 -036 -046 1080951 0018 -036 -058 -0160197 -16 -081 -0831225 -024 035 053 -05PTeJo 473 -1 • . i

STM1041 063 -035[ -173J 01680232 -034 0808330675 #####, >-2.39 0672 -12 -103 -062 -063 05 -04 -11| -18| -11

STM1042 0970304 -0 -0630101 03407190668 -052 ##### 00743678 -00207570387 092 126098 1890516 08

STM1043 -05 -073 -046 0165 002 -024 011 -028 -012 -0240302383605780426 -0020215 -07 004 -1 035 041

STM1044 -02 -0050115 -0320424 -025 -01 -01 0673 -0023916pTiτ| -034 -075 -011 -091 -09 -04 014 -054 015

STM1045 06208270525 05860389 0318 -005 -011 03580371 -0020203 -021 11130188 -021 -02 017 2020639 057

STM1046 -030155 -031 00440159 -025 007 -005 -0640623010607720482 -04608330745 -01 -01 0330353 03

STM1047 0650416 -045 -119 -082 0111 -06 -09 -059 -124 -068 -03402930541 03630519 179 101 2640421 035

STM1048 -07 -027 -007 -019 -002 -047 -0030005^028 2182.006 -015 -147pT56| -039 -014 -11 -04| -2.i] -134 -07

STM10481I -03 0290455 08440533 02510266 -003L-IjKj] -01 -028 -1370466 0160365 -013 013 031 -050089 059

STM1049 -0805160057 -0770089 -02400980007 -145 -07827490817 -053 -0331455 -024 -01 -01 -01 -006 122

STM1050 -07 -018 -023 01920015 -041 0253 -07 -084 -016 -054 -056 -059 -068 -03 -062 -11 -05 -19 -145 -04

STM1051 -04 -009 -044 01130237 -052 037009400860132 -048 -0220057 -106 -09 -02 -2| -139 -01

STM1053 -05 -081 -101 01230332 -004 -061 -097 -0340685 -1180793 078 -08 -16 -072 j_-1_7|

STM1054 -07 -046 -064 -013 -014 -040479 -082 -0610493 -083 -076QgT] -1 -23 -088 -13

STM1055 -1 -058 -101 -031 008

-13 -009 -084 -0030219 -034 -105 -1 -09 -1 -142 -1

STM1056 01 0275 -107 -191J -09 014 -025 -097 -104 -077 -125 -056 035003800440591 102 028 1880035 066

STM1057 -1 -0060003 0266 -005 •007 -016 -034 -002mm -058 -11 -059 -111 -0141468 -03 -06 -09 -065 -01

STM1058 0420842 -058 -086 -009 0129 -041 -073 -021 061 -0360476 -007 028 -0090344 206 057 162 -009 004

STM1059 -01 02340003 -115 -034 00790031 0163 -0 -032 -054 -0790515 -021 02850095 038023 1270722 036

STM1060 005 -0760125 0050015 11730125 1943 -071 -029 -0430513 1003 -019 -031 -039 016 -05 -070642 -06

STM1061 11 06930753 0749 -049 -0240089 -00405320263 P ■185! -003 -002 05100831005 -01 015 -02 -083 021

STM1061 089 0540764 1384 -056 -01601820078 0760092 -151 -0603140202 -015 093 -11 -02 -09 -104 008

STM1062 0770625019407050775 09480318 -1180155 123 -0330027129505971239 -018 -02099 -052281 096

STM1063 0280152 -03504980287 -025 -041 -0060206 -006044318830532 -1010344 -09 162 -11 ^~2Λ -1_95J 028

STM1064 ' 01 -067 -0060725 -021 -047 -026 -105 -080754 D683 -047 -018 -039 -129 -032 -11 -02_ -2 IpI 02 -08

STM1065 034 -021 -091 -141 -071 0453 -033 -116 -02 -051 -03 -05 -005 -006 -011 085 15 052 17 1817 075

STM1066 058 -0070007 -129 -036 -039 -009 -073 -099 -115 -046 -01600280475 -01 0664 175 129 2450968 094

STM1067 -03 -079 -05502360095 -092 -0090513 -016 -129 D 505 -111 -0760074 -084 -01 -05 006 -i[_-185] -09

STM1068 0150048 0090248 -02 -00703330329000601720545 -087 -06806050251 -04 -06 047 -13 172 064

STM1069 0690505092206260289 0554 -001 1001 02931084 -103 -032 -0430198 -0260191 -01 -02 -00949 -02

STM1070 0170327 -033 -123 -007 0386 -007 -056 -062 -02 -071 -012 059 -05900290455 157 19 2190349 128

STM1071 06502550102 -062 -002 -033031506960215 ##### -0231.2781561 0838 -0040055 076 116 147 039 031

STM 1072 034 -01906520084 -053 0741 017503750134 -081336 -0081538 -07 -011 0515 -01 062 047 -012 038

STM1073 08105060426 -047 -081 0152 -084 -056 -050316 -02700880494127507021031 064 05 1150076 094

STM1074 099 027 057 -079 -094 0319 -032 -013 -082 -056 -02801830415341303661174 167 093 1651031 11

STM1075 0710592 -041 -062 -051 0558 025 -0170153 -067 -0250112 -029035803431101 199 127 1851119 072

STM1075 0420555 -0δ| -184J -092 -024 -02 -056 -031 -003 -037 -0251163 102400990917 181 119 1670768 041 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1079 0490336 -0.24 -055 -076 -029 -033 -033 -037 -012 -06502890332069500960663 2 11 261 -006 095 STM1080 061 0129009707350338 00120513 101 13540378 0560177 -042 -071 0031 0867 034 -03 -05 -079 -03 STM1081 -00003015802410099 -027 -001 -01903050153 -046 -067 -0 -053 -102 -049 108 -09[^27] -069 -12 STM1082 -03054904180275 -007 -0330135028401580505 -011 -092 -0292131 05250535 085 054 -02 -094 -04 STM1083 -010284 -039 -125 -O 42 -006 -0030767 -074 ##### -0530273033508840251 0046 171 064 083 -037 005 STM1084 0350434 037 -026 -034 -074 -02 -0830378 ###»#0123 -026 -007014903860287 122049 141 1452 02 STM1085 0760418 -031 10020186 -02805540152 007 -1041672 -073 -06700980426 -048 _^ 3 -0 -080529 019 STM1087 -01 -002 -08311910438 0103 0350258 -005 -048 -031 -055 -02 -019 -022 -021 [

_-1s] -02 STM1088 -03 -111 -059 -0490148 0135 -089 -118 -047 -0680921 2349 -0180412 -0140077 -04 083 -05 -067 -05 STM1089 -01 -016 -06 -119 -024 -045 -046 -I44I-I72] -1 -044 -095 -003 -031 -00184 106 03 102 -054 -04 STM1090 -07 -089 -1 -095 -004 0184 -054 -088j -176| -052 -125 -1210436 -037 -085 -066 -0 -06 1140061 -09 STM1091 -02 -037 -027 0230312 -003 -05 -099 -05 -0320161 -108 -078 -019 038 -059 -05 -01 -06| -196| 018 STM1092 -050201 -012040400720252 -038 -027 -02307120479 024 -03712320834 -014 -02 -04 2180649 022 STM1093 038 -004 -059 -096 -0620265 -034 -129 -063 -052 -028 -0120719006902870702 156 147 2080112 039 STM1094 -02 -0050194 0150257 1045 -037 -015 -0870164052905191047 -0340369 -058 -11 -03 -22 0887 003 STM1095 -02 006 -0220212 038 -0310025 -11 -087 -038 -0640289 -073 -024 -0130158 -02105 -25 156 -03 STM1096 036 0470677 -09800050346 051421 0039 -051 1271 -0340373 -0150121 -031 088 143 2160421 08 STM1097 -00102 -07710370957 -01 06504890507 -1 ,r -:152 -067 -039 -1180101 -148 -09 -01 STM1098 -13 -0240409 -073 -056 -084 -012 -042 -049 -023 -173 -053 -14 132 -041 [TOTJ -13

-1 STM1099 -040135 -075 -054 -013 -Ijiβj -01i[_-1J_3] -037##### -07 -138 -085 -046 -1210867 -02096 -08 -011 -07 STM1100 0820292 -036 -126 -034 0559 -066 -04 -054 ##### -065 -03803470621 -001 0837 19079 2390292 055 STM1101 1060599 -06 -1 -044 0711 -036 -112 -011 -086 -015 -043 1230611 0241045 15 1 2221528 047 STM1102 051 0449 -04 -089 -01 09460748 1073 -019 -031 -08 -006 -004 -01811480347 197 123 202 406 064 STM1103 -0 095 -075 -0170824 0603 -02 -062[TiIj 0150655 -046 15305671093 -024 068 06 141 2099 104 STM1104 1350477 -038 -109 -054 0456 -044 -038 -082 -114 -054 -03704970247 10230922 19 126 2160584 1 STM1105 -11 -024 -123 -071 -031 -13 -O -078 -0880271 -O 34 -13 -065 pi 78 -1.5e] -133[^"-T? Q 22f-2i] -092 [ Ts] STM1106 -02 034 -048 -123 -089 0090463 204 -035 ##### -081 -062 -035011701970445 13025 160152 082 STM1107 -12 -04 -130475 -035 03550217 048 -104 ##### -079 -14 -131 -101 -129 -112 -03 -13 -02 -141 -08 STM 1108 -02 -135 -063 -125 -102 0327 -0390007 -12 -133 -O 15 -098 -054 -1081761 -016 04 -06 0610425 102 STM1109 -0 013 -006 -12 -014 -0640029 -034 -003 -017 071 049 2920784 -0 STM1110 -IJ? -104 -033 -033 -007

-078 -06500720076 -073 -04 -08 -1 -078 -02 STM1111 -07 -071 -003 -027 -072 0137 -026 -098 -056 -098 -103 -013 -121 -08 -05 -005 057 -01 051 -097 -03 STM1112 -04 006 -051 -037 -02 -057 -011 -03 _-106 -077 -0410356036900250589 -112 033 -04 0290032 06 STM1113 -01 01650519 -09 -043 0251 -058 -075[ -167 -0840117 -04903280467 -036 -002 132029 11 -007 016 STM1114 01601630222 -128 -102 0131 -117 -124 -111 ##### -086 -046 -0141854 -036 031 148098 1840439 036 STM1115 08604480102 -144 -028 0114 -076 -113 -006##### -037 -0090159054702970735 217 123 1961125 101 STM1116 -01 0449 -009 -135 -017 -0060111 -01 -123 -055 -049 -1.22 -014 -0480624 -014 115076 0890794 11 STM1117 -09 -0341358 -1050022 -059 -064 -142 -097 -036 -146 -096 026 07 -0 s[ -16e| -08 STM1118 056 0032 -018 -049 -101 -102 -04 -1410443 -01503240849 2.45 167 182 062 051 STM1119 -14

-103 -166 -374 -087 -199 -152 -043 -125 -137 -059 -137 -08 -11 022 -108 042 STM1121 002 -007 -066 -134 -052 -0592031 -034 -1160054 -055 -0850148 -036 -0020208 093019 178 -015 059 STM1122 0170416 011 -041 03720324 0790714 -039 -091 -0180047 -015012400680204 081 045 050234 104 STM1123 1290087 -071 -10201710511 -026 -049 -038 -09 -046 -04900270196 -0250982 177 15 1860461 123 STM1125 -05 -026 -035 -021 -0130171 -002010100160813 -01 -0071692 -0652115 O244Q2TJ STM1127 -01 0849 -051 -082 -028 -101 -048 -145 -019 -0181876 -063 -059 -024 -0860987 -14 STM1128 -05 -031 -0303740363 0337 -037 -045 -045 -0180614 -004 mm -0250322 -061 -08 STM1129 030231 -030661 0397 01440117 -020631 -03 -073 -0040382 -0141211 -014 -12 STM1130 -07 -075 -04806240297 -014 -043 -017 -065 -05602950117 -0640832 -112 -062 -12 STM1131 -13 -116 -131 -01 -021 0111 -05 -128

|_-325j3117 -039 -01 -105[_-1_7V -13 -077 -06 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1136 0660214 -004 047 -0460531 -081 -0660531 -013 -042 -02801621194 -01 -034 088092 0490141 -02

STM 1137 -061307 1145 -107 129402130121 0365^224] -069225507921005088911620461 022 062 -01 0989 085

STM1138 0540647 -0020739040505260516 -011 1080449 -0790262030504470975 -046 015 101 -09 1141 083

STM1139 -01 -012 0224042505490337 -0180171 0266 -02 -00400880002 -0770153 -025 -13 05 _j070152 -03

STM1140 -07 -064 -070514 -0580248 -0450726 -052[-1[76] -117 -043 -050537 -0860017 -13 -0δ[ _j-ijj]

STM1141 -0 -009 008 -066 -031 0341 -035 -02 -119 ##### 141605691045068607080189 -0 175 0870465 031

STM1142 02203970165 -124 -011 -039 -073 -044 -108 -073 -1 1905 -017 0301140598 105 01 1320412 045

STM1143 005 -007 -007 1021 0831 06340178 -0320391 #####3819024321420678 01 0085 -01 01 Z96 014 -04

STM1144 0320049 0068087202950164050907890547 -003 006 -017 -04 1411 -011 -051 -12 -01 084 1548 -03

STM1145 0590472 -04 -077 -0140476 -023 -117 -045 -03402440103 -041 008605530077 116 042 086 -048 045

STM1146 038 -071 01240624 -006 -012 -003 -0260059 ##### -065 -049 -052676 -120935 002086

STM1147 145 -034 -02308050235 -02805490451 -05SfTJ] -0

STM1148S 0780259 0542 -022 -0160092 -072 -0280449 -014 -044 -093 -009022500490376 014 017

STM1149 022 05 0006 13120147 0450257 -003 025 -015 D 571 -021 085405590889 -019 -02 -03

STM1150 -06 -064 -039 -094 -039 -055 -09 -074 -049 -005 -047 -084 -058 -098 -138 -104 -09 -12

STM1151 -05 -072 -071 -048 -057 -048 -02 -021

-0 SS | -156 -218 -174 ^"^U] -0 -06

STM1152 -01 -102 01470588 -004 -0350223 -008 1804 -034 -02806530148061705640426 -03 016 0220232 -01

STM1153 0730539 0212 -111 -047 047 -085 -073 -0080067 -025 -014 -023 -04204530873 133059 1880574 087

STM1154 0190407 06120693 -06304290336 -0560813 -0281543 -046 -0450482 -042 -085 -05041 -040802 029

STM1155 0380441 -03 -081 -00308960168 -061 -098 -0850077 -0740597 -01 01290542 207 058 2.250304 082

STM1156 -01 0241 13240687 -0181001 -04 -014077805131472 -05 188 -0217381146 -04 097 0010223 196

STM1157 0370816 001 0991 -061092807070204040705291571 08990946 -02202820531 006089 -030487 024

STM1158 03801310385078406020674 -00104 -0490228267604430231 -0150776 -026 -03 -03J ^~5T)0667039

STM1159 -000510214pTsT| -032 -017 -039 -068 -073 -125 -043 -06404360305 -0050211 188095 1740632 102

STM1160 056 -0080355 009 0140422 -021 0269 -04603310281 1687 -0091051 -0470486 065058 -132168 -02

STM1161S -01 -0240044031906570202046502830513 -05 -007 04 -022 079 -077 -051 -07 007

STM1162 071 -0080393 -10502190633 -055 -001 -083 -0402980636 -028 -0830294 -001 033 0 G 0?9330-ⁱ14^t)4² -°-⁵0

STM1163 -01 0030701 0406^-197| 0275 -04 019 -041 05122029040503980074 -072 -037 -08 108 -03 -072 -05

STM1164 13602940863 -072 -03300920316 -050618 ##### -079 -054 016 -0250406 1347 152 077 1490405 008

STM 1165 014 -06306160363 -02032402590411 0409 -021 -0230037 -018 03 -0370699 -01 -07 -14 -276! -01

STM1166 0260446 -104 -005 -038 -078 -07 -018 -089##### 039 -086 -133 -099 -045 -043 -06 -04 -09 -2.01 ! -13

STM1168 0740742 -012 -146 -0220434 -047 -067 -059 ##### -07501270341 005901461067 189 06 1040313 06

STM1169 0750194 -075 -141 -0720107 -069 -0570434 -099 -076 -0406420393 -0050867 135 07 2.430805 099

STM1170 0420543 06250402 024 -015 -038 -061 0156 1253055304130604 -01 0520828 091

STM1171 -01 -036 0317 -093 -0360425 098 060008 -028 -064 024 -062

132 -06 -2.05 -18

STM1172 043 055 -027 -131 -0680216 -067 -115 -105 -125 -0770053012601350531 0505 155 105 185 0995 081

STM1173 1060008 149 054 139 1239 005

STM1174 1121055 -043 -11 -02 -13 -151 -06

STM1175 0880093 -117 -039 -13 -08 -04 -207 -07

STM1176 0150822 -1 -03 -13 -114 -06

STM1177 0980653 -14 -12

STM1178 0590256 -08 -11

STM1179 1020584 -095 -1 -06

STM1180 0070563

124 055 053 -057 -06

STM1181 1320715 1451 06840081 06990066 104902940266 -078 -004 -047 -128 -06 -062 051 -04 -14 0753 002

STM1182 0386E-04 0730569 -04801330035 11230692 -01902240722 -0 θ[3| 5θj -136 -108 -08 -04 -07 -128 -04

STM1183 0950922 1739086208941137078309261101 0433 -008 -145 -098 -006 -149 -01 03 -01 -07[ -I82] -09

STM1184 028 -0 10320J92 -0190277 -02404430254 -05 -009 -13602160434 -028 -008 03 016 078 -03 001

STM1185 0670566 -014, -17! -035 -04 -02 -083 -011 -067 -0640094 1478037507691171 153 131 251 0642 115 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1190 023 -046 -04 -141 046 0051 12060321 1826 ##### -082 -0290497035605280329 155067 274 0017 062

STM1191 07203150298 -06 -083 -040515 -095 -01 -065 -079 -03 -034 -097 -062 -036 004 -04 181 -036 002

STM1192 -04 -0380462 0181 -115 008 -0660043 -047 -087 -060453 -136 -066 -06 -047 -1 -13 -09 -132 -07

STM1193 0520284 -001 -0640124 -045 -006 -122 -054 -073 -O7 -0650735 -O1603691289 201 11 224 1046 093

STM1195 118 -0390035 -075 -041 0053 -003 -111 ^36 -106 -031 -04504990871 02930885 244 09 170949 124

STM1196 -01 05940014 -0560065 -026 -022 -079J^~-Z42J -072 -114 -069 -0.2 -078 -031 0746 -04 013 -03 -144 -09

STM1197 00506380202 -0080314 -018 001 -109^-199)0414 -074 -122 -0670074 -0650643 -13 -02 097 -089 -04

STM1198 063 -0110362 041 -145 -085 -029

0460298154606720263 -044082503580722| -2J 514 018

STM1199 05301380226 018 -005 0401 0101 -019 -074##### -115 -099 -005 -079 -031 -017 -1 188 -01 -137 -01

STM1200 04 -020058 -136 -057 014 -06 -023 -059 -086 -033 -046006903670221 0897 19097 1870683 067

STM1201 0470744 -018 -109 -078 0466 007 -114 -092 -056 -065 -072 059021701631012 166 151 188 047 037

STM1202 005 11290071 07820553 01040609 -01 0653 015 -068 -072 -057 -1290458 -04 -11 -04 -14 -065 019

STM1203 014 -0070111 0388 -022 -0230402052408240133 -083 -054 -01 -10600870607 -05 -02 029 -016 028

STM1204 05908390013 17181113 -0550871 -02910970561 0068 -0390926 -0690062 -065L-15J -01 -11 -047 033

STM1205 001 0802 -054 -123 -105 -048 -023 -049 -02 -102 -079 -032 -0370433 -0450002 119 046 147 J)38 023

STM1206 -1 05140082 -044 -089 -033 -017 -0060288##### -07 -138 -129 -051 -084 -063| -18 -iTi -11 -zL⁸ll "¹¹

STM1207 006 -004 -009 0094 -005 -0130196 031 025 -021 -059 -0380134 -0690033 -09 -08 136J_-2 -06 03

STM120Θ -01 -051 -073 -142 -028 -0080048 -02 -01 -105 -0420449 -0204690172 012 091 047 062 -033 07

STM1209 -02 -001 -045 -045 -031 -085 -001 -0760257 -065 -032 -01 -1151599 -038 -068 -02 043 017 J) 68_-03

STM1210 09 -06 0220145 -012 -084 -003 078 1.299 -03 -021 -028 -137 -1041 -181 -Tδβ¹ -13 -2 -16 -185 -Te]

STM1211 -04 -012 -002 -004 -047 02460051 03870209 -107 -0370714 j -186) -074 -08 -046 -04 -03 - _1 1375 -11

STM1212 -01 035L-2J5J -013 -051 -0330117 -06 -038 -089 -0231016 -121 -127 -084 -078 -08 02i[ -182116 -12

STM1213 071 0272 -004 -0090509 -0570516 0551356 -044 -1390995 -053 -126 -031 0627 -04 038[_-290039 -03

STM1214 0040585 -046 -0740134 -014 -014 -09 -069 -112 -057 00420958 178 099 20618 069

STM1215 03 012 -0280721 -053 -127051703250577##### -045

123 -058 -04 002 -08 2392 -08

STM1216 089 -054 -12906520407 -107 -038 -042 -01 0589 -01 078 -0550554 -0431259 056 129 0080463 031

STM1217S 0760384 -029 -107 -O 85 -019 -065 -09 -053 -079 -117 -039037403750611 086 256 113 1760969 011

STM1218 070273 -016 -109 -009 0015 -011 06070618 -103 -04 -041 048 -03204560903 243 108 1240189 035

STM1219 0780312 -009 -083 -018 -0040015 -045 -011 ##### 0049 -0070762 05706340828 331 088 2260778 13

STM1220 1030844136409130397 1071 0254 115207740209009605530693 -022 161 -037 042065 -130197 155

STM1221 04406440046 -041 -0.22 0487 -039 -0770548 -072 -0908390177 -005 -001 -05 17 -02 150936 083

STM1222 -0 -0180927 -121 -022 0222 -016 -035 0391832 -056 -046000712460717 079 294058 156 0228 055

STM1223 046 038 -048 -025 -108 -044 -082 -O72[T85lθ237 -016 -0312449 -0420413 -028 668 -05 163 -052 035

STM1224 -14^192 -19S] -117 -176 -162 -187 -2.26 -1660061 0544 -071 -03 -078 -037 -059 -13 -07^34 -074 -05

STM1225 -05 -129 -016 -083 -079 -016 -037 -071 -008 -1030389 -134 -0060121 0188 -051 174 -01 002 -051 052

STM1226 02400570223 -105 -013 0133 -001 -001 0152 -043 D5881131 -0070471 0351 -001 132053 143 -034 022

STM1227 098018303340506 075 -02905180721 03670148 -096 -058 -104 -003 -041 -043 -03 003 -22 -11 -08

STM1228 025044308620491 0778 0830768 1480227 -004 -00507590493 -146 0340.219 -06 12 -2 1163 021

STM1229 046 0172 -015 -111 0192 0055 -021 --118888!| --114422 -070234 -0550292004803630288 161 118 1790572 011

STM1230 -07 -076 -136 -139 -126 -059 -1 -231 -183 -057 -128 -0520246 -00507360093 115 026 1320803 043

STM1231 -3 -415 -4.22 -396 ^73 -368 ■A7 -518 -5.23 -0660471 0681 -134 1846 -008 -O25| -24^"I -09 -140213 -06

STM1232 -040223 -146 -098 -095 -0370166 -1 -027 -101 -111 -086 -031 -047 -066 -029 08 017 056 -008 023

STM1233 -02 -028 -142 [-168] -117 -089 -057 -145 -103

-107 -036 -115 -07 -056 045 -08 -01 -069 -04

STM1234 S 0630745 -043 -088005402570418 -035 -049 -045 -048 -054011505220.2830825 154091 1760558 072

STM1235 054 -046 -046 -0050907 -0230919 -045 -019 -079 -078 -072[j 5j>] -019 -013 -045 02 -03 0781281 -03

STM1236 1380243 -039 -0230171 -005 -02 -064 -0350294 -033 -02 -019 -021 02950254 097 05 1860408 038

STM1237 1740493 -03910991203 -0931039 -05407631221 03730206 -047 -148 -027 -06 -04 -04 -03 -084 -04

STM1238 0850184 -013 -086 -070121 -024 -078 -048 -001 -0430188048603150937 1109 186 061 167 087 124

STM1239 -15, 103 -0680516 -001 -008 025 -111 -008 -055 0350804 -0250161 -127 -099 -191 -07 274 -205 -171 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1243 059 0495 -042 -146 0047 0559 -026 -034 -009 -075 -00603060134050707910677 179055 230572 06

STM1244 072 0232 -056 -124 0453 062 -049 -079 -098 ##### 023502270722 -02 -0190741 147 114 240519 118

STM1246 -05 -035 0168 0095 0507 0614014604750025 -01 -073 -0200150381 -078 -056 -09 -0 B| -2S) -123 -09

STM1249 098 029 -005 -044 0229 0113 -018 -050451 #####075801440108 -019 -00275 029041 1180652 -0

STM1250 045 0116 0472 -069 -04 02170012 -0300160223 068 -0690082 -01100370096 101 097 1250764 056

STM1251 -01 0175 0006 0642 0336 -0360342 -0390022 -038 -085 -057 -012 -0130053 -033 -13007 -25 -134 -05

STM1252 065 0125 0687 0965 0372 100503260125 0812004061408650706014127030262 -02 165 -270129 355

STM1253 108 0054 029 0247 0607 0174040907740612 -01 J) 761 -0520448025702170225 -03 113 0030244 006

STM1254 -04 0285 0384 -081 0552 055 -0140202 -017 #####^64] 0437 -05604280096 -077 001 -06 -050415 -02

STM1255 009 -015 ■017 0292 -028 -006 -022 -0106170388231909570313 -015 -0210319 -04 -04 0781813 -0

STM1256 04 0573 0587 0669 0059 02910446 -0140337 -016 -0630297 -0810008 -026 -058 -07044 0370579 -03

STM1257 057 0179 077 0419 -013 031405950673 034 -041 -076 -002 -048 -044 -001 -019 -04018 -040623 -05

STM125Θ -01 -015 -057 0605 -019 -034 -0450304 0190042 -142 -07 -085 -011 -095 -091 -03 -OβL-24 -212 -07

STM1259 -03 0751 -027 -046 -049 -0740093 -054 -043 -0850364 -05 054 -118 -1210108 -13 -01 094] -199j -11

STM1260 035 -029 -059 0984 0371 -020424 -0740319 -045 -022001413210231 -0040469 045 106 054 -01 041

STM1261 051 -008 -038 122 -038 0135 -01 -068 -071 ##### -035 -0091966006103280138 114046 1980579 127

STM1263 -01 -052 -036 0271 0037 -00701180056 -037 -0830334 -032 J>_18_0_708 -017 -084[_-18j -07| -17 -157j 1

STM1264 -02 0013 -043 0486 -012 -043 -011 -0381314040108440181 L-J 5JL₁I 65 -0210205 "¹¹ "¹³ -14 -072 017

STM1265 -01 -064 -031 128 019 0227 -057 -0750392 -0320458 0430192 -008 -03 049 024 -01 014[_-1_β7J -07

STM1266 049 0044 0232 1016 0268 0555011401650283029704970153028607140283 -015 -08007 1530723 05

STM1267 027 0508 0272 -051 -062 -017 -031 -04201480019 -046 -0520458 -005 -0040206 075 -0 244 -017 052

STM1268 [^] -089 -116 -013 -043 -06 -082 -082|_:221__-16βj -128 [ -Vra] -092 -1320041 -09 -06 -09 -11 -021 -11

STM1269 011 -098 -078 035 -028 -083 -029 0060153 -039 -049 -048 -082 -1 -031 -087 -12 -11 -13 -048 001

STM1270 -0 -017 -019 -022 0105 -034 -008 -011 -054 -0311314 -025 -0360097 -0410205 -02 -04 -0 -075 -08

STM1271 -01 0202 -024 -035 -013 042504730381 -04905760285 -063 -0820272 -073 -01 01 04 05 -077 019

STM1272 076 0496 -086 Gu§3 -016 -028 -048 -133 -017 -039 -031 -026009806720226 052

STM1273 084 -019 0042 0989 0384 -013020703520755 -007 -07503890816 -1040079

-04

STM12731I 076 0504 -098 -118 -065 013 -074 -139 -048 -069 -095 -0640373075510720498 17058 1640015 048

STM1274 006 -019 -038 0122 0193 -013 -027 -1110414 -083 -064 -075 -04 -0490056 -014 046 -01 07 -082 -04

STM1275 058 0278 -023 -098 0442 -00203330083 02 -0420091 -078 -03 -01 0170196 065048 1360001 045

STM1276 022 0242 0217 0429 -003 0271 -0310432080302261472 -118 -013[j^~ωj -0260038 -09023 -1 1906 -05

STM1277 044 1253 0159 1603 0994 0962 11590894039904520491020101480755 -07 -01 -051337 067

STM1278 004 -001 0017 -068 0599 0137

-112 -022 -003 -0060615 -1170022 -029 -04 04 -02 -001 021

STM1279 029 0197 -067 0361 -05 -035 028 -066 -034 -0.20673 -077 02065921512271 147 101 0780199 166

STM1280 065 0274 -056 -114 -061 01690367 -068 -055 Mtm -0390211 -018015208910404 201 123 1870874 136

STM1281 062 046 -026 -106 -051 0474 -032 -031 -077 -149 -021 -009 -026 -005 0220484 275 119 1090327 05

STM1282 -06 -131 02 0842 -089 00210171 -0060528195109690797 [TEB] -08705010072 025 -08 -09 -073 -03

STM1283 01 024 0349 0445 0303 0087 -011 -022 -0 -00410140098 -0430194 -015 -083[ -1 e| -01 -08 -03 -04

STM1284 095 0243 0736 0041 0904 0424 -11 [~-216 -2 :37##### 034510090271 -047 -013 -037 -08 -03 008 -054 022

STM1285 065 0341 0582 0608 -033 0280325 021 -00416260151 18130178 -037 -054 -042 0 -02 -12[_-16i] -04

STM1286 083 0351 -035 -01 0043 -0020464 -02407150022 -0430556 -034 -0290273 -043 29 -01 -07 -011 037

STM1287 045 0802 -064 0681 0862 -0340143 -0230664 ##### 13760302 -062 0030865 -017 0J2069 -09 -096 04

STM1288 -01 -016 0027 0062 02450159065801710668##### -0540084 -007 -079 -056 -048[_-1_s] -02[2Te] -109 -07

STM1289 05 0533 -03 -059 -03 -007 -036 -055 -047 -069 113 -0480408038803130429 135045 1020002 089

STM1290 123 0051 -037 0937 0192 03290201 -0308170534 -1491245 -139 -001 -0073297 -11 -1 08 -119 -04

STM1291 -04 -049 -124 -006 -022 -094 -082 -088 -018 ##### -0570098 -105 -124 -095 -055 -07 -09 -1 -128 -1

STM1292 009 0005 -121 0284 -034 -058 -075J -17] -00408580167 -025 -09 -103 -021 -072 -04 -11 -05 -066 -05

STM1293 097 0283 -047 -053 -08 -079 -01900380156 -062 -07 127 -0530189 -0470022 072009 1520152 062 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1298 04 -003 0276 -072 0552 0119 -0430854 -0820247 -0221016 -015 -0351277 -039 109041 0880457253

STM1299 107 0168 0546 0639 -017 -017 -028 092 -081 1323 -0510.28503550068 -0360523 036 04 -06 -036 -02

STM1300 084 -011 0947 0831 -042 -053035814570448 -06-ψ-2.3S] -068 j -161-198 -166J -066 -02038 -01 -13[TT]

STM1301 133 -003 1021 0964 -019 -042009117090734 -012 -003 -042 O33[ -1721 -124 -05 02 07 -01 -163 -08

STM1302 019 0289 -068 -071 -028 -053008801350171 #####22441231 -01804510529 -07 179 -01 033 -013 058

STM1303 109 1401 082 0844 0583 042108970731 110705233271 001 1069 -053 -0031055 -05093 -01 -011 04

STM1304 063 0418 -041 -094 0334 03070066 -0810264 -038 -05 -0070311040307470762 12087 196 039 056

STM1305 019 0815 073 -055 -003 -00503640545_0J68 -039 -0610075 -025 -068 -0070007 084 -02 157 -001 -01

STM1306 038 0141 1088 0275 -02 0253L-351__j-343 -5θϊ]θ7O6 -11 -1 -1230208 -07 -047 -07 02 553 029 -04

STM1307 047 0257 0268 1211 0555 0021 -027 -115 -095066309761104 -0221106 -024 -028 -04 119 317 -006 01

STM 1308 -08 -018 -062 -016 -04 -010232 -030058 ##### -0410045 -063 -005 -009 -023 -06 -01 -12 -101 -04

STM 1309 072 0657 0385 0176 0572 033404040047081608420308 052 -046 -03803010387 485 -06 0131977 016

STM1310 126 0529 -003 -107 -063 0181 -05 -078 -1 -077 -057 -0290463019401571037 195 12 2120771 031

STM1311 089 0455 073 0544 0033 0036 0130539 034##### -03 0191816 -123 -064 -031 -07013 0070641 -04

STM1312 037 0187 -012 -103 -021 0247 -087 -056 -046 -08 -037032103250201 ##### 0733 196095 2/|50225 011

STM1313 027 0384 0138 0517 0175 -0070045 -03 0140261 -134074810070133 099 -014 -01 009 f -17] -024 075

STM1314 -04 -042 -161 -042 -026 0055 -069 -114 -04403322597 -09 -06 -0730779 -054 -01 -06 047 -016 067

STM1315 -07 -108 -106 0878 -023 -018 -108 -09 -066038807450191 -063pT76] -029 -087 -02 -09 -33 -197 -03

STM1316 -02 -058 -001 0115 -012 -02 -03 -032 -087 -0510213 -00100320954 -068 -052 -13 -06 037 -084 -06

STM1317 -02 107 -033 1324 0151 -0080159 -02705690499 -04 -01 1331 -1420939 -119 -03 -06 011 0999 069

STM1318 007 0075 0814 0698 0282 -01403851157 0661336 -011 -029 -08 -0040231 -123 -12 -06 0260312 013

STM 1319 065 0496 0389 ..-¹M -098 -027 -048 -085 -039##### -099 -043 -013042702790727 212053 173 065 064

STM1320 077 1076 0835 0999 0906 05910885027306493594 -0472655 166034519380921 -06 175 -04 -145 153

STM1321 083 -015 -025 0411 0059 -0490045 -00901620297 -108 -02 -098 -135 -055 -003 -1 -09 04

STM1322 015 0233 -039 0105 -013 -019 003 -01507950385 -0321417 -086 -007 -0260447 02 -08 -05

STM1323 -1 -031 0255 0165 0767 0208017306181082 -032 021 -176J -027 -0931157 -034 -11 -1 -07 -057 09

STM1324 068 0137 0004 0423 -026 015600840331 1007 #####, -15β 0529 -04105530389 -05 -1 048 -2.3J 112 003

STM1325 031 0187 -02 0577 0527 0555 -0 -047 -0041959 -05404620516 -0 -033 -008 -1 -06 -2 -Z48, -01

STM1326 084 0214 -002 0572 -01 -097 -044 -041 -06 #####1251 -016 -117 -092 -065 -042QiT] -09 -21 -217 -11

STM 1327 -08 0064 -026 -057 055 -0480053 -0880122 -05717150073 -01 -09505290319 -07 033 057 -017 017

STM1328 053 0169 0217 0593 0474 0043 -019039803770186 -04 -002 028 -041 -012 145 -12 -01 033 -043 05

STM1329 021 0478 -032 -053 -049 0518 -002 -112 068 #####12630434 1247049901921136 139 081 2340484 034

STM1330 -01 0214 -022 102 -009 -03 -018 -00500540267 -02529220285 -03302170168 -15 069 -11 -092 039

STM1332 -213 -199 -13 -124 -13 -162 -245 -2.41 -119 149 -199 -111 -iβl 125 -094 -1 -1 -° ¹[dj59] -11

STM1333 049 027 0138 -044 -074 0016 -029 -067 076 -033 -0440367 -01 00300030525 068 02 121 1071 066

STM1334 C 029 -011 -02 -129 -04 -011 0355 -064 -053 -066 -058 -0120105039305440563 235 082 2070553 096

STM1335 067 0324 0415 -174 -106 -013 -049 -055 -028 -081 -067 -07311950359 -0280629 188 083 1750627 105

STM1336 064 076 -066 -155 -075 -0250279 -068 -074 -069 -052 -040443 -009 -034 087 231 108 2220447 117

STM1337 -01 -016 -11 -104 -07 -037 -046 -118 -028 -092 -061 -007 079030801220464 191 086 195 108 132

STM1338 -03 -048 -119 -009 -115 -024 -076 -11205170569 -114 -092 1602^11 -23i| -122 -07 -09 -03 -081 -07

STM1339 109 0436 -09 -128 -074 011 -031 -093 -032 -056 -11300360718 -00404460838 2 197 170954 092

STM1340 126 0127 1529 •023 -044 0818 -011791571 -024 -043 -026 -001 026500910513 144 099 1620697 094

STM1341 034 0586 0427 -02 -06 -007033306070568 -056 -098050701830833 -0030494 198 015 3052039 068

STM1342 105 0617 0035 -035 0091 006 -037 -057 -093 -10610882.219 013 -05 -0290423 088 122 061 -036 049

STM1343 -07 -054 -088 0149 -066 -049 -024 -109 -116039401891062 -128 -0050498 -003 [jj] 027 -12 -091 -0

STM1344 -06 145 -112 -008 -078 -052 -041 -05 -011 -04 -080277 1038 -060776 -073 -09 -07 -01 1134 008

STM1345 -01 0405 0551 0409 089 0901 02350843 -05901882398 -019021402740371 0433 -05 036 0950866 016

STM1346 055 0123 -035 -053 -027 0193 -05 -0080941 -042 -139 076 011 -031 -031 -047 082 -01 045 -05 -01 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1351 -03 -096 -073 -084 -046 -043 -011 -030578 -028 -08 -061 054704090359 -077 037 -04 219 -086 049 STM1352 061 0371 053 143500850301 -021 0321 00960168067408481653 -044 -0430818 -03 08 -22 -017 -01 STM1353 -04 -0502320162 -004 -01403150661 -024##### -126 -0940009| -1 s| -031 0725 563 -01 -25 -137 -08 STM1354 00701440039 074 -008 -0480324 -022 -013 -019 -06704851138 -05 044 -065 -02 -1 -22 0023 056

STM1355 -11 -072 -095 -0130168 -038 -065 -138 -132 -033 -0920061 -066 -096 -092 -072] -1 τ| -08 -34 -027 -09

STM1359 -040165 -04 -038 -0270293 -035 -0030241 037 -071 1830255 -053 -0280194 -1 -01 094 1245 -0

STM1360 -08 -034 -047 -0170087 -019 -029 -04 -087 ##### -022 -05 -126 -079 -011 -08i[jy] -1 -060379 -02

STM1361 -02 -035 -079 02940058 -018 -016 -025 -048 -001 -051 0141 -0440337 -051 0042 -03 -04 (^"^t] -026 -05

STM1362 -09 -072 -0702640394 -016 -021 0013 -046 ##### 0034 [ -158 j -061 1403 -036 -04PTT] -07 06 -135 -04

STM1364 -020089 -009 0030118 -014 02 -063 -029 -069 -01603051281 -018 -0030182 0 04 0381663 036

STM1365 050239 -032 0033 -012 02049905771003 -028 -0890519 -07806280747 -068 -02 -07 132 -095 07

STM1366 006 -003 -143 0231 0187 -005 05704560177 -111 -057 -026 -0062009 -001 -042 -13 -04[InJ -008 -0

STM 1367 -01 -102pT9? 0341 -001 -0460052 -0730544 -02 -087 -09 -146 -0130096 -102 -1 -13 1642103 006

STM1368 -07 -021 -018 ^Ll⁵JL⁰J²⁹JL¹³³ -⁰¹⁷⁰J⁷JL-?^0050178 °^{421019302θ30037 ~}°⁷ -^{057 ~}°^{9 ~}°^{z 054}Gl⁵?] -¹

STM1369 -02 -089^AM -163 -178 -178 ] -006 [-212 -2X5 Tδj -014 -044 -144 -1081789 -135 155 -06 01 -125 064

STM1370 -05 -031 -025 -041 -047 -012 014 -1030129 OWpTδi] -014 -048 -048 -1 -03 -050614 -11

STM1371 016 043 -065 0069 -004 -07 -044 -0463264 -0520225 -042 -0060217 156 07 1420397 -0

STM1372 -01 -001 -021 -0060484 -014 03408854638 -0140107 -04501180132 -11 032 -0 -04 005

STM1373 -0 023 021 03030194 05101840835 -0320762 -054 -09 -0040095 -11 043[^*-2~ϊ] -138 -03

STM1374 0140445 -009 040104530297 -003 -0383147 -0190384008900380001 089 106 1310176 002

STM1375 10206020132 -029046407550843 -0350729 -0290424094701340602 -04 1.28 020079 028

STM1376 00303960139 0101 01 -109 -108 -106 -022005301060053 -0141065 199 103 Z220517 105

STM1377 07507170136 -0 -028 -096 -Oβmmm -057 -041 -OI6 0390541 OβO8 214093 1880528 O 83

STM1378 012 -1330835 -061 -1160134 -067 ###fl#j^~T87 .iβ] -038[-3Ii] -077 -146 -12 -15 -12J 5] -07

STM1379 -0300580874 0536040509781032 -021 D794 -022 -012 -095 -031 -033 -09 -03 -1 i[_-1S^I -07

STM1380 0418E-O40779 -023037707340441 -02502130073 -0350211 -091 -034 -02048 -06 -081 -08

STM1381 -1 -0630034 0137 -116 -123^204] -0391641 -0410078 -021 -1450279 -08 -08 -06 -074 -1

STM1382 -03 -025 -032 0484 -026 -086[-2-1I_jO 22Θ 1776010100391464 -003 -02 206 -01 [^2.3] -121 -01

STM 1383 1540604 081 05570204 -095 -065mm -10425560463 -01310750712 087085 0491916 08

STM1384 00302580324 -00800850027 -0 ##### 02951607 -0390413 -0130266 -05 -03 -13Q₁Ia] -04

STM1385 -055043606681695 -10706080118 -029^VS?) -049 -102 -07 144 -07 -081 003

STM1386 115 11 1074 0952072508650377_^0847073406140499 -06 143429 -0 135 0250782 078

STM1387 1080368 -015 0034 -083 -122[-169J -040169 -0820285027714551352 -03 19[^i]θ197 087

STM1388 007 -028 02J -018 -011 039 -056 ##### -025 -050488 02208450247 163052 150201 036

STM1389 112 -014 -031 i 00350065 -0030226 ##### 0030244 -0060461 13530398 012068 -13 -052 075

STM1390 -0040252 -05 -10705190757 -11 026 -26 -021 048

STM1391 0238 0.276 -035 0066 -037 -11 -01 -16 -068 -02

STM1392 A 54 1356 -015007300870605 -044 -054 -08 -04 -1 0305 -01 STM1392 -402 0983 -012015403430555 -019 -045 -07 -03 -11 0405 -02 STM1393 02771096 -066 -06 -087 -13 -1 -08 -132 -08 STM1394 -001 -0130333 -059 -031 -116JGGi -06pTβ| -094 "°⁶ STM1395 0321 -025 -053 -042 -021 -0 -06| -24[O 474 -02 STM1396 -0020326 -011 0064 -024 027 012 104 1559 056 STM1397

-0780142 -0480385 -0260756 096 022 142 044 026 -0.9

-0.3 STM14O4 -1.1 -0.23 -0.67 -0.57 -1.49 -0.09 -0.97 -1.03 -0.21 -0.11 0.95 0.35 -0.5 0.177 1.288 -0.27 -1.1 0.2 -0.1 -0 1.22 STM1405 -0.3 -0.37 -0.89 0.038 -0.62 -0.78 -0.87 -0.78 -0.56 0.169 1 08 0.925 0.12 0.947 -03 0.177 -0.5 -0.3 -2.11 -0.04 -0.8 STM1406 1 295 0.481 1.072 2.23 1 59 1.89 0.084 051 STM 1407 0.066 0.589 0.588 2.19 1.11 1.91 0.306 0.55 STM140Θ 0.252 -0.64 -02 0.57 0.06 0.39 -0.51 -0.7 STM1409 -0.7 -0.9 -1.1 -2 -1.86J -0.1 STM1410 -0.15 -0.9 -0.1 -1.B| O.544 0.88 STM1411 -1 1 (_JJ6j -07 -1.7 -2.O2] -0.4 STM1412 -0.35 -0.62 -1 1 -1.2 -08 -1.34 -1 STM1413 -0.38 -1 5 -06 -0.9 -0.54 -0.5 STM1414 -068 -2.1 -0.71 ^JL§] θ 143 -0 1 STM1415 -0.75 -2.4, -0.5 1.47 -1.4 -0.2 STM1416 -0.1 -0.79 0.82 -0.3 0.56 -0.03 -0.2 STM1417 -0.07 -0.37 -0.7 0 12I -1.6J 0.655 -0 STM1418 -0.15[ -1.8| 0.13 -0.8 0.877 -0.3 STM1419 -0.07 -0.4 -06 -0.6 -0.89 0 1 STM1420 0.631 1.22 0.37 1.8 -0.03 0.28 STM1421 -1.4 -1.09 -1.4 j -2.1 ~UΪ] STM1422 -0.27 -0.68 -1.4 -0.5 -0.3 2.201 0.36 STM 1425

0.035 0.054 -0.97 1.77 -1 GM. ~¹-¹¹ -°^Λ STM1426 0.76 0.318 -0.29 -1.25 -0.61 0.075 -041 -0.45 -0.17 -0.76 -0.28 -0.04 -0.45 0.279 0.599 0.617 1.78 1.18 2.53 0.554 0.85 STM1427 1.02 0.453 -0.13 -1.39 -0.82 -0.08 -0.75 -0.32 0.233 2.538 0.429 -0.39 0.203 -0.44 -0.06 0.668 1 6 0.85 1.81 0.562 0.73 STM1428 033 0235 0.145 0.106 0.081 -0.72 0.221 -002 0707 ##### -0.5 0.344 -0.3 -0.51 -0.49 0511 0.54 -0.1 0.71 -0.28 0.04 STM1430 0.05 -1 2 -1.47 -093^1-63) -0.27 -0.14 0.147 0604 mm 0.514 -0.58 -0.82 0.543 0.138 -0.51 -1.1 0.83 -°-⁶Li§il °⁰³ STM1431 0.47 0.455 1.007 -067 -1.18 0.389 -0.16 -003 -1.14 0.307 -1.18 0.12 0.37 0 31 0.986 -006 028 0.43 0.86 -0.01 1.12 STM1432 -0 0.196 -0.21 0.065 -0.42 -0.14 -0.11 -0.19 0.385 0.421 -0.31 0.139 0.376 -0.31 -0.27 -0.36 -0.7 -0.5 -1 0.89 -0.4 STM1433 0.14 -0.26 -0.36 -1.04 -0.66 -0.37 -0.61 -0.52 -1.1 0.55 -0.66 -1 -0.01 0.473 -0.75 -0.79 0.24 -0.3 0.91 -0.52 -0.4 STM1434 0.51 0.543 -0.21 -1.34 -0.37 0.237 -0.55 -0.82 -0.48 -0.94 -0.39 0.348 0.053 0.095 087 0.904 1.22 0.93 1.85 -0.41 0.7 STM1435 -0.8 0.296 1.225 -0.46 0.398 0.824 -0.29 0.326 0.317 -0.85 O.314Q1V9] -1.02 0.169 -021 -0.24 -0.1 0.14 -0.5 -1.21 -0.5 STM1436 0.51 0.065 0.058 -0.67 0.194 -0.08 0.809 0.586 0.419 0.043 1.173 0.567 -0.65 -0.7 -0.8 0.2 -0.3 0.18 0.42 0901 0.04 STM1437 0.05 0.186 -0.65 -0.78 0.957 0.19 0.605 -0.5 0.587 -0.25 2.215 -0.69 0.425 0.07 0.465 0.118 -0.4 -0.4 1.05 0.907 0.46 STM1438 -0.7 0.212 -0.13 6E-04 0.258 0.138 -0.15 -0.62 -0.71 -0.07 -0.9 ^Tef] -1 04 -0.16 0.242 -0.01 -0.3 -0.4 -0.1 0.35 0.67 STM1439 -0.5 0.38 -003 0.671 0.096 0.117 0.162 0.201 -0 12 1.103 -0.01 -0.17 0.122 -0.3 0.271 -0.45 -09 -0.1 -1.2 -0.56 0.56 STM1440 0.75 0471 -0.31 QtEa] -0.51 -026 -0.37 -0.45 -0.61 -031 -0.62 0.308 0.169 -0.25 -0.56 0.71 2.33 1.47 1.81 2.098 0.5 STM1441 0.2 1 105 0.268 -0.66 0 199 0.063 0.42 -0.34 0.53 0.604 2.067 0.885 0.625 ##### 0.749 0.461 -0.3 0.54 0.42 0.585 0.85 STM1442 -0.1 -0.22 0283 -1.09 -0.92 -0.36 -1.22 -1.51 -1.77 -0.97 -0.39 -0.61 -0.51 -0.3 -0.6 -0.51 0.22 0.01 1.06 -0.43 0.28 STM1443 0.25 0.33 -0.41 -1.76i 0.012 -0.6 -0.07 -0.91 -0.97 mm -0.76 -0.23 0.204 0.278 0.584 0354 095 0.18 1.66 0.131 0.19 STM1444 -0.5 -0.52 -0.56 -1.57 -0.57 -0.01 -0.54 -1.08 -0.88 -0.56 -1.42 -0.78 -0.13 -0.07 -0.13 0.388 025 -0 1.13 -006 -0 2 STM 1445 -0.7 -0.9 -0.5 0.967 0.722 0.653 -0.15 -1.33 -0.3 ##### -1.43 -0.26 0.719 1.276 0.979 0.159 0.22 -0.3 0.69 0.442 0.65 STM1446 -0.3 -0.3 -0.03 0.041 0.184 0.343 0.814 1.369 0.426 -0.12 1 574 2.258 0.005 mmttmm 0.092 [ -1j[ -0.2 L^gJ -0.55 0.43 STM1447 0.05 0.026 -1.12 -1.61 -0.32 -0.66 -0.61 HtTi] -0.42 ##### 0.361 -0.56 -0.42 -0.55 -0.12 -0.92 037 -0.4 1.1 -0.5 -0.1 STM1448 0.32 0.16 -0.02 -1.72 -0.46 0.257 0.6171 -^{1 61}I "°-⁵ -⁰-⁶⁶ -° 27 -0.38 0.191 0.38 0.503 0.89 1.86 0.97 2.03 0.562 0.62 STM1449 1.13 0.244 -0.36 -1.83 -047 -007 0.198 -0.56 -0.91 -0.55 -1.21 -0.62 0.605 0.691 -0.9 1.019 1.77 1.08 2.31 0.968 0.83 STM1450 -0.5 0.208 -1.12 -0.28 -0.02 -0.38 0.823 0.548 -0.69 0.252 -1.13 -0.73 2.999 -1.31 -0.02 -1.07 -0.7 1.75 -0.6 -0.78 -0.4 STM 1451 0.38 0.249 -0.62 -0.62 -0.04 -0.15 0.206 -1 12 -0.54 -0.42 -0.42 -0.87 -0.15 -0.48 0.464 -0.3 -0 0.36 1.25 0.086 0.16 STM 1452 -0.8 -0.54 -0.46 0.165 -0.25 -0.08 -0.38 -0.35 -0.05 -0.65 0.003 1.726 -0.8 0.435 -0.31 -1.651 -1 3 0.13 -o.βl -1.94I -0.3 -04 0831161 068 -04 1730769 02 1680086 101 -0 199 001 055 0241783 019 -05 0081154 031 -01 0710012 -03 -126 -11 -01 |_-1_6__-Z07J -15

099 097 -06 034 -072 058

STM 1469 045 0830069 -0040465 009 066 -0 -0111217 -049 -003 -073 -122 -087 -076 183 -02 -14 -133 -07

STM1470 02 -0 078 -025 -0580579 -055 -01 -143 -081 23 -1020372 -011 17050017 031 004 026 -082 177

STM1471 -0202720485 0531 -03401030116 -030133 -01708130403 -116 -006 -045 -041 -01 02 -080458 -04

STM1472 -0108820278 0787028805270201037308060307 -06903120397 -0870236 -029 045 -03[IM] -053 -02

STM1473 -0100620242 02240064004200960195 -028 -01701850075 0770173 -074 -024 002 133 074 -05 -09

STM1475 07307160505 088105680719 -0060426 0090043 -0050718##### 4680082 -038 -06 -05J^~-17 -16ij 016

STM1476 0421178 -015 -11 -03906970183 -034 -101 -053 -00202360973081805280666 141 083 259 058 063

STM1477 12203450098 09990503 -005 048013804110169 -062 -10619850337 -025 -057 -08017 -05 -121 009

STM1478 02210371432 -009063804691226066402630361 -0940785 -001 -051 -022 -016 -01 168 -031758 058

STM1479 -010153 -065 0759 022 -10604010141087701050211 -014 -005 -077 -047 -058 -04 -02 ^80697 -0

STM1480 -05 -0660621 0138 -01512740547 087 -0330276 1151039 #######«##### 0555 088072 L-IjSj 2047 -06

STM1481 03601470393 0265 -004 -043 -00174064704210543072801690784 003 -028 264005 -091211 -03

STM1482 -0102310516 -04 009 015040200660499 -0130732 081 -01204880303 009 041 086 061 1128 046

STM1483 021 11670144 0640203 -12208210701 -0760959 112 -061 -107 130577 -024 -06012 -081072 083

STM1484 -040046 -019 02470316 000055004466440022441100333311 --001188 --00662200112244 --11005500772211 --006622 --003388 006699 --0033 --O0θ9f[--172) -06

STM1485 02805640286 -0604350195 -094 -081 -059 -066 -069 -041 -03607920176 -022 089025 073 -054 -0

STM1486 -0804860491 -025 -052 -0280347 082 -0181824 -01809130028 -0070373 -029 -02 -03[j2L3]θ304 028

STM1487 06708850551 004 -013 -105047401770153 ##### 012715610042 -09 -058 -047 -14 -05 111 -08 -04

STM1488 -03 -022 -004 -054 -038 039 -0390746 -005mm -046 -094 -024 -0910173 -027 -03004 19 -004 05

STM1489 01505160281 022101480004 -01 -03501080183030801050257 -092 -0760107 -03039 177 -018 -03

STM1490 -00173 -00104520146 -019 011 -00405940643 045 -074 -028 -079 -06 -018[ -17| 016 1 >1 139 -02

STM1491 -000140144 0270687 -043095805250704 -1 -032 -05 -03401560336 -091 -12 -1

002

STM1492 024 021326024301220786 -0080368 -0480186 -08 -015 -0120239 -037

-03 -1 -084 055

STM1493 010436 01 02690104 -03013408690672 -028 -0390467 -0520592 -0070153 -07 -01 -02 -001 0

STM1494 014 -006 -007 0543 -0040048037802280678 -026 [-15βJ 029901920221 -0110119 146 -08^-24] -032 -03

STM1495 0040197 101 06830367 -04404520557036205370583 -025 -071 038 -1110373 144 -03 -05 -143 -04

STM1496 069 032 0530224 -029 -0030361 15130637 ##### 0719 -1060758 -0690494 -082 -08022 -05 -119 035

STM1497 0330676 -052 -044 -029 -051032607970517 -031 -125 -091 -0532155 093 -015 -06 06 1 -034 008

STM1498 105 0250337053501050317082708471058 -006 -0210056 -037 -00105120322 006054 -09 -059 044

STM1499 -01 -019 -071 -0320285 017 -083 -038 -08706450897 -021 1178 -0170133 -0 -0 -04 0110841 091

STM1500 07903910686 -087 -0310485 -011 -052 -038 -0620432 -0450561067207040945 191 119 1691149 021

STM1501 -04 -O 22 -112 -024 -06 -070164002508880408 -102 -0260531 -106 -017 -01i[2uϊ] -0 -031263 027

STM1502 0690009 048 06860716 -0040437026213180576 -0772354 -009 -0471099 -074 041 073 -0 -039 144

STM1503 -06 -037 -009 0151 -027 -056002701950326 -091 -1170118 -131 -138 -065 -104 -04 -09J -16 -227] -13

STM15O4 10515460109 -071044301850481 -0040702 -04 -089062501980451 07450304 098087 0380873 107

STM1505 07109110343 120501880164110310391151085404140403097800020751 -039 -08052 -140278 038

STM1505 06512760264 114101950081 11080821 1327 022704090889 -031 0768 -032 -04049 -10235 034

STM1506 025083204771053027805440386 -01305751162144408381083106710270214 -08079 0710286 063 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1512 0320062 02640018 -014 -04601810348 044030304490429 -056010501570569^1^] 018{_-2β] -13 -04

STM1513 0150255 -056 -123 -062 -022 -052 -037 -091 -1283151 -0470668 -004 -025 -014 066005 039 -046 -06

STM1514 -02 -06 05820161 -0160145 -0530223 -102 ##### 0894 -0080769 -025 -016 -032 314 -0 βQTδ] 1151 -04

STM1515 -12 -025 123 -007 -0470454 -0590259 -112 -085 -133 -0490719J_-1J>6J 0476 -091 03 2310042 -01

STM1516 0760063 -022 0690475 -00804910049054606980351011308361237 -0240251 -05

-02

STM1517 0340183 0507086803280873 -0371141 1137070525551319060704381804 -012 -02077 -121973 237

STM1518 038 085 0542084606140368 -O83[5θi] -009 -012069500680105 -083 -082 -056 -11 011 2631637 -02

STM1519S 0410803 07230463081404080687022707660283075908720644 -027 -014 -0 -12051 1331518 038

STM1520 0721142 -0510210336 -0090623000210780084 -0740646 -027 -054 -035 -016 -07 -1 043 -01 -03

STM1521 0480489 o 5131387 mmmmmm o 232017710060409_| -16 o 625 mmmmmm mmm o 855 -oβ o 24f -2.3(1818 -02

STM1522 -04 -019 -059 -027 -093 -106 -131 -073 -108 -068¹ -2.02 ■O78[-Z17|35140086

-11 [ -19 -175] 002

STM1523 0790517 10780727057901330668022806120225 -02420540125181600741129 191 128 1660812 075

STM1524 0790395 -004 -123125510972133 293 -025 ##### -0520071 1121065807430882 171 119 1952095 143

STM1525 0770892 01151412 -0160617074707641128 -0030681 19513619270766 021

605 063

STM1S26 0010119 0506 -1110388 -0320692 -0331519 ##### -0550107 -0221260136 074 144032 0870372 -01

STM1527 009 -023 -033 0590201 0120163 -00106280214 -061 -007 -0 -0540443 -035 -11 -0 sj -15 ' -082 011

STM1528 0430436 0175039202260066 023 -014 0650636 -030167029208720278 -007 -04037 -16 -029 036

STM1530 -01 -029 -021047301320204 -005 -003 -0290014028313180683 -002 -064 -035 126 -05 -1 -106 -05

STM1531 -030561 -017 -02900510369 -032 -0120383 -012pi^~77J -024 -054 -0191094 -023 -02 -06 -1 -039 104

STM1532 0650575 0055043100880479050206930833337302990122 -051 -0740284 -046 -1 006 -023 -02

STM1533 0890531 0735056906530675 -034 -0340314122122260642 -0702210369 -026 -02079 -16 -052 081

STM1534 144 048 0046 -13201090858003702081299 -003 -0530143168906470081 01 11 133 170559 097

STM1535 0650731 -005 -111 -005 -029 -00800120351 -10616121137 -015 -061 077 -006 152 1 1440731 025

STM1536 -01 -036 0630086 -033 -109 -0102690947 -O 540005 -056 -1040985 -068 -073 -09 -1 027 -048 -09

STM1537 1380351 11630811 0380982 -018 -099 -026 047 177908480847 081 044 0940623 112

STM1538 -010026 -11105640139 -039 0490161 074 -009

38180291 -094 -04 -12 -1 -145 041

STM1539 1370648 12650844062907610601080808520561 052603641062 047057| -2[ -015 093

STM1540 0830418 0548029102010013001804840343 -02306080436 ##### 178702860185 -09 02 -150657 -01

STM1541 -O 50376 -016 -02 -026 -0460469 -0830619 -062 -002 -023 -073 -103 -084 -095 -02 -07 -01 -128 -1

STM1542 0830076 0730844049103170253 0420934 0230377210904891093 -040386 135006 -1 -088 -01

STM1543 -00051 044701430188034800610418 -0280536032904641085 -006 007 -019 -08 -03 -090375 -0

STM1544 -06 -124 0649 058 -0220244 -032 -003 -042 -05215860216 -013 -06 -0410338 -03 -06 -12 -126 -05

STM1545 -010587 084 -0.270416022803460056022105721306 365 -03502530765 -067 -09 -03 -09 -019036

STM1546 079 -002 055 -055 -05 -013 -0231096055700642223 -0160008100109972228 056014 0873358 148

STM1547 -01 -009 -083f-172| -062 001 -015 -056 -065 -13 -052 -045 -0270568 -0030785 169059 183 -039 -05

STM1548S -03 -056 -03303620233 015 -058 -O 73 -059 -039 -044 -072051501480152 -072 -03 -12

STM 1549 027 -002 085058902780162 -0190194 -009 -029 -004030707631379 -043 01 -07 -02 -23 -207 -09

STM1550 04 -032 -02 -089008304410077 -0580711 11730874 -056 -04801650734 009 -05015 03 -026 075

STM1551 063 093 -055 -129 -0740058 -031 -093 -042 -089 -06 -03403040448 -0080488 236 134 2120893 066

STM15511ι 0290501 0266 -022 -01305680037 -003034902110942072105440023 054 -023 052055 1590734 155

STM1552 016 -02 -0220375041410710142 -043 -0120512 -05317330162 -0080387 -031 -17 -06 -08 -058 -04

STM1554 -06 -017 -0120195 -018 -0270276 01906230799 -135 -048 -076 -0910356 -055 -17 -1 -2 -019 -03

STM1555 0890423 -11903870103 -0250067 -0790173 -0 -1260354 -115 -0480173 -14 -1 028 -19 -077 -0

STM1556 030886 0509 -00402270544049403840655071304561144 060221 -040506 -07 -04 -2.4 -027 003

STM1557 036 -012 -01702020483 -0070324 -037077214511005 -04 -04003400420309 027007 -020795 -01

STM1558 035 -014 0980317 -0210731045709590391 -0021192 -06 -052 -04200120214 029 -04 -031298 -03

STM1559 0880776 07851037 -002028801880571029800530218037503280909 -091 -088 -1J 027^-24] -007 -04

STM1560 019 -002 -00503210155 -0610426025702430909 -01 037 -067 -048 -0420062[-19^ -08 246 -125 -06 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1565 -01 0194 -045 -064 0642 -032 -052 -061302 -06103840143038807180728 122054 1641443 106

STM1566 -01 0372 0677 0388 0149 028500410503004122852686 -01618630043 -0710074 -08 148 -121571 -06

STM1567 -01 0369 0437 -042 -01 -0050122025802320007 D392 -080408 -064 -066 -017 03 -0 014 -021 -09

STM1568 -03 -02 0114 0745 0347 0478 02608050775 -073 -041 -043 -045 -0350318 -055 -07 -02 155 -1 025

STM1569 116 1373 1056 0999 0433 0507 -044 -053 -0730305 1210195 002016404710407 -01 033 Si -125 091

STM1570 -0 0296 0162 0584 -00503770272027206770352033504390751 -084 054 -084 -04005 '≠ '-310725 044

STM1571 -01 0156 0342 058 0271 04160504082606410181 057 -011 -015 -009 -012 -045 -03 -0 1820922 -01

STM1572 -0 0247 0316 -024 -0390084004201090289 -079 -029 -098 -096 -055 -030037

-02

STM1573 S.046 0929 -053 -028 -018 006205030031 1027 ##### -0280134 053 -033 069 -009 127032 150087 017

STM1574 -04 0161 0423 0783 0387 09410072040600980647 -042 -039 -018020706270544 056095 095 -023 013

STM1575 054 -009 -052 -118 -0520387 -067 -081 -108 -054 -092 -0601090317 -02 088 238131 1870514 12

STM1576 04 0458 -019 0748 0017 -053 -008 -0201160353 -0990039 -068 -024 -071 -04 -13 -06 -11 -103 -05

STM1577 -05 0608 0666 03 0457 -03 -0110243[-1JB7J03570154 -009100500840625 -039 -02088 -031115 081

STM1578 -03 -117 -063 -052

10215820529 -096 -139 -088 -056 035 -112 -01 -09 0730203 014

STM1579 -02 0669 -004 -015 -066 031 -01802660183 -064 -050261 -067 -121 -0180335 194026 145 -057 007

STM1580 046 0641 0757 0624 0202 0296 -007 0010288050101250269 -074 -06702210149 157 03 2520547 -01

STM1581 -01 0226 -039 0421 -081 0431 07 0551894 ##### -1090211 -123 -084 -063 -04Sf-Te] -06 041 -089 -04

STM1582 -04 0378 -102 -076 -035 01210308 -074 036 -063 -0680713 -083 -053 025047 072 -045 -03

STM1583 -04 -051 -057 -038 -021 01930411 -036 -015

-07601631243 -065 -032 -08062 2512188 -05

STM1584 085 0062 0221 -085 -064 0437 -054 -105 -088 -045 -072 -1130647 07600231387 256 143 1520694 032

STM1585 -01 0109 -052 -136 -022 -003 -048 -044 -009 -055 -03 -05500430094 -030292 363 02 078 -024 016

STM1586 075 0694 017 11 -017 02820123 -0230922 -1 -067 -057 042074704031021 172075 1940023 065

STM1587 066 0286 -024 1097 0233 -019 04901360368##### -05602140001 -086 -011 -014 042042 -11 1026 013

STM1588 053 0426 0532 0669 046703040153 -005034903130971 -012 -01106130074 -058 307 -0 -18 -046 051

STM1589 -0 -017 0126 0368 -011 0108 -0060391 -04 039 -00904421007 -093 -0320185 074 -04 -2.2 -088 -06

STM1590 034 0809 0403 0817 0367 0735 -01308150647 ##### 03470504 -007 -03104420173 -02 -06 -08 -067 078

STM1591 089 0828 -025 0693 0189 -0850551 -01207610724 21 1845 -052 -0531761 -084 -06 -11 0390104 1

STM1592 077 0355 -012 KU -025 0421 -074 -096 -075 -097 -039 -0980755003103271009 225 142 249 051 -05

STM1593 -o 0564 0725 0383 0.257 0259069709160271 026 -072 -0080381 -054 -105 -049[[TJ -1¹L±§]⁰⁸¹³ -°⁵

STM1594 11 1047 117 0098 0408 058304910429040805411151 021 -04508370118 -052 034 06 -06 -018 076

STM1595 098 0524 1015 0732 0321 0644045710470321 0028 -0840453 -058 -021 -022 -007 -09057 20019 007

STM1596 066 -01 -016 -098 0223 0023 -052 -0430143 -073 -013 -00804420678 -010407 185078 164 -031 063

STM1597 115 0713 0418 1552 0728 1180269094603920294083712710398006701720681 -05054 1380055 008

STM1598 034 0808 0596 0458 1079 0832128607531289 -03410910432045404961518 028 028022 -020267 149

STM1599 051 0398 112 101 0767 101401 0130116 -033027304170296 -03 -04 -07 -095 048

STM1601 -01 007 0539 0403 0817 0365 -0 -048 -009

STM1602 L-¹Z¹ -117 -133 -008 -008 -053 -0 -106 -068

STM1603 043 -008 -054 -048 0175 -08101730248 -011 -016035601680058 -075 -04 009 -01 003 125 -064 -05

STM16O4 095 0397 -007 -059 -055 -0140003 0180402 -009 -075 -03 -1080216 -043 -007 077 -03 113 -002 -01

STM1605 047 0466 0765 1001 0469 0305078807891672 -0131253 -009 -009 -057 -041 -042 048 θ[^~ijOO12 -04

STM1606 142 0669 0983 -044 -023 -034 -04500320145 ##### -07200390385 046 -0430777 204 -03 124 -022 034

STM1607 135 0482 1467 0843 0234 08940239098900710175174102241427 -08100540137 342056 _-10952 -01

STM1608 -03 0152 0583 0103 064 -017033402130498 -061 -11411841296 -066 -0430598 -07 -07[^44] -021 -08

STM1609 054 0848 1223 -004 0204 067707141125 040819 -138 -038 -03 1221402 013 01 002 -14 056 143

STM1610 073 0634 0152 0778 -012 0311063901841282 -0350966 -002 -035 -0270462 -072 003029 -140681 08

STM1611 06 0232 -034 0162 0227 0101 049603270989015900330077 -0290003 -011 -014 -08 055 -36 -104 -0

STM1612 046 041 0242 0097 -075 -0170219046306420509, -19 -0390246 -038 -022 -062 -05 -03 -17 -027 -05 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1618 0230442 062208720711 -0580126|||§f 10830487 055 -0440918^I₀Tg] -054 -098 036028 053 -022 -02

STM1619 -09 -031 -00600470007 02280009 -0330279 -032 -055 -091 -047 -026 -0720066 -14 -02 -04 -1 -11

STM1620 063 -001 -0020291 -O 07 0168 -001 -0150096 -041 08360131 -017 089 -0390794 172 -01 -07 -064 -01

STM1621 1580613 0315 -0080541 0670307 -028 -032 -003212922580359125903450598 032 09 0590762 087

STM1622 0750331 01020841 -002 -0580464030403740101 -111 0959 -065 -144 -070436 -03 004 -11 1086 -01

STM1623 061 101304960087 -021 -015 -040335 -023 ##### -001 1624 -099 -04803840317 053 017 0850273 064

STM1624 043 -013 1161 10690045 -04604581155149703370486 035 -0252.6330159 -023 -04 071 078 1462 -01

STM1625 091 1468043217960341 062306140269 -05600490488 -05913131551 15420785 143 -0 1270103 124

STM1626 0240142 -0330455 -001 033900470574 -022 -008 -026 -0650109 -076 -005 -034 073048 291 -127 -03

STM1627 018 006 -01705140119 01420453 0261099 -01404980302 -043063401550628 112 034[ -ie[ -o 53 o 06

STM1628 -00058 0077 -053 -011 -0390054 -011 -0540134 -0560217 -039 -00908850045 12022 173 -013 094

STM1630 0590165 -015 -022 -0 0708 -023 -007§H§ -093 -069 -024 001 0106 -051 -014 158 -02 061 -056 028

STM1631 -11 -O 69 -106 -065 -052 -081 -064 -05 -053 -0480814 -125 -040458 -071 -067 -1 -05 -01 -011 -07

STM1632 -02 -025 01020504 -0140581 -055 -0250247 -0350704 -048 -099 -06 -04 1915 -08

STM1633 -12 -122 -047 -037 -061 -026 -1230037 -14 -

04 -033 -039 -097[-167J -08 -11 -11 -11 -09

STM1634 -05 -011 -054 -1 -036 -05

-107 -061 -064 -039 -0440047 -042 111 -02 1190067 005

STM1635 -03 -068 -1280023 -071 0006 -012 -048 -041 0355 -045 -068 -051 0339 -0220317 -08 -03 059 -008 -0

STM1636 -14 -051 -088 -034 -033 -041 -089 -052[3jg] 0353022901380309 -022 -054 -016 -08 -11 -1 -11 -11

STM1637 -07 -007 ■068 -005 029 -01 04950101 -059 -006064209371385 -026 -1170059 -04 -04 -2.3 0078 -09

STM1638 01 -034 -0620561 -04 -047 -04800320052 -058 -039 -097 -043 -006 -066 -057 -09 -07 -26 -146 -08

STM1639 021 03840142 1079 -009 0861 0054 -069 -081 03243196100506052661 -0040578 056 054 -09 -067 -08

STM1640 048069801740675mm #####04750234 07821982005 -012 ############### -055 -05 047 -04 -095 005

STM1641 0360228 1067 -0170137 -04407951299138600621825 -084 -115 -019 066 -001 014 -06 -03 -064 092

STM1642 0240776 -00603640131 0079 0560511 -06900831568 071 0406 -0970291 -013 039 -06 0042969 046

STM1643 00423 -01 05790353 0485 026 -037 -0050625 -011 -015 -054 -0050373 -011 -06 -05 054 -019 075

STM1644 033 -05 -0170761 -018 -0550403 -01 0808 -029 -091 -022 -071 -03 -014 -011 -02 -04 -05 1125 019

STM1645 054 017 -022 -127 -011 0005 -008 -057 -014 ##### -053 -05 101 -043 -0190029 12 086 199 118 054

STM1646 0510367 -008 -040223 -004 -052 -024 -02810891011 -01501960142 1281 -023 017 014 -00741 11

STM1647 00401190637 -039 -011 -031 0151 06690926 -03300850518 -0752452 -094 -026 -07 009 -23 -2.221 -07

STM 1648 05702860548 -0770082 01720182 -019 -1250607 -088 -045 1161 -02 1281201 168 01 109 -047 112

STM1649 067 -004 -011 -086 -0.25 -0140137(3Pf -042 -064 -063 -0.2806980377 -0390982 274 15 1920367 066

STM1650 0640477 -077 -12 -043 0357 -006 -0330487 -046 -067 -0030885019405631454 236 121 2540991 083

STM1651 0570517 -062 -123 -025 0537 -017 -055 -071 -082 -038 -0770791 01621216 158 239 143 1791153 063

STM1652 0630118078807530251 04530091 -0180307 -0020271 0641 0.2230558 -0740319 13 -02 !^ϊ^~j| -086 -05

STM1653 047 074 -024 -088 -039 0309 -043 -047 -0190159 058 -040771 -02402970278 023 038 1230225 052

STM1654 0210566097908170959 09761035062603870827 -041 2317 -0.2800980122 -071 027 036 -079 049

STM1655 074041907480029 -002 00130364 -0060354 039 -0340436 -048 -150209 -027 -12 -05

STM1656 042054806230033 016 00570092060808220069 -111 0267 -06339740412 -013 -11

STM1657 023 011050403590094 -0 -003 01502560169097521290346 -013 -0090264 -08 028 092 -007 -02

STM1658 136 -013 -04300850347 -002 -0170915 -00600080319 -01602860511 07622659 -02 -03 -110392 106

STM1659 0691032056705520611 -0130105 -009 -011 0802 2150824007^3905^11 015 -06002 042 -082 -02

STM1660 S -080254 023 -084 -01 -149 -04202120918 [-1*55 1430055[V75 -189 _-1 βθj -109 -04 -11 -0 -12β[Vβj

STM1661 0150136 -0260637 -012 -004 00600860684 -009 -001 0361 -015 -03100890374 -09 07^-3^2206 004

STM1662 -01 -024 -047 -002 -026 0535 -02800180987 -03,-18β101240293 -054 011 -063 -07 -03 -1 -079 -01

STM1663 -05 -015 -01504420204 -017 -003 -007 -0170131 03470327 -037 -023 -033 -01 -08009 IJβj -158 -07

STM1664 0310425 -04204940266 -0250238 -04 027 -02 -0770054 -11 -019 142 -074 -09014f-26 -28 084

STM1665 01 -0291066 -102 -04 -0150293 -0420378 ##S## -049 -06 -006 -0320334 -012 052 002 0750134 032 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1673 -01 -045 0269 0574 -019

-08

STM1674 131 0079 0077 -046 -045 -016 -007 -0730106 -064 Z207 -0220704040503920552 381 135 1780814 043

STM1675 133 0695 0465 -062 -052 031051603932668 -003 -054 -0590035 0103040597 19 138 1320257 069

STM1676 052 0386 0555 0662 0004 0030156 -0690784 -017 -009 -0220482 -0310066 -022 -07032[^β] -078 014

STM1677 099 0756 0997 1116 0297 0435 -0040154037705660072 -0270884 -004 -071 1585 -1 -044 016

STM1678 007 -015 0565 -017 -038 -0390338 064 -038026100710408 -042 -077 -036 -053 -

08 A72 -07

STM1679 011 0522 0521 0487 -022 006801380192051901280257 -004 -02 -1390297 -028 134 179 -11 -058 01

STM1680 135 0142 0092 1059 071 0728 -004 -063 -054 -089176310480041 -103 -0210185 066074 [ -17] -064 -07

STM1681 038 0355 -005 0308 -029 02380965 0440037 -086 -08615080654 -077 -038 -037 093096 129 -01 001

STM1682 024 0305 0724 0263 0787 014 -005 -081 -0841373132222262644 -117 -002 005 055 -02 147 -026 -04

STM1684 1 1 0398 -004 0438 0705033401880221018513820693 -0521392 -037 -07 -08041 -04 -034 008

STM1685 078 0669 0658 0116 0086 -003 0020014 -00508581! 101 -04 -07902870711 -1 -05| -2.1 -237[ 064

STM1686 041 -016 -023 0384 0415 06040213 -008 041 -035 -086 -0060135 -0190106 -013 154 -03 105 -131 -02

STM1687 057 -016 -061 0338 005 00690195 -0090579 -066 -062 -104 -033 -004 -0221739 01 067 0550948 -01

STM1688 094 0406 -019 0895 0801 0412 -008 -0571019 ##### -029 -0990824353302610362 088 -01 0341607 024

STM1689 119 0584 -024 IdZ -051 0367 -063 -089 -072 ##### 0283 -040816 -004 -0291289 175 154 2640278 048

STM1690 -09 -024 -07 0039 -057 -078 -046 -1110425 -1451752 -076 -073 -035 -101 -017} -2.41 -03| -23 ,1] -07 -09

STM1691 08582234103802160791 -0190882 -032 -05238 -061483 078

STOI1692 -083 -029> -2J25] -136 -12| -2j -138

STM1693 -022[-1_56) -0472339 -141 -051

-017

STM1694

1471 ##### 0028 -0370459 -02406460711 162069 220576 078

STM1695 049 0146 -004 -14 -002 -01 -086 -042 -051 -077 -034 -0680153038104610943 237 101 2360945 117

STM1696 -01 0385 -1 -049 -087 0497 -021 -101 [Ts4| -0812084 -0260843 -04704790099 138 191 121 1014 072

STM1697 158 0503 0649 0834 -05 -007 -034 -003045502292025 -018 -033 -031 11082507 -01 -03 0210351 196

STM1698 -05 -125 -07 0725 -028 -058 -033 -0150118 -046050902950118 -03104351243 -1 -11 130146 -01

STM1698A 074 0056 -001 _iL⁵. -096 -009 -013 -118 -028 -032 -069 -0840276021802850816 167 107 2110288 -01

STM1699 046 -004 0513 0559 05 0491 -00310531629 -052 -141 -006 -014 -064 -053 -035 -02 149 008 -138 -04

STM1700 -02 -038 0076 -015 -041 -033 -0470057 -052 -006 -037 -038 -041 -048 0220168 08001 1780017 053

STM1701 023 -007 0726 086 033 033706910695 -007 -0320052 -0041141 -111 0340561 029006 -08 -022 -03

STM1702 106 045 0369 -131 -01 0025 -0130147 -135 -009 066 -0630359 -029 -068 -047 -09098 2310051 063

STM1703 073 0544 0491 1315 0025 1 08508331234 ##### 06180182 -0703851126 -025 -01 034 -08 -103 102

STM1704 -07 -022 -047 0487 023 -069 -048 -013 -0350742 -0150257[-ij55J -072 -0890295 -14 -04^7)0791 -11

STM1705 042 012 0606 0307 0087 -006 -0230264 -0090212 -02 -0250079 -1030771 -117 -13 -08 -110321 097

STM1706 -03 -097 0007 0244 -032 -0140363 -027 -0170196 -052 -065 -024 -048 -019 -094 -08 -0 -05 -046 -04

STM1707 -03 -058 -032 -063 -064 -018 -0550167 -006 -088 -096 -0 -063 -058 -0910259 05016 076 -006 -03

STM1708 017 0438 -069 -124 0011 -0110142 -054 -034 -026 -063 -0410427034905990576 207 105 1990988 087

STM1709 051 044 -016 -144 -029 0062 -004 -114 -053 -086 -051052908060707 -0390528 189 1 2JH 061 052

STM1710 057 1111 0885 1661 053 020215041121 127103551351012912630456 -023 -036 -04049Q-IJj] 005 025

STM1711 04 -024 0769 0119 0204 -0960914070910040464 -01001801720459 -0270144 123 -05 0630174 -01

STM1712 066 0544 0463 065 0817 04850484 -00403891248308711220417 29104480196 011 -0i|^~Tτ]i835 038

STM1713 -01 0268 -036 0191 -003 0025 -033 -0270026 ##### -0620694 -078 -066 -068 135 -07 -01 T| -1 θ( -03

STM1714 101 0471 0466 -177 -029 -0180664 -0120649 -052 -02901860985016708540624 194119 2591271 107

STM1715 -03 -021 0017 -021 -031 0013 -0090583 -107 -065 -07 -042 -083050505090206 035076 0270416 059

STM1716 001 -027 -057 -022 0191 -0330343 -0420197 -046 -048 -049 -023 -0650705 -014 -02012 -09 -029 006

STM1717 172 0758 0216 1652 0023 08970899051707160898 -001 1575 174 -035 0660682 -06078^ -17} 325 077

STM1718 051 0699 -005 -137 -01 0376 -072 -113 -093 -0240327 -010347063500690781 209 108 1750298 107

STM1719 -01 0071 -066 -075 -087 -058 -131PT7] -113 #####00590265 -025 -014 014 -013 076041 1210042 039 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1726 0990188 -06 -147 -001 0119 -058 -015 -061 -059 -025 -0090361 0541 00940968 166 1 2370826 041

STM1727 07706250295 059901420334 -04203490361 11910821 17160581 -040554 081 019 022 -01 0774 101

STM 1728 -0401790434 -011 04530746 -016 -005 -1130473 -0471633 -103 -034 -042 -052 -07 -01 073 -022019

STM1729 008 -02304330032 -004 034 -04 0076 204 -029 -O68JTτ|θ68 -18JO 113 009

STM1730 -06 -0090231 02890617 0470317

014215880121 -047 -04 -11 351L-192J -05

STM1731 079 -0010484 08470287 -041 0552 13691471 ##### -149020701270313 -046 051 -07 024 -01 0172 012

STM1732 0880421 0499 0619058304750889046311460034 pm] 0255 00304420134 -025 061 017 -142682 044

STM1733 043 0440346 I -15i[ 0161 0461 -063 -108 -11 -058 -047174702670618 -0140746 172 094 2410326 031

STM1734 -020281 -03 -0570075 -058 -031 -039 -042 -047 -0932062 -102 -016 -062 -044 117038 016 -055 -08

STM1735 -030609 -021 -0170337 005 -01 -0250249 -029 -062 -011 030604050372 -039 -05014 0990533 035

STM1736 0620295 -089 -119 -0240093 -083 -071 -017 -0850045 -062 -022028505650925 185 041 1760506 05

STM1737 121 06470403 -033 -00608780001 07380423 -001 04870482 067 -07407120075 098 126 111 -033 054

STM1738 -020513 -058 -049 -049 -058 -05 -0560722[TJeSl 0673 -052 -035 016 -05 -046 037 -01 0850182 002

STM1739 0603170315 -004 -025 -035 -024 -0160517024613380854 1168 -00505550584 026 036 -060524 092

STM1741 06406060482 0686 0630282019900050814073401440929 -027012308170237 -06 -0 -030138 077

STM 1742 -01 0074 -021 -037 -014 -088 -004 -056037600390346 -0021609 04401060201 -02 -01 -030071 044

STM 1743 04403950186 0549018300630402 -061 -0640736 -135175223970309 -018 -004 -13 019

STM1744 -0503750419 -075 -02 -0520069 -0080991 0622 -047 -12 -086 -059 -043 -041 -09043|

STM1745 -02 -0330355 0360448 -059030902460395 ##### 08040462 -106 -0390165 -095 -09

-05

STM 1746 S -04 -00144 0415 -0270078 -047 -08303141442 -031 -043 -077 -078 -1 -049 -07 -04 -02 -035 -06

STM1748 1030613 Z313 -06703151732 051 10930891 067800771116 089 -046 -0731303 108 109 1560865 045

STM1749 10304160277 0494 -03 -0350345033214630355 -091 -032 -084 -023 -0330477 -09016 G-J-] -^{115 o36}

STM1750 -01 0221 -0 0549 026 -006 -0030581 0782 -021 -0361832 -103 -07 -108 -027 -05 -06 035 -013 -15

STM1751 057 -O94pTi8J -020367 -0520571 -087 -058 -0730614 -055 -003 -037 -038 -039 025 -02 -02 -04 -02

STM1752 -02 -045 -053 -082 -04 -107^19 *-224 -173J -049 -03 -104030501621405 -015 074 13 080099 067

STM1753 07705261058 0927 -014 1390327044404280957094604830172 -005 -0020235 -04 035 -1

STM1754 -1 -08 -068 -1271 -156 -186 -Z01 -208 -174 -127 -128 -114] -199 -166 -221 -122 -12 -14 -o

STM1755 -07 -0080159 -0402650098 -016 -0562793 -091 02730768 -115 -07 -05 -07 -02 -036 -09

STM1756 -07 -0250345 -0260249 -001 0174 -021 075 -071 -0251331 -075 -131 -03 -0θ[ _-19J -074 -09

STM1760 001 -001 -019 -056 -016 -021 0931 -036 -094 -062 -06304940041 -097 -01 -0 077 -079 -01

STM1760 031 -04 -031 -032 -0360027 1155 -031 -089 -075 -0570871 0078 -087 -02 -01 -12 -066 -01

STM1761 05208160201 05080362 -071 0831 -074 -03 051 -00302850766 -037 201 -02 -051867 011

STM1762 12309160739 1004 -014 -076 -015 -0351919 -0190444 -00510930079 425 -04 -02 -062 06

STM1763 0680121 011 0083 -084 -0840429 -032 -023 -0280161 01660691 0816 094 065 1660443 099

STM1764 060329 -004 02380351 0804 -019 -0380257 -030804 -051 11090547 19097 1530414 103

STM1765 05602280012 -011 0197 -0040256 ##### -1130514 -091 -106 -0740107 058 -04[ ^~£8]θ355 -02

STM1766 02 -0040191 0383009506751206 -101 -118 -059 -06 -073 -0250193 085 055 061 0666 043

STM1767 -05 -001 0198 -0470353 -067 -031 -073J -1 β] -091 -084f -1 s| -05 -085 -0 -03 086 -087 -04

STM1768 097 -0560309 Te]O 928 -0803080395 -089 -079 -042 -042 -0020076 182 -01 -03 -106 -01

STM1769 048 -017 -03 -036 -017 -053 -098} -1 δ| -036 -0660196044600880017 183 097 2381006 13

STM1770 0630552 -021 0008 -015 -122 -09 -041 -109011814560163 -001 035 172 051 061264 031

STM 1771 -0402040536 -067 -101 -044 -087 ##### 0854 0261227 -11806940043 -09 -08 0040474 -01

STM1772 1140583 -026 -005 -001 -106 -084 -044 -02 -0520221 0428 016 1018 235 086 1650935 02

STM 1773 038 -054 -013 -038 -029 04610590112 -083 -02202260827 12252458 049021 1220422 147

STM1774 0540434 -029 0735 -021 -0640305 -053 -039 -031 0097 -02205231541 132 136 1430803 126

STM1775 -12 -131 -148 -078 -065J -18β|θ456| -157| -044J -169J -1080063 -03 -052 034 21 -04 1167 -05

STM1776 0570663 -003 0524 -012 -08 -083##### -034 -0120429 -009 -0030853 231 134 2.320592 071 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1782 -05 -028 -07 -118 -088 ^■051 009207990305 -01δ| -2J9J 02250053 -0430268 -037 -06 -04 059 177 008

STM1783S 093 -0 -018 -1113689 0007010200150644##### -068 -032 -089 -059 -0360092 144 038 108 -02 065

STM1784 -04 -074 -073 -12107 0045pl 691 055| -232; -056 -124 -0550275 -0730303 -034 075 004 055 -054 011

STM1785 -¹⁴GiJf] -056 -119 -012 0014 -118 -119 -148 -072 -073 -047 -023 -061 -067 -085 -08 -02 -04 -149 -04

STM1786 01 -00300020374 -021 -05404340869 067 -045 -073 -0750188 095 -0170333 -03 -0 002 -049 04

STM1786 008026401840356 -01 -014046307390637 ##### -086 -0670392130301340018 -02 -03 -02 -067 -02

STM1787 0 027 -00502310263 042903380214 1232 -07310890349 -0280054 -0370273 072 092 029 -002 -0

STM1788 -05 -074 -0440509 -119 -054 -085 -038 -08312571038 -004 -084 -1440163 -081 -05 -04 032 -1.27 029

STM1789 0730403 -032 -099 -067 0222 -044 -05508830052 -029 -048 -051 0199 -01 01 114 126 1180596 034

STM1790 05904010115 -0610242 050303720846 -036 -048 212 -01303030337 -0370863 201 097 240926 036

STM1791 012 -056 -06303140039 -061 101701440105 -0142764 -027 -07200650109 -026 057 118 0442067 001

STM1792 091 02200870169 -01 -0630866 -0990694 -026 -081 07320044 -035 -0040262 022078 1091246 023

STM1793 0270346 -065 -082 -086 -062 -037024404560522 177 -054 -045 -082 -0170234 054 051 049 029 087

STM1794 099 -012 -098 -125 -094 -046 -037 -14 -025 -111 -025 -0790605057600620758 214 107 1530359 031

STM1795 -0202640398 -145 -129 -075 -012 1487 -055 -057 -068 -065 -105 -108 -038 -035 019 012 0290147 021

STM1796 076014910710618 -006 1468 -005 13270656 -0411520771 0127063610640073 -08 092 -04 -009 094

STM 1797 013 -046 -0430241 -1 -020222 1197 -042 ##### 01350288 -047 -107 -085 -086 -03 -01 039 -03 -07

STM1798 019 -039 -021 -133 -074 -009 -052 -0520205 -017 -075 -018 -026 -02602470009 116051 1621136 036

STM1799 1710507 -0571073 -042 0318 05204331629 -058 -1201161002 -015 -030155 011 084 033 1268 002

STM1800 05105970078 -0450454 -0380898 0970242 -053 -05 -011 -0390217 -0080076 116 046 16 -018 012

STM1801 106 091 0205880588 -0140297 -001 05740756092600080316 -023 -0290011 057 -0β[~2] -025 009

STM1802 -01 -033 -00300390214 -021 041 0215 -02901260324 055 -003 -0270495 -027 -09 096 -07 -044 031

STM1803 02302890518 -038 -049 -0390481 049905950322 -0460699 -061 0107 -094 -072 -02 034 -04 1926 -05

STM1804 S 02 -015013203880102 0288 03505730894 -054 -01801090301 012503870076 -06 O25Q26J 1071 038

STM1805 -01 -0810205 -072 -046 -006 -101 -0131122 -016 -148 -106 -104 -047 -059 -112 -03 -06 114 -123 01

STM1806 069 03 -0130621 -078 -023 -021 £333 -0507360273 -028 -081 -07405020003 041 -03 -05 -12 -03

STM1807 040124 -04 -1240006 -04 -062|_-V66l 016 -121 -072 -085 -015 -082 -0181041 122 03 106 -033 014

STM1808 0980222 00912590296 -0270181 025402781032 06605351645 -04202420046 098 -03 132 -121 069

STM 1809 05300630616 -021 -007 -0040261 02660469 -0270284 1031 1814 -0430809 -002 105004 014 -093 032

STM1810 10108230361 -145 -064 0355 -057 -105 -005 -011 0502 175095 1840011 086

STM1811 0810525 -06208330281 -047 -018 -071

-142 -126 -065 -14 -11 -09 -198 -15

STM1812 025 -0270493 -067 -023 -031 -034 -06300120427 11 056 1090225 035

STM1813 -04 -102 -09 -017 -023 -131 -002 -022 -031 -037 -04 033

-13

STM1814 -020096 -052 -046 -101

-02 -118 -12 -119 -11 -05 -03 -01 -044 -09

STM1815 035 -002 -067 -106 -074 -034 -097 -006 -077 -057 -04 -039 -0390139 -013 -043 086007 1320003 033

STM1816 -02 -011 -034 -128 -048 0153 -053 [ -15il -096##### -045 -0460509 -0180251 0658 12 -0 170412 031

STM1817 -02 -028 -056 -06 -011 -045 -043 -025 -036 -012 -078 -032 011 -052 -024 -031 -06 -0 -Z7 -22 -02

STM1818 0950069 0320596 -008 -013 -021 0389 0240705 -1 -047 -068 -063 -102035β| 3069 -21 -159 -09

STM1819 0850442 -018[-1JKj] -024 -007 -028 -071 -015 ##### -063 -065 -01503080281 049 205 132 2360656 095

STM1820 -01 -003 -117 -012 -091 -0870012 -029 -037 -129 -04 -05|^" -1 β| -136 -13

STM1821 027047103870486 -128 -0270291 1029 064

-048 -05032 1391542 -07

STM1822 049 -024 -024 -0150182 01490387 -0660768 -11 -144 -056 -05210680871 -08 -03 -03 -07 -069 056

STM1823 050661 -O 25 -128 -082 00660196 -020232 -099 -058 -099 -011 -023 -0060257 169 1 1230381 061

STM1824 -12 -037 -015 -046 -013 -056 -074062511820562006307060403 -0440777 -018 034 -04 -01 -007 071

STM1825 0730296 -078 -086 -017 -046 -024 -046 -053 -1 -033 -0160787014805550405 185 089 2271158 091

STM1826 1630643171601510237 05680512 141 110506491435 -03401020618 -0273448 -01 02 -050742 109

STM1827 S 0330164 -00908390205 -025 -031 -052 -052 -026, -2UJ 1116 -002 -022 -011 -071 059 091 -150295 -02 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1833 057 019 -027 -081 -02 -0090009 -0350211 -055 -0680226 -0020331 01030364 056022 1350006 04

STM1834 050733 1157 0446 -0050557 -022 -064 -027 00518470357 -138 -074 -048 -078 -13 -08| -2.2J -095 -07

STM1835 13608070779 0967042908240712 -041 0742 -01 -0191953 071 060208740811 06 012v -19J0874 064

STM1836 10506860764 0921 0444 0780563087212230621 1151 0994 -032055703391805 -O 013J -2.31 -029 08

STM1837 162 11622196 -0080531 1546106213950657 -014136616430579 037 11040561 091 119 0660067 069

STM1838 05612350065 -0640097 -0020131 -0660061 -042 -026 -04053804230158 017 151 136 1460034 041

STM1839 059 -0470614 05470144 -08705850653 -06 -104^-189~ 1^*ξi ~ϊ -18*y-i*79J -067 -07 -12 -11 -05 -141 -11

STM1840 024 -045 -081 08170431 -0350388 -0020908 -077 -005 -061 0129 -011 -092 -049 155 -1 i|__jj -035 -12

STM1841 10305560832 -01406520125022311380372 -0570853 -0450219 -01 00821018 092 069 124 -034 074

STM1842 066 -0040323 096 -0290304 -036 -028 -005 -022 -14 -0260337 1417 -098 -01 -02 -05 196 -024 -11

STM1843 09905980407 09320135 -0330382 07201630047 -003 0561676 -046 -0641401 -02 015 509 -006 -07

STM1844 05706691244 0646 -001 1011 -003015714180811 099907350389 -01305820619 054 082 -02 -012 083

STM1845 081 01950518 009907970529027805390172 -079 -083 -095 -082 -079 094 133 -06 029 116 -078 091

STM1846 176016708931185 -0507040031 1240086 -04913130397 -011 14770793 -017[-1_8j 005 -05 -14 078

STM1847 10203170887 127017300120756 06 117 ##### 104303890019 -060739 -042 -06 -02[3[9~T94j 039

STM1848 0940534 1017 1028 09803570713048406150393 -112 0761037 -013 -038 -052 -03 -02 -1 0466 -05

STM1849 11504331178 0984 -00071 0407039606670476153406091128 03301490239 -02 -02 -0 -054 059

STM1850 12405990683 1201 072408660427106503741465 -04704640262 -0290271 0321 -06006 -1 -073 069

STM1851 024 093 -041 -107 -0640015 -028 -093 -001 -061 -037 -0170319 021 -0070916 174 118 1460126 086

STM1852 0370142 15 020205981174 059 1091 0536 -081 038 007045608830397 -005 098045 0480055 033

STM1853 098 -0830128 110403620371 075302531161 -059 -058 -036048416890538 -017 -02 -03 -110717 -01

STM1854 043 012 -047 -1jj4J -004570232 -0080497 -0730041 -0290136 -009 -0490626 132071 0860896 014

STM1855 005 -017 -011 -0080157 -028 -032 -059 -0320177 -058 -042 -075 -037 074 -015 -1 -03 -09 -149 044

STM1856 052012400430881 0343018803560238078402910054 -O735E-O4 -031 032 -017 -06 -05 -08 -048 -05

STM18561I 043 -018 -0611840068 -024 -022 -065 -078 ##### 101 015 0330002 062 -080902 -07

STM1857 043 -012 -0290841 -020045 -0030189 -025 -038 -0690523 -0320094

-11

STM1858 0980015 017 -01201160394 -01901580.2490819 101 10920216 -04200650625 078044 1540642 018

STM1859 -0303230083 -033 -001 0192 -035 -068 -088##### -098 -085 -087 -055 -057 -001 048 -04 -051357 035

STM1862 -1 -075 -0690274 -024 -040125 -011 0695 -033 -0050674 -032 -0090022 -01 -1 04[1MJI 906 -03

STM1863 0480023 -029 -096 -041 0543 -086 -086 -106 -063 -117 -0590342020400150454 238 119 2330717 081

STM1864 02 -033 -0460463010800830062 -069 -001 0931 -021 0115 -083 -083 -0480127 -08 -O2[j-1jl_-758] -02

STM1867 -02 -047 -049 -021 -033 -029 -038 -087 -116 -0310656 -0780813 -019 -025 -024 136 -02 173 -044 004

STM1868 0390057 -023 03760025 -0030306008802350275 -03 -059062900750193 -033 055

036

STM186811062 -03 -078 -11400930254 -036 -1350017 -023 -049 -0420544022202521263 103047 1640244 049

STM1868A 0740244 -007 -056 -018 -0320021 -039 -046 -028 -051 06440233 -021 04890269 128026 081 0005 072

STM1869 011 0771 0288 02330145048700490687 -073 ##### D 32303640924 -035 -0070589 -05 -02 [^] 0728 -01

STM1869A -020315 -045 -093 -0 -027 -04 -008 092##### -037 -0603450633 -0160636 13 039 1540071 051

STM1870 0780162 -012 £599 -017 -043008606240222 -025 -02503750368 -03 -0840137 026 024[_-1_5J -059 -08

STM1872 090232 -029 _-1J57] -091 0502 -064 -069 -089 -127 -068 -0840625075801591188 228 082 1660568 -01

STM1873 0960392 -014 -086 -063 098 -10502450887 -053 -0530084 1064030402790631 127 08 17 -012 053

STM1874 05900830539 0598 ########## -0290338 -0990161 -03 o 045 mtmmmmm -026fTs|o2i -24 -Z0 ? e2) ---112

STM1875 041 0365 004 0471 0204 -0650295 -04606790469 -0780048 -038 -061 02660374 -11 -05 -17 -052 021

STM1876 01901480197 -017 -00229 -00210080455 -026 D 259 0060299 -03205520542 -03 04 0390018 05

STM1877 081 -022 -0 0317 -07306020348 -07310180237 -052 -039 -048 -011 02690647 067002 0282156 -01

STM1878 02905150538 •0290308 -0640261 -00202490241 -03 -0430391 -11 01730387 -01 -04 -070925 -01

STM1879 086 -0040361 1 0162 1286 110912420561 -017 -024 -008 -001 -0470571 1205 053 131 0772986 096

STM1880 0551221 -001 08660626 -0651023 -0320934 -1 0696 -018022602850178 -039 -06 -04 -05 -099 -03 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1886 001 -105 -066 -015 -035 0090344 -112 -029 -106H-TsT] -0660552ITa)I -075 -046067019 -08 -148 -07

STM1887 012 -049 0971 021 -034 -027009501861288 -065 -05 -081 10680158 -046 -028 -01 026 ^~5] -067 -04

STM1888 022 -06 -119 -126 -1 -104 -065 -157 -023 -014 -062 -0870172 -00303540396 075 229 049 -028 044

STM1889 -00099 -073 -154 -061 0199 -053 -157 -006 -062 -021 -0230371 0301 06090434 156 076 1340766 034

STM1890 0650382 0891 0664 0131 0551 -0760065 -002 048J -187[ 0337 -111 -117 -0850774 -14 -09 -11 -121 -1

STM1891 044 063 -017 -137 -096 -040121 -081 -043##### -061 -05400070402 -006 058 219085 2350261 015

STM1892S 017 -056 -116 -084 -122 -027 -11β[j244J -14 -065 01 -058 03607921458 -02 062 106 1550115 187

STM1893 0880059 -076 -017 -002 0492 -051 07791519 -05401470381 0106 -036 0140465 122 208 1070604 055

STM1894 1490438 -027 -148 029 -0450016 -068 -0580067 -015 -00807180331 06771064 219 116 24 1215 12

STM1895 006 -021 --002233 --117799 0225 0036 -089 -122 -086 -097 -101 -0640889 -000220469 192 094 201 0108 021

STM1896 -111 -1 e| -117 -07 -162 -125 -136 -122 -03 -13-2) -2.1] -141 -062 -131 -089 -045 -15

STM1897 037 -013 -040411 -0330349 -004005905090495 -014 -108 -065 -115 -054 -034 -2

STM1898 0540533 -015 -0940733 -0140136 -077 -105 -02 -046 -064 1018 ^09602820735 055 005 1180564 085

STM1899 -±§1 -¹²²I -Z58[ -03δ[]z37 -123 -063| _:21 ^203] -078 -045 -001 -136Qi_5§j -097 -064 -06 -07 355 -076 -1

STM1900 0250297 -04 -0680243 0714 -075 -1050069 -11 -016 -0019804460591 0974 235 135 231 0632 073

STM1901 0340678 -026 -113 -059 0205 -082 -108 -047 -089 -058 -09 07077609140725 211 11 1790927 048

STM1902 05420330033 -083 -033 -0 -038 -019 -0560298 -0407150311 -01 03051098 107 11 170298 068

STM1903 07315451106 -056 -024 -020114 -019 -005 060395 -068 -052008205451726 -0 09 1350743 003

STM1904 0930131 -008 081 -009 -01209230512 158 ##### -1 -02700051257 13970251 -01 074 2170664 122

STM1905 0610609 066 -0080322 0687056205570434##### -0580645 -041 -0360995 -023 -12 049 -05 -122 143

STM1906 037 -0030188 -034 -054 -008 0220176 -025 -012 -04 -036143500681263 03 -03 069 287 -094 114

STM1907 0 -039 -045 -01 -052 -0180041 074305020194 -0840101 -149 -127 007 -06 -08 -04 -1 1261 -08

STM1908 080451 -007 -115 -036 -029 -015 -137 -09 -076 -094 -085 -008002400430936 158 088 2250551 06

STM1909 0980567 -022 -112 -058 0059 -009 -106 -048 -027 -020306006305160667 108 21 164 2820624 068

STM1910 -03012601330551 -014017608441571 1585 -047 -192 -019 -127[TM] -020014 -09 -03J -Z8 -22e| -11

STM1911 0360261 -01806970446 00520197 -023 -014 -008 *-16 -132 -04208860449 -029 037 -02 -12 0162 017

STM1912 044 -001 0163 -12 -03 0036 -05 -055 -078 -089 -066 -012 -00602450098 1026 212 101 Z33 0884 014

STM1913 0290035095203080104 0793048611770878 -009| -417 -162 -149 -139 -031 -113 -11 -05 -3! -139 -02

STM1914 00800580911 05 -016 0237037812280774 -059 D 475 -03 -0 θδfTas] -118 QiJS- TJi] -15 -106 -13

STM1915 081 00080321 -039 -052 -089 -0820349 -092 ttmm 4611 4101 540341181398 326 -01 261 098 -026 172

STM1916 -07 -107 -052 -055 -066 -032 -102 -088 -061 -00837630864 2380502 0390838 02 169 -08 T94] -06

STM1917 03 -07 -033 -113 -075 -05 -067 -0060267 -0233421598386712040648 1332 04 194 02 -068 081

STM1918 -02 -034 -017 -0690388 -024 037 -078 -06 -043 -123 -142 -041 -0970767 -036 -08 -08 -02 -097 052

STM1919 -1 -105 -Z1 -111 -052 -06810240621 0975 -221 -153 -031 -O74FT55] -101 -13 -07 -13 -11[ Ts2] -09

STM1920 040031 -059 -IJj -04600320135 -114 -036 -105 -08 -073051504440285 118 118 1,9 224 08 -01

STM1921 -06 -013 -089 -058 -0350223 -02 -099 -0690232 -124 -117 -019 -076 -019 -013 033 067 06 -086 -01

STM1922 0010141 -0230481 -043 0254 -016021811230333 Tθ2 Ts] -098 -123 -081 -1341 -1 δ] -15 --1166 --224422 -09

STM1923 -090023 -03 -093 -081 -04103470506 -036 -016 -1821-059 -104 053 -087 -034 -03 -09 00 --111122 -16

STM1924 S -070265 06410279 -043 0563 -067 -037 -0830024 -143 -119 -114 [T∞] -124 -134 -11 -14 --1111[ -234 -05

STM1925 -020033 0569 -021 -0 02620018 -005 -019 -001 002 -062 -139 -09 -1060483[^"Ta] -08 424 -091 -09

STM1927 0240193 037204950637 -00601690392009402060654 -01 001 -0290165 -023 -13 03 -26 1212 -01

STM1928 0130065 057 038 023 -005029604020358 03803240399 -071 -052 -0620067 -11 -0 -18 -064 -04

STM1929 0960959 094 1387 -006 035501690531 -00600480167 -03901741422 -106 -02 -14 052 -16 032 -08

STM1931 140358 027908520168 0462 -03 0130417 -0340647 -03706330435 080483 02 038 338 219 077

STM1932 116 -005 -07203271142 04140885 14750271 0008 033 -0420133058409130569 185073 1550633 179

STM1933 -0 -005 0352002701890217122802260612 -017 -080272 -071 -046 -084 -043 -08 033 -13 1011 -05 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM1940 01 01760253 0261 -004 -02402190386056901570739 04602620501 01290973 -08068 -05 -038 016

STM1941 -03 -004 -00505960178 0022 -029 -035 -003 ##### 0287 -016 -113 -109 -052 -044 118 -05 -11 -031 -1

STM1945 01 0928 -086 -027 -049 -014066802150424##### -043 -005 -042 -1 00460245 048 -03 048 -046 008

STM1946 -05 -008013102560354 00860097 -0460434047415190642 -0660792 -011 -069 -05 -03 -12 -064 -04

STM1947 -03 -024 -026 -0070089 -043 -031 -071 -119 163257529282319334618052035 -08 256 2272697 184

STM1949 0890354 -036 -0810025 -042 -021 -106 -025 -0630408 -031 01570107 0220128 078 029 169 -02 -01

STM1950 -020111 060202530235 02490307022400231101 12260784 -044 -042 -055 -032 -1 -05 -13 -002 -03

STM 1951 0370305 -00603680459 1126011803420119 -068 -0050189 -088 -028 -056 018 ^05017 -05 -11 -01

STM1952 -07 -044 -059 -016 -015 -094 0340105 -012 -101 -003[T 97 -155 -Tai| -066 -069MSl] -09[TM] -063 -11

STM1953 0130465 -064 -013 005 -08504730239 -025 -038 -05 -054 -083 -136 -082 -071 -12 -11 053 -044 -09

STM1954 009 154 -037 -011 101 -01507290124 068 -02 -137 -0380441 -043 -007 -011 081 034 084 1775 046

STM1955 0150072 -04705290204 -1130016 -036006301030238 -109 -007 -124 -007 -007 -12 -06 [^] 308 -03

STM1956 -14 1101 0864 -1160322 03781034 10540.294 -043| -293| -1351 -184 -224 -185 -165] -09 -13 -140325[^"TT]

STM1958 -06 -038015101220143 0051 00920346 -032 -0190439 -054 -061 -056 -0540249 -03 -05 -05 -077 -07

STM1959 -020454 104905790458 1264041609180764 -025 -038 -143 -12 -068 -129 -138 -02 054 2.27

STM 1960 -04 -048 -0030218 -029 -027 -024 -0440253 -0180394 -1321 -Z06 -175 -Z03J

-15

STM1961 149 -011 0532[TS] -072 -003 -062 -135 -112 -0630509 -0230052 -04803280776 191 13 161078 088

STM1962 0580193 -007 -111 009 -012 -118 -091 0658 -052 -037 -074237701920425 -011 171 097 135 -029 069

STM1963 -040486 0620344 013 024806560252 11271365 -0380032 -058 -049 -111 -03 -05 -01 -1 -103 -05

STM1964 0120165 -044 -124 -074 -006 -013 -01 -127 -1030173 -0650368012406920664 14 137 2350609 1

STM1965 0770502 -013 -0620036 -001 0436034601240031 -0571565 -092 -054 -0780256 122 014 06 -051 031

STM1966 0520125 -045 -135 -071 0117 -022 -081 -081 -131 -008 -069 0130546 -01 0651 146 141 2040293 1

STM1968 -03 -034 016 -08 -01 0268 -0250755 -127 -0.2 -11 -009 -082 -083 -047 -036 022 -02 -01 -104 -02

STM1969 -080004 0050708 -014 0130084 1330271 -

1 -11δ[^" -1 S -192 -212 -19^* -14J~T6~ -27s[ -12

STM1970 087 -009 -062 -115 -O 81 -0490031 -046 -041 ##### -036 -0220296 -00504560851 197 101 20678 086

STM1971 -02 -018106502350064 -072 ^■18,_2?! "⁰⁹LiIl '¹³² -°⁸

STM1972 -01 -0180763 -012 -095 036308861877 -069 -15pii 015 -01 -076034

STM1973 -0305770346 -007 -006 054 -048 -062

-101 -0090928 -062 -063[-1J36J -0420307 005 -1 -02 -109 -06

STM1975 004 -005 -021fTeβj -022 -03800160095 -0691598 -009 -001 016 13 015 2080507 -01

STM1976 -030092 001 -1040129 -02401630428 -015 -05 -112 -077 -082 -041 -047 -032 008 -01 063 -028 -01

STM1977 -06 -050053 -045 -029 -025 -0140675 -015 -056[TUT] -141 -047J_-1J>5 -0850536 -05 -1.2 -03[TeSl] -09

STM1978 089 -011 013 -092 -045 -017 -040757 -051 ##### -014 -106 -046 -108 -074 -03 029 026 075 -06 -06

STM1979 0950126 -038 -105 -082 -0 ie[ -1.62] -004 1519 -071 -021 -014 -034 -001 00430767 164 078 1640215 048

STM1980 071 0103 -061 -13 -101 0094 -012 -106 -095 -132 -034 -0530537049202450756 188 152 2621268 038

STM1981 -030181 0494 -005 -002 053102650667 -105 -0670943 -117 -10δ[Tκj -06β|Tβ7~3 -04QzS] 0204 -07

STM1982 -02 -049 -04601450105 -028 -036 -069 -066##### -128 -013 -139 -053 -0860417 -06 -03 -07 -066 -1

STM1983 027 -015 -014 ^*~ -1^"65' -027 0477 -056 -119 -103 -06 -044 -0140276 -01 -0220145 076 054 1350317 086

STM1984 0490778 -074 -158 -089 0183 -03 -051 -129 -028 -008 -02605720083 -0171149 263 122 1520594 054

STM1986 -080351 076 -068 -008 03660201 0187 -0060149 -0850857 -051 -076 -026 -025 -05 037 0380014 -04

STM1987 051 11080406095603850238 067005503750574 -1361058045912690685 -028 084 02 042 05 11

STM1988S 081 0503148505680503 1116110815081075 -0030231 0283 -004 -011 -01 0798 09 021 1280026 -02

STM1989 02802760074060306680422076600820351 0587 -048 -0870192 -018 024 -028 13 -1 -05 -035 037

STM1990 0780129 -002 -003 -0780023 -040322 -08602442824 027 -016 -08500230243 -01 -03 009 -028 094

STM1991 06703380053 -141 -005 -0030084 -025 -093 #####1249 -031 03602740091 0915 141 084 190603 035

STM1992 0350194 003 -0790702 -02502920222 063 -051 -073 -0980155 -04202820477 113009 1280038 038

STM1993 1 -025 -05 -054 -01601540491 11760621 1769 -111 0837 -0 -03201833217 065042 1090548 058 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2001 112 0065 -0660956 005 -05 -068 -01307030231 -1260229 -1 -084 -045 -048 044 -06L₅JjT

STM2005 0780057 -014 -1240163 0028 -075 -077 -049 -089 -061 -012 06700920424 1217 216 111 187 0922 064

STM2007 -01 -O 3501590097 -005 0344 -023 -004 -015 -022 -015 -004 -064 -059 -05 -03 -06 -07 -12 0106 -08

STM2008 0190179008706340408 0093028300290277 -00200610082 -0481227 -0160256 -14 -01 -21. -111 -03

STM2009 09405090314 0420068 0102008909470594031608652306 #####0316 -021 -007 -06 069 -16 0207 -01

STM2011 03503660073 -O 25 -047 00440379 01408850315 -1090141 014048401030243 096 037 123 -041 006

STM2011 1ι 0620212 -02 -131 -008 -0130316 -013 -014 -081 (M7502150895 00401890725 181 072 123 0527 038

STM2013 1040765 01 04740872 -0830849 -003 -057 -066 -06802860284 061 116 002 -031 -05

STM2015 104 1159 0961202 1292 124306740015 059

2681*0854 1592 1288 126 159 379 1531 177

STM2016 1170318 -0060516 -008 036212231398062700631541 2357 -041 -034 -0450057 162 045 133 -01 -04

STM2017 0630242146603670554 034703141329 -027028315640941 -057 -101 0551 -013 -070 isfjTβ] -012 101

STM2018 -06 -O 750436 -114 -02 -05802871382 -064 -085 -081 -025 -059 -01 -03 007 148 057 056 -015 031

STM2019 148029712190419 -056 1061 0291694 -0.2 ##### -103011801320105 -020783 026057 -13 1665 042

STM2Q2Q 0480047 Z201 -093 -057 0566 -081547 _-1_76J 023128690683 -094 -089 -006 -069 -0 -05 022 -06 -05

STM2021 046 1252 -078 -0040875 0070434 ^*-156 _084 #####06881022 -048000300090695 06023 2.25 0394 033

STM2022 148 012 -03400460078 026 -086 -174 -065 ##### -052094 -0 -013 -0470292 108028 152 044 077

STM2023 0460714009603250075 -046 005 -0480696 -021 -03 -054 -149 -086 -112 -014 -1 -0 -22 1327 -12

STM2024 0380203 O 30706960103 -057 -001 -0020673 -052 -051 -088 -141 -084 -103 -032 -09 -O3[_-1_71241 -14

STM2025 061 0472 -021 -143 O 016 054 -01303270005 -04 -0340076 027 -00706760555 09099 1750465 154

STM2026 1060287 -018 -091 -089 -027 -03101230239 -046 -01501250737 -02302510728 225122 2210823 11

STM2027 357 227517642373 1419 1757069804461454 071 -0990506 -028 -07801910053 064 -02 6741611 027

STM2028 0980029 -03709070452 -113 -O05 -0750213 -0471645 -078 -072 -083 -043 -014 -07 199 1330262 07

STM2029 070265 -008 -059 -048 0323 -029 -049 11 -003 -0320177011103851708 039 17063 240266 122

STM2030 0861627 -00901870206 03450393 -0050738 ##### 11650043 -00900050368 -04 -02086 09 -009 069

STM2031 063 0169 1 B7 -101 -064 0179 0630048 -14 -O 2 -026 ~-0450503 -04803070091 132069 2020111 019

STM2032 112 1241070504710854 0802 -086 -108[ -2 Oβ) 171 -01908760242 -03 0810185 02 09 0250518 058

STM2033 0461147025711380131 -04708470647094405560456 [ -15B| 0718 -098 -019 -006 -06043 -11 -119 -04

STM2034 04410210943 -0090253 024504370463085818880969 -0222134 -02 -0071211 094 06 -03 -058 014

STM2035 0501660411 -094 -067 04430342 -001081705650123 -078 -042 -05700240753 063045 1510574 047

STM2036 0130088 -00902560.207 01330198 -060708 ##### 0108 016 -0120337 -006 -002 1030371^2 -017 015

STM2037 -0102240471 _j016 -028 002501990028 -052 -0460621 -018 -1080011 -01 1534 086 -02 -110336 -01

STM2038 -0 -0250179[-16J] -032 0316 -015 -044 -063 ##### -03 -0301620181 -030218 154076 1990338 099

STM2039 0070132 -0360171 -028 -027 037 -0020264 -0510403 -014 -06 -115 -063 -095 -09043 M 0405 025

STM2040 068 00030008 -026 -083 -064031600420535013201792582 -106 -021 0459 -052 -01

064

STM2041 0270153 -009 -0930553 -0170218 -0431686 -034 -04 -0430448073908370773 127 119 1370788 136

STM2042 060384 -01 113 -083 0458 -0 -044 -058 -0470062 -0420691 -033 -013 057 198 123 234 J-LIiL ° ⁷⁹

STM2043 -020447 -07103250604 -0460468 -003 -0080211 1898 11090256 -O 571522 -064 075 -03 156 ___-32j 145

STM2044 0340351 -064 J 42 -054 0316 -045 -088 -105 ##### -031 -0370359018903770735 161 107 186 0448 033

STM2045 0430209 -02β[-189J -106 05590061 -086 -034 -082 -065 -031 0256 -0130157 069 201 114 219 038 112

STM2046 050263 -O21[-1Jβ] -013 -001 -046 -075 ^052##### -044 -01 0251 -00501770076 227 201 144 0539 093

STM2047 078 -019 -0310368 -004 053200840195^ -233] 1284 -072 -015 107406650335 -085 04 -06 241 -078 112

STM2048 0810386006IpTsTj -067 0111 0282 -0160396 -046 -0430089 -012060601970427 123 03 186 0287 139

STM2049 0380251 -036 [ -161 j -069 0636 -008 -069 -059 -083 -049 -019 0280176 -0070553 089 115 19 0506 066

STM2050 -070536 -01 -0320366 02650474055306780834 -11 -041 -021 399403231014 026012 -1.2 -062 114

STM2051 0290199 -022 -076 -03 0116 -055 -1430131 -021 -065 -0130079 00601450853 173 07 24 0307 105

STM2052 -04 -014 -123 -02 -148 -14 -05 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2059 0.03 0.459 -1 -1.12 0.644 -0.02 0.275 -1.36 -0.79 -1.17 -1.23 -0.37 -0.22 0.393 0.032 -0.02 0.88 -0.1 1.38 0.275 0.64 STM2060 -0.2 -0.23 0.034 -0.06 -0.67 0.004 -0.25 -0.7 -0.01 -0.13 -1.25 0563 -0.87 -0.26 -0.42 0.036 -0.8 -0.4 -0.5 -0.98 -0.6 STM2061 0.06 0.253 1.164 0.538 0.441 0.751 0.682 0.104 0.144 0.24 0.853 -0.38 0.521 -0.88 -1.02 -0.51 j~a] -0 -1.6 -2.36 -1.1 STM2062 0.21 -0.58 -0.11 1.134 0.371 0.213 0.385 0.363 -0 -1.18' -37610.125 0.419 -1.37 -0.75 0.138 -1.1 -0.7 -1.5 -2/rø -1.3 STM2063 1.04 -0.3 -0.16 1.313 -0.681 -1.5j -1.04 -0.72 0.084 -0.6; -3.04 -2.89| -0.74J -1.69| 0867 -0.43 -1 -0.9 -2.2 [-086 0.06 STM2064 0.3 0062 0.001 0.373 0.093 -0.22 -0.06 0.145 0.188 -0.16 -0.02 -0.13 0.407 -0.05 -0.09 0.295 -1.5 -0.6 -2.5 -I.64] 0.2 STM2065 -0.2 0.597 -0.46 -0.18 0.221 -0.24 0.958 -0.17[3Ua] -022 0.859 2.977 -1 -0.33 -1.22 0.679 0.83 0.12 -0.5 0.033 -07 STM2066 0.14 -0.05 001 0.56 0.458 0.146 0.342 0.339 0.113 -0.48 0.215 -0.27 0.086 0.339 0.381 0.152 -0.8 O.19fϋτj 0.733 -0.1 STM2067 0.37 0.63 0.445 0.653 -0.17 1.613 0.316 0.635 0.163 0.011 0.081 0.472 -0.21 0.53 0.834 0.117 0.4 0.59 -0.1 -0.34 0.72 STM2068 0.87 -0.13 0.156 -0.25 -0.27 -0.24 0.159 1.335 -0.2 0.84 -0.53 0189 1 42 0.131 0.383 -0.17 -0.1 0.17 0.73 0.064 -0 STM2069 0.93 0.003 1.099 0.738 -0.25 0.393 0.004 0.759 0.917 -0.16 0.437 0817 -0.36 -0.51 1.101 -0.66 -0.2 0.53 -0.3 -0.99 1.44 STM2070 0.11 0.58 0.111 -0.37 0.02 -0.94 0.4 0.532 0.559 -047 -1.22 -1.31 -034 -0.84 -0.49 -0.22 -0.8 -03 -0.7 -1.15 0.33 STM2071 0.72 0699 0.394 0.484 0.056 0.41 0.429 0.846 0.351 0.223 0.237 -0.27 -0.94 -0.49 0 136 -072 -1.3 -0.5 [_-25J 0.733 -03 STM2072 1 38 0.461 1.161 1.268 0.122 1.293 0467 0.894 0 154 0.99 0.88 1 635 0.369 0.051 0.315 1.442 0.14 0.11 -0.5 -0.19 0.72 STM2073 -0 0.217 -0.51 -085 -0.71 -0.05 0.284 -0.19 -0 12 -0.57 -0.58 -0.26 0.268 024 -0.04 0.46 1.34 0.24 1.87 0.873 0.44 STM2074 0.31 -0.03 -0.76 -1J2 -0.09 0.074 -0.41 0.414 -1.03 -0.39 0.042 0.43 -0.08 0.782 0.227 0.307 1.29 0.16 2.62 0.006 0.48 STM2075 -0 1 0.279 -0.17f-1.5i] -0 53 -0.54 -0.29 -0.19 -0.21 -0.37 1.393 0.945 -0.35 -0.45 0.37 0.458 0.29 -0 0.61 -0.35 0.03 STM2076 -0.2 0278 1.043 -1.15 -0.56 -0.47 0.405 0.043 -029 -0.34I -1.62 0.446 -083 -1 21 2 356 -0.21 -0 1 0.49 -0.1 -1 36 1.12 STM2077 098 0.649 0.767 -0.14 -0.47 0.344 -0.01 1 908 -046 1.405; -1.95 2.233 -0.23 -0.34 1.909 -0.11 -0.1 0.33 -0.6 -1.28 1.32 STM2078 0.41 0.112 -0.09 -0.82 -1.05 0.113 -0.89 -1.43 -1 08 -0 19 -0.17 0.4 0.721 0.016 0.183 0.4 1 0.55 1.55 1.004 0.22 STM2079 -0.9 -1.07 -1.05 1.518 -0.7 -0.86 -0.43 -0.78 0.31 0.327 -1.19 -0.73 4.44 0.016 0.831 0.08 -0.6 1.23 3.43 2.183 0.72 STM2080 0.27 0.317 0.344 0.492 0.139 0.313 0.347 0.181 0.265 -0.27 -0.28 0331 0.387 1.033 -0.05 -0.18 -0 0.01 -1 -0.24 -0.1 STM2081 0.21 0.071 -0.09 0.109 0.055 -0.08 0.024 -0.54 0.272 -0.27 -0.23 -1 2.815 -0.15 0.312 0.111 0.2 0.83 0.9 0.262 0.68

STM2086 0.4 -0.17 -009 -1.18 -0.32 -0.02 -0.51 0.414 -1.36 -0.67 -0.82 1.177 1.063 0.522 0.113 0.53 1.71 0.46 1.66 06 0.27 STM2087 0.34 0.284 -0.24 -1.37 -0.9 0.849 -0.1 -1.22 -0.88 -0.18 -04 -0.53 0.151 -0.05 0.226 0.935 2.29 1.7 2.01 0.361 0.03 STM2088 0.71 0.212 0.014 -1.01 -0.86 0.013 -0.48 -0.58 -0.47 -0.92 -0.49 -0.63 0.265 0.761 0.757 0.393 2.45 0.9 1.74 0.75 0.69 STM2089 0.17 -0.05 -0.39 -1.12 -0.38 0.36 -0.06 -0.78 -0.54 -0.89 -0.59 -054 0.44 0.066 0.411 1.45 223 1.25 2.19 1.212 0.83 STM2090 1.06 0.031 -0.11 -1.07 -0.75 0.219 -0.33 -0.56 -031 -0.58 -022 -0.19 1.063 0.409 -0.36 0.896 223 1.17 1.92 0.856 0.42 STM2091 0.63 0.35 -0.4 -0.96 -0.56 0.48 0.12 -1.06 -0.38 -0.37 -0.69 -0.1 0.784 0.146 0.675 0725 2.71 1.68 2.56 1.234 1.05 STM2092 -0.08 0.393 1.72 0.73 1 ?fS 0719 0.58 STM2093 -1.29 -1.03 -0.3 -1.1 0.59 0.17 -0.7 STM2094 -0.99 -0.78 -1.3 -1.2 -1.3 0.296 T₇] STM2095 -1.24 -1.1 -0.9 -0.4 -1.14 _-iZi STM2096

-O.73| -1.67J -1 -0.9 -1.2 1 359 -0.8 STM2097 -08 -1.06 -0.83 -0.12 -0.32 -0.07 -0.49 -0.14 -0.28 -1.13 -1 07 -0.44 -0.23 -0.32 0.161 -0.03 -1 3 0.33 -0.4 -0.46 0.16 STM2098 -1 0.327 -0.02 0033 -0.03 0.223 -0.14 0.514 -047 -0.54 -1.61 -1.71J -071 0.667 -0.31 0.036 -0.2 0.13 -1.1 1.329 -02 STM2099 -0.7 -0.59 -0.4 -0.59 -0.16 -0.59 0.04 0.053 0.135 1.046 -0.23 0.003 -1.15 0.027 0.03 -0.66 -1.2 -0.5^ -1.1 -03 STM2100 0.25 1.273 0.681 0372 -0.17 -0.35 -0.57 -0.02 0.471 mm 0.402 0.232 -0.62 -0.06 0.375 -0.42 0.56 0.23 -07 -0 11 0.31 STM2101 -0.4 0.092 -0.42 -0.12 -0.23 -0.31 0.253 -0.26 0.353 -0.07 D.371 -0.14 -0.24 -0.67 -0.55 1 104 -1 -o[ _J] -0.68 -0.5 STM21Q2 -1.4 -1 15 -1.03 0.287 -0.28 -1 07 -06 -0.92 -0.69 -1.38 -1.09 -1.76 -1.7 -1.651 -1.4 -0.88 -1.2 -1.3 ^~O8[ ^⁴³J -1.2 STM2103 0.15 -0.09 -0.27 -0 15 -0.6 0.942 -0.04 0.568 -1.13 -1.17 -0.06 -0.69 0.999 0516 0.111 -0.31 0.67 0.67 1.23 0.931 0.47 STM2104 -0.4 -0.18 -0.7 -0.79 -0.5 -0.53 -0.42 -0.29 -092 -1.49 0.083 -1.4 -0.7 -1.1 -1.01 -15 0.11 0.16 -O.θf -1.92! -0.3 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2111 i -077 -0640295 -0520087 -076 -136 -068 -071 -023 01402820512 -023 007 -03 0670368 -02

STM2112 00830332 -001 -017 -01 -0.2 -05306871165 -04 -032 -052 -0241126 -09 -02 -15 -1 -06

STM2113 021 05250.228 -04401740.2240454 -0131003 -068 -04 -063 -0550687 003 -02 335 -014 -02

STM2114 01470222 -0570332 -0780421 0059 -028 -095 004 -038 -055 -039 -02 074 -04 165 -004 021

STM2115 19481101 11771411 0388105501790101 -14423630973 -149 1560199 -07 017 -05 -066 09

STM2116 0885 -131 -031 0707018424020558 #####12880824 -1 -036 -06 -052 06 0 -07[Ta-I -09

STM2117 -008 -071 -050191 0412 -019 -129 -076 -014 -01 05270179 -0530648 179 118 2060294 -03

STM2118 i -096J -168[ -09 -0030074 -0.21 0009 -042 -034 -054 -02 -066 -0220298 102 022 132 -01 -01

STM2119 i -0560546 -013 -0580783 -05602680012 -106 -04 ^|,-183 ^"^ -172,0437 133 -08 -06 -13[TfHi] 07

STM2120 -178 -154 -2.66^19] 0153 -0020258 -081 -119 -011 -11 -149 -088 -114 -08 -07 016 -051 -02

STM2121 -063 -147 -096 -016 -063 -122 -1 -056 -041 -036041704280382 07 195099 2380609 146

STM2122 -021 -0140441 016 -0 -063 -138 263 -12703480047 0940355 -031 -02 06 0990567 022

STM2123 -07507140193 -037 -022 -012 -1220727 -009 -023 -072 -05406340153 -06 -02 -07 -098 055

STM2124 0005 -0550995 -096 024 043 -044 -140841 -12 -068 -1080171 -118 06 -07 008 086 08

STM2124 0024 -0660908 -0520371 031 -087 -1420772 [TwJ -052 -1180267 -088 -06 -08 035 -093 079

STM2125 0192 pm] -132 -037 -067 -071 -044 -06 -136 -131 -149HT5B~1 -028 -119 -03 -04 0240875 -04

STM2128 -063 -14 -116 0451 -039 -119 -045##### -089 -0561319 -02408890779 155 118 1670144 091

STM2127 -045 -0320166 00070391 044 -037 -028 313 -123 -059 -1121719 -063 032 -07 0520145 185

STM2128 -129 -068 -101 -017 -016 -086 -036 ##### -062 006 -0420717 -0340048 -02 05 023 -023 -02

STM2129 0186 -122 -07 -13407590588062203070804 -079 -087 -14705850274 095 -02 019 1783 085

STM2130 -016 -094 -04 0941 07430311 0179 ##### 005 -0460323* -1_710239 -035 16 023 005 -091 042

STM2131 -021 -086 -099 -003 -056 -106 -135 #####0547 -0304450348 -0180007 086 049 Jj660547 106

STM2133 01570177 -021 0324 -0220098 -036 ##### -035 074 -067 -082 -074 -047 -14 -θj -24] 0755 -06

STM2134 -0660432 -004 -04704220084 -022 ##### 1232 -02607060201 17730284 058 03 072 152 176

STM2135 -023 -027 -004 -11 044008901920262 -0820183 -05 -043 -034 -067 116 -09 -06 -113 -04

STM2136 -06 -011 -061 0216 -057 -004 081 ##### -030459 -012 -103 -05 -006 08 082 -0 -049 -06

STM2137 -139 -042 -062 0044 -127¹ -1 ^■6*-1^■"'* -1 ^'0 ^"6 -1 — 25 r[^" yt 8^9| -091 -045 -095 -053 -072 007 -04 007 -098 -05

STM2138 -122 -061 -03 -021 -015 -177' 0636 -053 D 062 -084 -0020056 -0080279 059012 1490033 -0

STM2139 - -1I 8 O_j, -065 -132 -04 -003 0116 -043 -109 -012 -0130478 -142 -131 -02901030021 -11 -07 -06 -089 -03

STM21392ι -004 -11 -077 -031 -038 -083 -107 -086 -089 -089 -007 -01 0124 -038 -005 168 057 115 -008 017

STM2140 01061106 -129 -077 -002 -080757 -M52681 -003 -051 0733 -01904430871 049083 115 -016061

STM2141 010415130114 015 0621 -01803370813 -008 -1JK -031 -051 -0 06 278 -012 -06

STM2142 -0960182 -106 -11 -067

-024 -00700140032^^75] -112[ <-21 -204] -106 -137[^~Tτ) -O4 -12 -073 003

STM2143 0151 0988 -104 -065 0089 -041 -02 -121 -042003800350501 -04309960678 06 034 2140275 077

STM2144 0307 -003 -125 -054 038306940385 -008 -012 -063 -031 1173 26614220402 105 129 122 1686 139

STM2145 -039 -115|_-1_5βj -123 -072 -116 -043 -105 ##### -109 -0771626 -015 -017 -036 012 -0 089 -013 05

STM2146 07270493 -126 -067 0278 -036 -054 -099 -074 -038019708730541 0747 1004 149 365 1780895 126

STM2147 036 -0231-1631 -081 0101 0493 -0580028 -085 -046 -067067704170751 0685 217 134 2130598 154

STM2148 -16 -043 -05 -009 -042 -009 -075 -005 -1060223 -114 -133 -089 -102 -024 -029 -14 -15 -11 -106 011

STM2149 -17 -084 -0870002 -0390225 -071 -076pT77J -036 -121 -03[TM] -063 -124 -094FTS -01 -26 -216] -08

STM2150 -05 -033 -009##### 094 -085 -112 -0580051 1514 |_-1_7J 021 -16[-O 63 -02

STM2151 [Jgj -122 -147 #####[_-1 Sr] -064 -077 -096 -072 -051 -15 -13 -1 102 -09

STM2152 -05 -027

-079 -02303090304 -020345 -048 -02 089 -02 1360241 -02

STM2153 029 -006 -042 -128 -037 -002 -034 -095 -096 -057 004 -0670157019300790142 102027 145 -018 02

STM2154 118 131 -089 -0490477 04230184 -0740606 -032 -01200530203075515830299 -01 053 08 -048 139

STM2155 04605080199 -075 -01 0644 -076 -098 -113 -048 -032 -051 0036 -0040844 1046 2 113 230881 085 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2161 0220192 -O27 [^159] -055 00460028 -087 -079##### -005 -0080408 00904420812 219 111 2690306 074 STM2162 0520338 -016 -099 -012 01830513 095 -052 -05 -066 -0160189068600290934 181 061 2080476 039 STM2163 0071249 -01207120493 -0620667 -0180032 023^-178] -083 -075 -016 -052194 -09041 337 -071 -01 STM2164 08706580393 -027 -046 -078020700481023 -122 -027 -050085 -007 -0321062 242 165 -120702 008 STM2165 -020328 09904430286 09930057 -0191421 -0020336 -105 -028 -1480311 -104 -04 -12 07 -05 025 STM2166 040241 -030998 -057 -045 -01100331053155805060003 -038 -0321031 -029 025 -09 -13 -028 087 STM2167 05400340104 -017 -072 -008002904951371 -069 -009 -0431196 -049 -036 -001 053002 -050754 -02 STM2168 0490073 -01 -044 -013 -009 -089[TS] -086 -071 043 069 -012 06604360389 213081 114 -004 106 STM2169 -02 -025 -049 -048 -035 049503760967042θ[T«_-1_66J 05 -091 Qijfflj 02610108 -09 -0i[~Jil "°^{5 157} STM2170 1050484 -026 -001 -07 -11 -079 -036 -057 -0400820269 -0010697 195 194 2550524 091 STM2171 0140289 -121 EΞ 0ϊz24ϋ] - -⁰0⁶2⁶3 -036072618571768 #####,' -Zi] -1243036004711971098 021 122 -0 s| -1621161 STM2172 0410518 -011 -073 003 03 -0150509 -062 -005 -073 -065 -011 -00811260782 073 02 0850234 016 STM2174 -02 -04 -058 01 -028 -014 0360225 -019 -059 -142 -059 -0650011 -006 -089 -13 -01 -081292 -03 STM2175 0561564 -034 0781057 -10713060969 054032307312443 019 -048 -1060264 186051 -010055 -04 STM2176 048 -006 -033 -143 -011 0716 -026 -105 -112 -055 -021 -010066068700240999 19 108 1980426 076 STM2177 -05 -081 -072 -0050075 -082 -084 -

06900970578[^255^~^207] -079 -071 -13 -12 -OβQϊjj -05 STM2178 05305030047 TiM}] -006 0602 -01402790661 -034 -014 -04302530083 -0130207 187 102 1830954 061 STM2179 071 1.2250262 05250301 -0180616 00707791215 -0690628 -056 -058 -0590297 043062 -05 -046 -01 STM2180 -05 -021 -014 _-12 -061 -032 -0670739 -083 -119 -057 -034 -116 -137 [ -I₁Si] -092 137 -0.2 0510622 001 STM2181 0680842 -022 _^7i] -038 -0120156 -105 -079 -093 -057 -0412210018 -0281451 233098 Z47 -004 126 STM2182 -020124 -084 064 023 ^r~U -° ⁶Gi?] -¹²⁸ -¹² STM2183 -01 -069 -105 -072 018 0292 -0050868 -0540291 -1191184 -058 -121 -O 0644 -04053 216 -059 -01 STM2184 043 -039 -042 -066 -058 0207 -005 -009 -049 -072005912510434022404080829 135091 1390047 085 STM2185 -04 -0230697 00560431 -021083611482037 0420216 -0041551 -0990041 -021 -03004 -05 -042 -0 STM2186 -0105110344 02620346 02010153 03 -03907360774 -02504110756 -024 -043 -0041 -051713 -03 STM2187 -04 -054 -025 0123 -033 -044 -039 -027 -011 15821076 -089 -071 -042 -085 -121 -11 -1 s\ -1 B] -115 -1 STM2188 -0605980611 04080091 -07 -016 -13 -0410875 024 -008 007 -1270648 -137 -06 -04 155 -043 087 STM2189 -0 -0090205 06690194 0351 -013 -013 -03402170004 -0190124 -058 -037 -048 -1 -04 -140186 -05 STM2190 -04 -041 -03 0245 -007 -001 -045 -011 -036 -0841318 -041 -083 -078 -07 -026[Tj]

-1 STM2191 071 026 -038 -043 -05 05640247 -06 -081 -065 -091 -0280546012107021123 22 14 217 114 104 STM2192 09807440595 10870427 029701050777 -0160353 -0960755 -093070103270577 -05079 -040857 048 STM2193 011 0830331 Tsϋ] -037 -039 -098 -029 -126 -0560461 -02502230501 228 111 1951132 084 STM2194 -02 -049 -034 0412 08 0587

-0350078 [^∞] -143 -0661493 -12 05 -10628 -03 STM2195 047 -001 1031 217 178 2020455 081 STM2196 042 208 105 1620412 -0 STM2197 -07 -136 -054 [^T) -08 -15 -082 -15 STM2198 011 -027 -029 -12 -06 -08 -003 -01 STM2199 048 028 -03 094 -028 114 STM2200 062 -056 -01 -06 -020003 012 STM2201 101 -06 -03 -14 -06 -02 STM2202 05 17085 2110552 084 STM2203 095 -077 -008 225 168 0740892 016 STM2204 105 086 -001 046017 -08 -047 006 STM2205 -11 -095 -14 023 -02 -040683 -01 STM2206 042 -025 -13 -03 043 093 -06 STM2207 005

-074 -037 -11 025 028 -006 -0 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2214 0.24 0.191 -0.04 -0.21 -0.45 0.114 -0.98 A2 -0.84 -1.11 -1.15 0.017 -0.42 -0.6 0.107 0.032 1.09 0.23 1.16 -0.12 0.43

STM2215 -0 -0.25 0.343 -1.05 -0.43 0.595 -0.74 -0.11 -1.2 -0.6 -0.45 -0.32 -0.3 -0 -0.13 2.426 1.06 1.47 1.35 0.391 0.56

STM2216 -0.5 0.424 0.282 0.242 0.867 0.119 0.593 0.247 0.664 0.207 -1.24 -0.22 -1.19 -0.92 0.098 1.034 0.26 -0.5 -0.3 -0.38 -0

STM2217 -0 0.125 0.178 0.049 -0.43 -0.79 9E-O4 -0.17 1.074 -0.26 ,"²T³¹ -0.99 -1.37 -0.86 0.174 -0.43 -1.6 -1.3 -2.3 3.915 -0.2

STM2217 0.11 •0.06 0.269 0.153 -0.36 -0.68 0.037 -0.2 1.051 -0.4 -2.33 -0.86 -1.26 ^■0.63 0.291 -0.26 -1.2 -2.3 4.219 0

STM2218 -0 1 0095 -038 -1 41 -08 002 -077 -1 13 0644 -047 -1 01 -0.48 0.194 0.034 0051 0259 1 12 005 1 55 1 284 0.24

STM2219 0.72 0.077 -0.21 0.473 -0.8 1.011 0.258 -0.65 -0.09 ##### 2.666 0.292 -1.24 -0.12 ÷0.09 -0.42 0.33 -0 -0.3 -0.55 0.45

STM2220 0.57 1.29 0.64 0.37 0.413 ■0.25 0.063 -0.02 0.356 -0.47 -0.39 1.005 -0.15 0.397 2E-04 0.587 0.2 -0.2 -0.8 -0.26 0.35

STM2221 0.17 -0.14 -0.11 0.581 0.351 -0.44 0.647 -0.22 1.195 ##### -1.02 -1.27 -1.1 0.167 -0.13 0.7 ^* -0.72 -0

STM2222 -0.6 -0.02 -0.78 -0.31 -0.67 -0.53 0.54 -0.3 1.395 -1.26 0.868 -0.22 -0.98 0.072 -0.43 -1.1 0.61 -0.1 0.7 -0.3 0.06

STM2223 -0.1 0.425 -0.17 0.115 0.121 0.319 -0.14 0.881 0.554 1.092 -0.98 0.097 -0.69 0.145 0.562 -0.05 -1 -0.3 -2.7 -0.68 0.44

STM2224 0.63 -0.13 0.298 -0.87 -0.87 0.023 -0.54 -0.49 -0.97 -0.52 -0.19 -0.2 0.695 0.171 0.286 1.127 2.07 1.34 1.56 1.156 1.25

STM2225 -0.7 -0.28 -0.08 0.501 -0.69 0.183 -0.31 0.023 0.691 -0.14 -0.54 -1.07 0.046 -0.45 0.593 -0.21 0.31 -0.6 0.35 -0.64 1.35

STM2226 0.49 0.581 -0.48 -1.32 -0.73 0.458 -0.11 -0.53 -0.19 -0.23 -1.28 -0.55 0.393 0.535 0.263 0.81 2.23 0.97 2.47 0.609 0.57

STM2227 0.6 0.056 -0.42 -1.38 -0.08 -0.16 0.318 0.02 -0.65 -0.09 -0.28 0.271 0.254 -0.17 -0.3 0.472 1.05 0.13 1.83 0.062 0.94

STM2228 0.67 -0.32 -0.12 -1.1 -0.75 -0.09 >i:β "-1-87, -0.44 -0.88 -0.58 0.732 0.32 -0.42 0.603 1.28 1.12 1.63 0.793 0.76

STM2230.1 0.82 -0 -0.44 -0.52 -0.43 0.197 -0.34 -0.82 -0.9 -0.97 -0.07 -0.16 0.168 0.424 0.414 1.129 1.8 1.38 2.21 0.808 0.91

STM2231 1 -0.12 -0.54 -0.42 -0.04 0.065 0.179 0.054 0.503 -0.88 -1.25 -0.07 0.133 0.535 -0.26 0.326 0.85 0.19 0.14 0.21 0.14

STM2232 -0.4 -0.2 -0.02 -0.27 0.089 -02 -047 -034 002 -057 0663 1.349 -0.39 0.215 -028 -0.45 -1 1 -08 -2.4 -0.98 -0.4

STM2233 -0.6 -0.38 -0.8 -0.48 -0.06 -0.28 -0.16 -0.45 -0.18 -1.04 -1.23 -0.5 -0.78 -0.34 -1.25 -0.75 ^"Ml -0.2 -2.4 -2.56

STM2234 -0.2 -0.55 -0.71 -0.02 -0.09 -0.83 -0.32 -0.71 0.821 0.056 0.322 -0.34 -0.31 -0.1 -0.8 -0.3 0.46 -0.95 -1

STM2235 0.22 0.493 -0.23 -0.04 -0.12 -0.13 -0.46 -0.09 0.005 ##### -0.04 -0.86 0.263 1.595 -0.21 -0.5 -0.6 0.13 -0.2 -0.36 -0.4

STM2236 -0.2 -0.45 -0.44 0.234 0.021 -0.08 0.161 -0.19 0.519 UIIIIUH -0.73 0.934 -0.5 -1.33 -0.7 -0.31 0.29 1.16 -0.1 1.55 0.55

STM2237 0.261 0.138 -0.19 0.954 -1.18 0.005 -0.8 0.804 -0.41 0.905 Q-169 0.37 -0 1.026 -0.23 -0.8 -0.6 -1.3 0.403 1.17

STM2238 -07 -1 02 -1.08 -1.24 -0.26 -0.11 -0.48 -1.3 -1.35 -0.55 1.007 -0.34 0.526 0.47 -0.52 -0.35 -0.1 -0.6 -0.3 -1.47 -0

STM2239 Q₂T -1.35 -0.07 -0.69 -1.21 -0.63 -0.23 -1.26 -0.74 -0.77 0.09 0.756 0.079 -1 -0.7 0.18 -1.5 -2.39 -1.1

STM2240 0.1 -0.44 -0.11 0.504 0.128 -0.44 -0.19 -0.5 -0.32 -0.84 -0.81 -1.04 -0.44 0.715 1.222 -0.13 0.07 0.13 -1 0.997 0.84

STM2242 -0.5 0.189 -1.1 -0.74 -0.15 -0.13 -0.19 SiI -0.61 1.146 -0.46 -0.75 -0.33 0.178 -0.35 0.048 -0.4 -0.1 0.07 -0.61 -0.4

STM2243 -1.1 -0.38 -0.83 -0.27 -0.15 -0.37 0.339 0.421 0.267 -0.38 -0.44 -0.72 -1.49 0.151 -1.3 -1.1 -1.1 _-ΪL _-J/7 -0.3

STM2244 0.69 0.867 -0.13 -0.87 -0.42 0.042 0.315 -1.14 -1.18 -0.92 -0.87 -0.6 1.003 -0.42 0.557 0.544 1.56 1.13 2.29 0.718 -0.3

STM2245 -0.7 -0.46 -0.46 -0.26 1E-04 -0.24 -0.12 -1.15 -0.79 -0.31 -0.65 3.062 -072 -0.71 -0.44 -0.21 -0.8 0.13 0.78 -1.33 -0.7

STM2246 0.81 0.457 -0.02 -0.57 0.259 0.484 -0.99 -0.96 -0.99 -0.15 -0.29 0.652 0.874 -0.11 0.87 232 1.05 1.43 0.783 1.15

STM2255 0.72 0.25 0.029 -1.05 -1.44 0.722 -0.38 -0.62 0.399 -0.75 -0.59 .:9i°jL 0.429 0.274 0.228 0.441 2.39 1.91 2.28 O907 0.45

STM2256 -1.8 -0.47 -1.43 -0.85 -0.53 -0.62 -0.85 KΛΛT -0.27 -0.78 -2.34 -2.17 -1.8 -2 -0.62 -0.53i 1 -2.3] -0.7 -0.1 -Z56 -1.5

STM2257 -0.6 0.346 0.433 -1.11 -0.06 -0.93 -0.3 -1.63 -0.69 -1.54 -1.27 -1.64[-0.38 -0.14 -0.53 -2.52J -0.2 -1.4 -0.7j_ -1.65 -1.3

STM2258 0.61 0.222 0.072 -2.12 -1 19 0.255 -1.13 -0.25 -0.91 -0.52 -0.02 0.384 0.42 0.535 0.768 1.59 0.7 1.98 0.995 1.11

STM2259 -0 0.072 -0.63 -1.34 -0.34 0.262 -0.14 -0.68 -0.66 -0.72 -0.37 -0.64 0.562 0.378 •0.09 -0.15 0.77 0.34 1.9 0.314 0.9

STM2260 -2.2 -0.87 -0.24 0.846 0.04 0.619 0.043 0.677 0.934 -264, -001 0982 0836 1 07 -1 92] -1 4 -08 -1 1 -0.86 0 92

STM2261 -0.8 0.419 -1.22 -1.01 -0.9 -0.48 -0.8 -0.89 -0.98 0.005 0.676 0.161 -0.06 1.03 0.987 -0.26 -0.4 0.25 -0.1 -0.73 1.01

STM2262 0.04 -0.53 0.026 -0.68 -0.49 0.181 -1.02 -1.35 -1.45 -0.07 -1.23 -0.69 0.842 -0.94 -0.2 0.02 -0.3 0.02 0.27 -0.87 -0.2

STM2263 -0.7 0.062 0.916 -0.28 -0.46 0.407 0.044 0.398 0.16 0.397 0.817 0.787 -0.58 1.731 0.236 -1.37 -0.1 -0.2 -1.3 -1.01 0.65

STM2264 0.86 0.03 0.081 -0.81 -0.11 0.439 -0.34 -0.42 0.495 -0.65 0.589 -0.17 0.442 0.32 0.107 0.308 2.17 0.63 2.13 0.76 0.41

STM2265 0.22 0.398 -0.18 -0.35 0.071 -0.21 -0.25 0.461 -0.3 -1.02 0.125 0.233 -0.11 0.103 0.35 -0.84 -0.7 -0.2 4.21 -1.22 0.18

STM2266 -0.78 -0.06 -0.93 -1.64 -0.72 0.651 0.429 -0.72 -1.42 -1.17 -1.25 -0.8 JL85J -0.92 -0.79 -0.5 -0.4^-2.2 -Z54 _-ⁱ3

STM2267 -0.5 -0.73 0.189 -0.32 , ^',U6 0.47 -0.95 -0.03 -1 48 -0.22 -087 0.805 -0.33 0.394 021 -046 -O R 1.86 -05 -1.721 0.09

STM2269 0.62 0.238 1.012 0.604 0.287 0.091 0.191 0.451 0.392 0.212 -0.36 0.165 1.764 -1.1 -0.51 -0.3i [_-1.8J -0.1 0.39 -0.78 -0.7 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2276 016 0319 -073 -133 -078 -036 -089 006 -047##### -092 -10319186802581141 089092 1812411 036

STM2277 082 0408 -038 -109 -057 0791 -018 -087 -047 -11 -072 -037079206010481 1466 18 14 209 094 072

STM2278 073 -018 -044 -133 -069 0030724 -017 -084 -032 -055 -0250355 -04402841228 217 105 2241292 099

STM2279 077 0208 -024 -031 01120097 -105 -046 -065 -01902340181 -008 -0410824 136 119 160611 079

STM2280 078 0411 0731 E 01s36I 0317 0325 -005066402190301 1412138 -001 -022 -0213027 024 -02 003 068 016

STM2281 -04 -015 0245 0274 -0170049 -065 -067 -1340793 -134 -0670464 -063 -088 -102 -2 -04 -25 -101 -09

STM2282 -02 -045 -007 -014 -001 0456 -047 -013 -023 -0460554 -013 -054 -06 -053 -13 -15 -02 -42 -016 -06

STM2283 078 1384 1131 0697 0207 07430742 10306261273010906480989120508340039 085042 051 023 085

STM2283 123 121 136 1217 -017 118705480968 061 1602011407460706 171 0974 -006 106041 0180895 146

STM2284 004 -017 -101 -106 -091 -03202780142 083 ##### -087 -014 -008 -038 -067 007 066 -03 079 -006 027

STM2284 037 -049 -129 -124 -1320359075902850777 -02600180319 -038 -08 -084 -022 01 -01 0830227 -04

STM2285 061 -007 -018 0536 -028 03130323032808080162 -119 -094 -0170112 -0660316 -05 -04 -12 -045 -03

STM2286 -03 0646 1107 0552 -023 1581 0443184513520618 189 -015 -119 -092 04 -07[^"TB] -136 j -1 s]

STM2287 -05 -045 -007 0425 01820527 -016 -051 -077 -036 01 -112 -037 -071 -065 -04^-34 -Z19 09

STM2288 -02 -043 -086 0134 -0390171 -027 -004 -075 -032 -069 -07 -

084 -01 -015 -086 -01 -03 -01] -164 -02

STM2289 045 -01 0474 0253 -001 1213 -0240694 -06807451276 -087 -07604531557 -046 -03063 -080071 131

STM2290 104 0723 -062 0371 0741 -0160437029712850856 -0310455 -019136913960167 -05056 1272076 094

STM2291 055 -022 1314 -05 -021 -03 -01 -03201990267 01203770556008607841406 12095 18 117 137

STM2292 087 0247 -027 -122 -086 01490059 -092 -041 -037 -052 -00108340716 -00549 077056 190347 1

STM2293 003 -002 -073 0423 -043 -0960063 -0070322 -023 -098 -048 -084 -113 -093 -061 -06

STM2294 -03 -037 -111 0021 0032 -0110438 008 -085 -

042^4i] 1365 -032 -077 -0940093 -09

STM2295 -06 012 0836 0518 0285 09110208 -0820315 -0830032 018 -013 -0780057 -028 -03 -03 -070648 006

STM2296 017 0068 -033 0432 0087 0011036302040251 ##### -148 021 -09 -071 -004 -009 -03 -04 -12 -017 -0

STM2297 049 -039 -021 1207 -036 -1210286 -0290531 00213860438 -014 -1040004 -003 -09 -03 396 -09 019

STM2298 -02 -02 004 0469 0162 -0850332 -0580145 -067 -0650263 13 -021 -005 -013 075 -06 022 -089 072

STM2299 07 0258 -03 -057 053 0774 -003 -068 -125 011 -097 -0090543 -01508361612 17095 160939 129

STM2300 -006 -044 -134 -05 -041 -098 -032 -096 -044 -030027 -131 -075 -007 -073 -14 -03 5Uu4 -05

STM2301 -09 -024 -034 -092 -117 -042 -066 -024 -066 -065 -0820287 -099 -1170263 -07 -08 -03 _j2JI_-1_54J 009

STM2302 04 0111 -002 -08 -075 -005 -017 -053 -119 -097 -055 016 -009 -01204480593 183 105 1990765 08

STM2303 046 0196 -02 -107 -06 0447 -011 -0440771 -062 -09512270211 044202891212 214 138 2380451 088

STM2304 088 0056 -05 I -193J -03 0185 -035 -085 -046 -0680079 -018089701860121 1089 114 106 1930668 017

STM2305 049 094 -034 -073 0124 0014 -01 -021183 #####01570141 0784000806721316 089 123 1760401 087

STM2306 07 116 -042 -107 -025 O164pT63[θ188 -01 -07 -1 -084 -023 -092 -068 -014 029 -03 009 -114 -04

STM2307 069 0308 -047 I -16 j -04 -0040135 -085 -071 ##### -059 -0570389 -023117406762221492341072081

STM2308 029 0038 0587 -038 -01 0473028305880562 -061 -064 -023 -134 -2.2 Z1J -058 -046 I₁ ¹⁰⁹ -030317 -06

STM2309 01 0429 -008 -053 -032 -088029406690224 ##### 0082 -072 -088¹M 55 01670669! -1 β| -08 -15 -047 03

STM2310 037 -04 0046 0142 0285 08990657 15160582 -1290899 1914 -119 -057 -0190983 -13 -03 -05 -115 -01

STM2311 049 0323 -005 -04 -059 -023 -027 -0070136 ##### -096 -065 -015 -012 -044 -01 103 123 103 -014 094

STM2312 062 0326 -003 -112 -064 -011 -098 -067 -075##### -026 -03806080141 05680428 198 176 230238 -01

STM2313 -0 0088 0354 -129 -075 -016 -032 1056 -061 0623 -05403942583|j-1^*6i| -016 034 019 -03 071 -03 067

STM2314 046 0936 -05 0682 1186 11321004 1211 0430711 1032 -07203832194 -0970844 021 085 001 0005 046

STM2315 -05 0079 0303 -01 -018 -026 -005 -072 -03200440165 -032

-016 -11

"¹

STM2316 S 019 032 0604 -093 -0120014 -032 -04 -089 -033 0290211 076 -01600452127 058 007 123 -03 043

STM2317 042 0007 0066 -109 0146 -011 -073 [Tiθj -075 -026 009 0040611 0421 06030721 196 083 1790769 124

STM2318 059 0031 -032 -085 -0540462 -06 -15 -037 -027 -064 -02609040275 -0081028 197 091 2.020745 046 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2327 101 0106 -029 -125 -055 0227 -054 -094 -07 -086 -059 -020486 -01 0089 137 225 154 206 073 096

STM2328 041 0054 0363 -148 -088 -03 -087 -092 -062 -097 -049 -01 0812 -00304070388 224 126 1860183 067

STM2329 043 0835 -039 -227 I -071 ■021 -011 -099 -021 ##### -086 044071704O403490951 233 144 160824 051

STM2330 -01 0304 0283 07 0416 -02 -053 -082 -051 -034 -01 10280635 -029 -0260078 153 -04| _;24 -183) -06

STM2331 -0 0039 -017 0251 -081 0053 -0770187019215960776 -091 -078 -0220042 -057 -02 005 -03 -136 012

STM2332 -05 0101 -026 0189 1007 -042 OOβ[Ty]θ334 -056 -022 -027 -065 -0320188 -08 014 -07 049 -046 -01

STM2333 -1 -042 0204 -038 0194 -0420221 00160422 -111 00070498 -082| -15βj -055 -002 -11 -Oβ[j22j -021 -05

STM2334 072 0952 0035 -112 -058 -008 072 -0.25 -085 -102 -013 -017 1129024302671552 218 13 1750578 027

STM2335 059 0157 -093 -137 -055 -018 -011 -099 -045 -076 -041 0162 060128 -0030662 146 12 1720497 043

STM2336 082 0606 0075 i -054 0608 -08 -106 -06 -04 -053 -0820293 -02404551014 206 102 2280769 116

STM2337 -01 -049 -115 ΔU -105 -037 -114 -126 -118 -084 -08 -061 -01 -033 -045 -052 076028 179 -025 002

STM2338 08 -007 -055 -112 -028 016 -056 -088 -045 -035 -004 -0640564 -00905030243 193 075 2050541 087

STM2339 -04 -0 -029 043 0583 0326013601170502 -034 -095 -116 -025 -0271961 -005 -07 08 -06 -045 214

STM2340 028 -086 -02 0343 128 -0270893 -119 -023 -032 -018 -034 1005163902931161 -01 031 -03 -099 045

STM2341 087 0989 -005 -049 0079 03270852 -0790171 -074 -036 -0170937058901650322 031 034 1251142 022

STM2342 004 0616 0079 0148 0271 -0180269017703290108 -0520327 -048 -0420661 0623 -01 118 044 -016 048

STM2343 091 0163 -034 -116 -048 -020034 -085 -054 -036 -074 -0840211 -039 -032 032 075 136 152 -008 004

STM2344 -12 -071 -129 0087 0023 -047 1249 -098 066 -06SJ -1 ββ] -032 -112 -043[ -154J -093 -14 -05 -12 -041 f -17]

STM2345 -06 0114 0298 0076 -019 -051 0214 -0430324 -004 -0030652 -043 -071 00130004 -15 -04 217 -005 -07

STM2346 -04 -021 -074 -108 -056 0394 -017 -017 015 ##### -021 0781 05862011 021 0323 101 065 053 -034 -01

STM2347 -0 0516 -091 -124 -025 07260319 -020798 -0380089037202452291 -0141175 035073 0970231 -01

STM2348 0289E-O4 111 0582 -02 0657 011 11240248 004 379 053 -109 26312390309 019 -06 -05 -08 147

STM2349 049 0393 0262 0797 0443 -042 -009 -074 -0230071 08790517046307750152 -016 215 062[Ti] 0754 07

STM2350 087 0493 0372 0729 051 0420111 0541 -0350971 31105182153 -0180522 -005 224 053 -1 -131 003

STM2351 046 0223 0877 1237 0743 -002 -01 0231 0247 -0210269 -064 -11603320462 -046 017 03 0690966 079

STM2352 017 -051 0443 0577 -001 -005 0430501 0587 -03602430266 --0077 --005588 --009911 -11 -02 004| -25 -25) -11

STM2353 086 0451 -004 -074 -083 0233[TOT] -076 -0850529 -007 -08401760214 -0330598 131 074 140568 054

STM2354 035 0214 -041 0168 0016 -02 -01200590374 -051 0115 -064 -042 -021 -0440165 -04 013 -080287 -05

STM2355 058 0204 0127 0374 0198 -02707340068 -061 -048 -093 -07702780809 027 -02 223 -023 001

STM2356 026 0102 0667 -034 -054

-031 04990294 -109250409420791 05871214 207 165 1380951 039

STM2357 -04 0746 -035 -064 -051 -01 05360024 12730201 1581 0003[-1_55| -008 -116 -055 -05 168 -05 1328 -04

STM2358 -06 -033 -027 0262 0283 000700440091 -032 -0621063 -02 -011 -0230562 -063 -13023 -2.5 -066018

STM2359 -0 0138 0191 0404 -0190465 -036 -072 -018 013 -046 -0512570706 -0270248 -1 011 -270773007

STM2360 -02 0493 -024 0512 0385 -063 016 -087 -011 -067 -044013717650535 067 -07 -05004 1 138 029

STM2360 -03 0418 -025 0842 0416 -114 012 -072 -002 -016 -0170301 17630.281 1019 -036 -03007 -07 -093 045

STM2361 -04 0609 0367 018 -011 0260288 -048 -035##### -101 -057 -0032305 -1 -1 -1 -03 016 -009 -04

STM2362 014 -032 0251 -145 -182 -031 -068] -236 -176 #####0268 -074 -082 -0870316 -065 056 03 1131453 037

STM2364 -02 0072 -043 -151 -006 -27 -Z52 -095 -097 -0730011 -041 -081 -009 019 -02 142 -011 -08

STM2365 109 -022 -019 -128 -025 00130441 -069 -075 -017 -005 -022083203990301 106 265 142 2550528 108

STM2366 102 0483 -08 -103 -046 -032073604810252 -086 -055 -033 -012 -009 -0070702 216152 181 -011 056

STM2367 033 -07 -068 -075 -01 -019 -132[T85~T93) -052 -095 -0430104 -034 -031 -033 042023 071 -03 -05

STM2368 062 004 -054 -146 -059 0130319 -038 -104 -042 -091 -0530268 -08802110678 185114 2080492 065

STM2369 -02 -046 0249 -131 -03 -02 -04 -017 -037 -051 -128 -0840808 -061 004 -033 111 049 112 -009 076

STM2370 -04 0426 -096 0184 007 -0240561 -056 -145 -092[T59] -131 [TTi] 047602770031 -09 04 371 -11 -07

STM2371 03 0799 -038 -107 -054 0629 -047 -097 -043 -053 -004 -0580901 028 0250991 206 116 1880298 079 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2380 1280279 -066 -131 -079 -039 -03 -113 -106 -121 -0140236 -006 -01403671155 205129 202 0362 047

STM2381 -1361007 -012 -040173051900510394 17 13 181 0809 051

STM2382 -104 -058 -036 -03 -0780009048405481052 207099 184 1405 071

STM2383 -128 -061154101330322 -026 -0150219 108 168 124 -003 057

STM2384 ##### -1180305 -076 -074 -051 -111 -1 -01 -11 0225 025

STM2385 -025 -073 -077 -139 -02 011 -06 -11 1502 -05

STM2386 0374

1898 -1120412 014004 -06 -097 -1

STM2387

-133 -102 -054 -1 -068 -043 014 019 022 -058 -1

STM2388 025040300780736 -022 -046030600591225034600070585 -01506370198 -019 047001 058 -005 114

STM2389 13309020531 0653 -019 -081 077204170622 ##### -0060539Qn] -13 -0180257 -01 123 -12 0111 013

STM2390 -0201830919 -0970089 0984 -023 -029 -089 -086 -081 -122 -034 -0350192 -103 032 -05 09 0522 026

STM2391 07805991149 -044087401680208 -06 -0750087 -097 -03408710125 002 -011 162082 095 -015 073

STM2392 1320924 -06 -0140677 -0530028 -144 J -2.37J 1825 -098098607650154 -077 032 036 -04 043 -077 038

STM2393 0780461 012409080685 ■0310467 -017073600990037 -069 -0770568 -01 -015 08 0 -03 -006 -06

STM2395 -01 -049 -0380151 0084 01120121062805010033 -067 -103 -0030294 -0020086 -14 -0i[_-29J -141 -04

STM2396 -01 0362 037 -124 -044 -0420379 -078 -041 -044 -06 -055 -008 -01506870418 161 09 149 0075 092

STM2397 056 -002 -078 -081 -059 -045 -066 -086 -057 -067 -058 -022 015002703081053 211 124 17 0976 098

STM2398 05707570325 -001 0204 0393 -043 -066 -041 100503640334 -007 -094 -0410591 -03 04 -08 -007 -05

STM2399 060249043608520019 0081 -0190287 -0320436113712280947181104330084 388087 -14 059 017

STM2400 -02 -014024309760673 03330488 -011 1031 0960675 -074 -006 -0390392 -003 034 -oQli 1015 028

STM2401 0050777043609160462 -O09 041 05350228027607530331 -03203030083 -002 014 019 -09 -043 -01

STM2402 056 -02 -0691015 -011 -0520737 -02809170052 -0980103 -021 -047 -017 -044 -07 081 -07 1389 057

STM2403 0650455 -006 -1 -023 0003050900960372 -095 -067 -0860321 037406770102 144 072 1970034 018

STM2404 06 0770276 -101 034 0320491 0106009202150281 2003 -014 -061 04080604 104 089 -05 -062 037

STM2405 012 -021239 -062 -044 -034 -1020294 -0070237 04 -038 -1 OsfTsilj 0941 0472 -07 051 004 213 058

STM2406 -1 -098 -091 -084 -09 -02403120905 014 -0630991 0306 -087 -068 -058 -068 002 -03 004 -039 -04

STM2407 0720384 -04 -144 -043 0149 -064 -102 -064 -049 -101 -0320461 00030041 0921 2 104 2.29 0546 072

STM2408 04800550638 -056 -044 0567 -04400520359 -02 -0980531 0509 -050084 -026 033 064 066 -038 083

STM2409 -02 -026 -012 -107 -078 -058 -109 -O6i[jJ8l -094 -06 -079 -08 -014 -1180679 06 -02

STM2410 -01 0065 -076 -034 -004 -1060219 -023 -032 -061 -011 -107 -021 -1220416 -054 -05

004

STM2413 0840132 -032 -13 -008 0563 -012 -036 -076 -034 -045 -02603290002 0120947 241 131 198 1317 076

STM2414 08901540236^-197^ -019 0286 -066 -114 -097 -088 -016 -0420356039206850616 216 157 262 0875 025

STM2415 020427 -036 -072 -04 0007 -09 -056 -014 ##### -01402880537052203970905 22 107 187 1193 119

STM24201ι 0510055 -0i[5_KJ -084 02840359 -103 -106 -101 -023 -04702940855 040339 146095 163 0317 095

STM2421 -09 -066 -108 -040238 -092 -025 -0650003 -018 -1 -13 -054 -108 -079 -077[JM] -05 101 0645 -09

STM2423 016034300440267 -065 -066 -031 -05 -075#W##D893 -0440043 -073 -055 -074 -1 -1 -15 -112 -07

STM2424 0120284 -O 46 036 -001 -0050342 -037 -0741682 -0720441 0723 -086 -042 -038 -06 099 -19 -14 -06

STM2425 -030389 -015 -038 -018 -099 -035 -039 -143 -015 019 -116 -027 -012 -11 -03 -22 0049 -09

STM2426 0840728

-O08 00650236 -092 -039##### -051 -059 -034062203261211 227 119 2 0672 038

STM2427 0810561 -064 -063 -067 0015 -03 -047 -073 ##### -065 -0190423046300681141 196 176 2.52 0445 099

STM2429 072 041 -012 -134 -066 0113 -086 -04ifTs6 -169] -065014105220175 -0420459 209 076 154 0833 047

STM2430 037 -004 033 -088 -119 -053 -02 -069 -053 -059 D 495 -018 -134 002 -065 -05 -07 -03 031 -111 -06

STM2431 05903910038 -115 -067 0239 -07 -049 -128 -09 -142 -095007504750431 0419 22 115 256 0917 076

STM2432 0580363 -035 -0J3 -026 0642 -036 -097 -075 -095 -062 -04308180216 -0150414 182 136 197 1109 089

STM2433 0540387 -06i[-15sl -011 0132 -013 -079 -037##### -029 -02605830208 0780309 234 084 183 -011 051 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2441 -02 017 0482 -016 -01 03803881331 -012 -027 104 -001 -048 -07403150032 018 056 015 -006 026

STM2442 01 0209 0433 -027 -014 016 -0580415051607420581 0093 009 -065 -001 -073 -1 015 -12 1287 025

STM2443 018 -07 -123 -08 -013 -139 -022 -062 -095[TiTj -121 0023 -037 -073 -092 -086 -02 -05 -08 -11 -05

STM2444 -080076 -028 -042 06501080847 -0371565 -043 -043 -057 0720150161 -132 -1 -02[To] -013 071

STM2445 026 -009 -038 -0403420058 -016 -112 -10707880785 -1040383003202860629 073 051 1560628 107

STM2446 -07 -049 03640113 -024 1322 -00504170054 -0160238 -0740561 026409931465 -01 -02 0722025 107

STM2447 043 -023 0193|-jJ8J -0570245 -074 -027 j_-j_72] 0255 -0700020463 -00908020965 186 102 180753 031

STM2448 -01 -023 -065 -095 -0780039 -085 -043 -016 -045 -1070093 -073 -021 0357 -024 086 05 027 -03 058

STM2449 S -130237 0081 -094 -021 -012 -005 -0160123 #####[_jijl9] -142 -183

STM2450 -09 -017 079 -00013 -035 -026 -087 -043 -102 -138 -028 -223

STM2451 -020129 -065 -057 -026 -040115 -032 -008 -0570471 -064 1702 -096 -043 -077 -06 -07 -07 -136 -05

STM2452 -15 -047 -042 -022029802890153 -0090087 -087 -003 -0351857 -123 -074 -082 -15 -04

STM2453 -08 -004 026 -0140197 -0880138 -056 -03 -017 -030403 -122.711 -023 -039 -14

-02

STM2454 021 0038 ■09 141 ^,Q460502026721930177J -16ij -003 -0290465136205570753 21 2170534 07

STM2455 1280587 -076[-18i| -067 -007 -073 -097 -077 -084 -024 -0380476002506440213 249 11 2.030484 075

STM2456 0850902 0217 -091 0170595 -00500320315 -002 -106 -0840798 ########## -01 037 105 277 047 093

STM2457 071 -005 -014 -071 -056 -032 -065 -039 -0560795 -00502870462 118 064 1850438 055

STM2458 -1 -091 -022 -097 -067 -037

-057 -063 -012 -106 -104 -027 -101 -03 -03 -021117 -02

STM2459 0580323 -039 -093 -0470557 -041 -069 -105 -058 -085 -052 146 ########## 1472 188 139 2220932 062

STM2460 -12 -O 81 -099 -015 -084 -00306280355p|72]

-031 -104 -03 -03 -07 -04 -041 -04

STM2461 0670482 0204 -148 -062 -0270287 -060546 -119 -05028503961171 04340378 163 16 1930822 057

STM2462 009 -008 0215 -136 -0220267 -079 1331 -123 -0640601 -045 -055 -011 01950102 12 032 165 069 028

STM2463 02603120128 -134 -004 06 -02504240005 -083 -065 -064 1.2840832 180375 163 093 1440964 148

STM2464 -00475 -081 -134 -076 -057 -051 04860818 -0750274 -0020279065204030824 2 108 2380983 098

STM2465 -00884 -018 -0708580741 05230328 -053 -05 -105 -091 0621 -0391101 0519 085 142 170279 129

STM2466 06 -004 0197 -114 -02904670107 -043 -124 -098 -045 -055 -0070043 0220676 298 138 1670696 078

STM2467 0490506 -065 -146 -083 -0080402 -056 -058 -062 -065 -048 -043 -076 -001 0367 29 025 113 015 058

STM2468 -07 -072 0521 -046 -1040327 -012 -00704380639[-173 -217] -082 -091066 -072 071 -08 -1 -117 039

STM2469 0160457 -06 -1250038 -062 -016 -058 -068 -115 -072 -053 034040608631048 223 127 2JM 0854 029

STM2470 -07 -023 0109 -035 -021 0735013704430034 -072 -1460885 -028 -021 -005 -O39[~5] -04[^Ij] -1 -02

STM2472 051 0508 -007 -09 -05501960242 -0730378 #####0606 -0161134075805540687 158 095 181 1J121 06

STM2473 -020237 05540125 0980486077205280971 -0790237 -080273[-759J 03360014 071 041 -13^1 δj 04

STM2474 -02 -013 -049 -038 -138023806960431 1185 -085 -079 0180343 -013 -007 -036 172 187 -020059 065

STM2475 -040759 -114 -03509050227 1260061 -029 -073 -054 -092 -07 -0080839 -002 03 04 083 -017 062

STM2476 -02 011 -04705750449 -023037701690396 -06505950226012309060295 -046MT]

STM2477 -1 -086 -096 011 0421 -0320109 -081 -086 -0460333 -046 -08 -075[_-1ββ] -081 -11

STM2478 -01 -009 0279 04 -0150024 -02 -021 -00302650689 -0 -042041200520182 064 017 0290204 014

STM2479 081 0618 0105 -081 -02901130106 -019 -068 -059 -089 -0050311 -00200980312 129059 172 -007 092

STM2480 0070238 1353031603430331 -00668047302080383036408750631 0015 -005 -04068 -03 -077 008

STM2481 -03 -0550301 0393 -006 054 -01 -001 -11 -10502120005 -1160364 -049 -005 [Tf] -0

-06

STM2482 -O 0862 -014 -0660546 -0070313 -0.2505910247 -002 -001 0720704 025 003 06 11 022 -079 002

STM2483 07 -005 -004 -121 -0720099 -03 -081 -004##### -047 -00902890042 1090507 174094 1680892 087

STM2484 06 -014 -037 -146 -091 0127 -052 -104 -092 -098 -102 -031 0375 -061 07170939 172 14 1640528 063

STM2485 -00086 -019[i1_⁸¹J ^{^0560096} ~°^{M ~}°⁶⁵ -⁰⁶³ ^^{88 006 ~}°^{320747097504030686 225}1883121032064

STM2485 0740936 0231 -068 tmmmm 1126 -02 -137 -058 -048 -026 mmmtmmtmm 101 203 132080972 107 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2493 018 -001 0447 045 -039 -0430452 -0420681 -023 -031 -086 -046 -004 -052 -066 -02 -02 029 -081 -05

STM2494 056 -002 -031 -104 -08608960175 -009 -076 -064 -031 -015 051085106511085 192 115 1910662 119

STM2495 030883 0186 -123 -077 -039 -026 -085 -085 -1 -017 -077018507590481 066 194 132 1620405 09

STM2496 0970161 -057 -142 -081 -038 -047 -119 -134 -059 -045 -079 -032 -04403730307 139099 1970415 032

STM2497 -020906 122507B2 mmmmmm o rrβ o 0371305 -004 074 -ΛTzmtmmmmmm -088 -12 -02 -oβ -016019

STM2498 025 -011 0028 -14s[T84^~j 0531 -015 -108 -094 -085 -077 -003 -031 -03805130381 137059 1560789 029

STM2499S -01 -077 -007 -081 -065 -008 0010477 -048 -04^0790233 -008 -032 -0030164 127032 1060152 05

STM2500 -07007200881155 --1144f [_--11_8899j| --002266 --004477 --003311 -03 -⁰³⁵L-IZlJ⁰⁴²⁶ -088 0794 -005 -128 -08 -12 -04 -14 007

STM2501 -03 -102 -131 0339 -053 -046 -051 -105 -003 -033 -081 -047 -085 -147 -055 -044 062 -06J ^I -115 -07

STM2502 -01 -048 0214 -001 0343 0335 -009 0716 -089##### 1136 -062 -038 -027 0656 -041 -05054 -08 -13 -03

STM2503 -09 -074 -001 -024 0006 -013 -036 -006 -056 -025 -009 -02 -084 05 -083 -059 -07 -O 5 J -17j -098 -05

STM2505 0540478 0184 0764 1322 0651 -0 0013 0341 0284 -147 -125 0327 -037 -0 0879 -08 -05 -12 -048 -03

STM2506 0330448 0046 [T72] -014 032 -035 -099 -028 -049 -078 -053 0382 0764 0355 0487 187097 179 03 043

STM2508 0230799 0494 -034 0018 0092 0726 -025 0877 -023 -085 0022 0988 0064 0237 0475 137098 1582241 051

STM2509 0850355 0148 0618 0097 0547 -005 0264 -076 218β[ -159) -096 -038 -114 -052 -015 -04 -07 -090473 -09

STM2510 -0 -026 -061 -138 -082 -038 -049 -043 -037 -094 -056 -056 -009 -04 -013 0034 112033 135 -013 051

177088 23 048 117

0¹0⁹2 ° 02⁸3¹²0⁰2⁸10 -⁰4⁰36⁷⁰0⁶7⁶4

STM2514 0230001 0026 -128 -0660027 -012 -079 -008 -056 -068 -0310644007806770706 181 119 Z320654 079

STM2516 -03 -05 -⁰⁶³GlS?] -°^{9 013} -¹¹³ "¹⁴⁸ -051

-09 -077 -03 -053 -00178 067025 1360251 022

STM2517 -090182 -013 -0530016 -018 -026072703890247 -0022132 -03801130721 -075 -06 -01 -080097 055

STM2518 036 -015 -048 -118 -077 015 -034 -015 -141 -028 -058 -05 -004 -0640015 -05 066 03 209 -006 -0

STM2519 0970324 -031 -157| -05 -019 -057 -069 -059 -084 -004 -0430753009200460385 167 149 2330994 072

STM2520 008 011 -056 -1^*74|-076 069 -039 -09 -075 -042 -095 -117 -0060619 -0250874 208 125 1550748 072

STM2521 -02 -015 -064 -245J-088 -006 -011 -068 -046[VSj -039 -06 -056 -056 -006 -048 069007 140527 016

STM2522 1140308 -039 -122 0060746 -0080489 -009 -0930008001406760172 0240571 174092 2.530405 083

STM2523 0660297 -002[-18S* -059 -009 -014 -0.23 -068 -054 -094 -08806210135 010754 178 126 2020654 044

STM2524 -02 -047 -135 -22£-067 -045 -042 -082[^"JiJj] -068 -098 -104 -059 -007 -053 -033 065 -01 161 -009 043

STM2525 -06 -091 -⁰⁶⁴Ql⁶?.^10380282 -°⁷³ -°⁷ -°² -⁰⁴²L-I⁹⁶IJ⁰..⁸³ -^{033 0410951} -⁰⁹³ -° ⁰⁵⁶⁰³³ -¹²²¹⁰⁷

STM2526 -1 -11 --004444^ -009933 --002255 -1360139 -006 -06811221971 [_^34] -O 98 -077 -039[-1Jwj -12 -04 -06pT83] -03

STM2527 -08 -02 -0311 -165] -0570436 -0160018 -1050175 -015 -1230426 -0810075 -024 016009 1021699 071

STM2528 069 016 ⁰⁰⁰⁹Ll⁵Ii -⁰³³ -^{022 0537 3774} -°¹⁷ -¹¹⁴ -°²⁴ -°^{41 00050298} -0141036 195094 224 113 066

STM2529 -10477 -022 -01 -019 -040258 -026 -023 -09904370431 -038 -1050198 139 -15 -05 -061534 051

STM2530 0650334 -063 -14800290252 -024 -069 -079 -05 -038 -0560701 03902071031 126048 2.16 019 036

STM2531 075 -024 -028 -179 -00401930128 -089 -059 -091 -053 -0430101 -03309990792 246072 2020505 085

STM2532 -05 -005 -139 W -06506060272 -0510246 -009 -0460177 -063 -02211160327 126061 1732277 108

STM2533 0090158 0452 -088 -0230144 -0050102 -044 -10904750095 -01 01700720717 046 -0 081 -043 053

STM2534 -130099 -09903220291 -0230314 -072 -124 -1 -019 -129 -06 -065 -014 -069 -14 -02J -2s| -125 -03

STM2535 0290248 0232 -079 -0980247 -004 -043 -022##### -0510322 -037 -022 -006 -029 067015 086 -016 018

STM2536 010347 050402250673014400460616 0090558029906810768108100860323 -01 083 091 -005 029

STM2537 003 -011 -09 -111 -1030043 -057 -093 -077 -093 -065 -0150041003404870096 138113 1970697 033

STM2538 089 024 -048 -099 -108 -013 -102 -077 -131 ##### -072 -055 021 0616 -0530767 187087 2150755 108

STM2539 062 -002 007 -122 -0850099 -039 -083 -076 ##### -0540107005800540519 -019 162051 1980655 073

STM2540 041 -008 -053 -104 -0960056 -01 -102HTsTI -07 -073 -0620126 -03 -0550324 161 035 1380279 004 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2547 -02 0028 -002 0024 0433 001 -069 -091 -028 03 -053 -086 -0340243 -016 -057 -13

-02

STM2548 -01 -012 0297 -017 -015 -036 -0120399 -010629 -0750951 -036 -087 -063 -016 -08026 -09 -07 007

STM2549 033 0667 0393 -036 0882 0521 01 0302 -0030997 -098 -025 -016 244 -0370475 106043 1261184 037

STM2550 034 0469 0465 0862 0506 0328 -0070113056706770065 -016028807970004 -039 -09039 -060586 -01

STM2551 048 -005 •051 0584 0043 0042 -0220487 -1340617 -052038803260765 -0060576 178057 1550656 093

STM2552 178 -058 0537 0989 0651 0121 1279 -04 -1030378 -066 -070176 -017 0161148 05 01 072 -0 026

STM2553 026 0064 -041 0635 -068 0746 -007 -064 -01813620855 -05811980356 -0480336 011 059 063 -043 002

STM2564 -07 -044 0171 0467 -008 -04603750031 17490002 -072 103 -064 -017 -0820536 -07

037

STM2555 067 -002 -036 -125 -086 0356 -017 -008 044 -033 -047 -029083903540621 1286 161 101 161026 112

STM2556 061 -011 0379 0082 -007 0245001403460683 -019 -056 -089 -082 0550189 -062 -03017 -12 -101 083

STM2557 -01 0416 0454 0371 034204560071 03408450395 -006 -079 -064 011 -044 -014 -13 -02 -330189 -01

STM2558 -02 -051 -079 0176 -015 -066 -001 -0020085 -05 -017 -095 -0250755 -103 -024HTT] -05 -37 0398 -11

STM2559 029 -041 004 0545 0614 -0080356 -0290621 ##### -0361171 -015 -01704650502 -07 -08 -08 -046 008

STM2560 -01 0364 -027 0069 0626 029 024 -10432 -109 0550192033401050061 -027 -02 139 067 -005 051

STM2561 065 -028 -028 -178 -132 0608 -014 -126 -073 -1150347 -03104470573 -0160146 126017 Z050236 047

STM2562 -06 -074 -174 -O 32 UUUUii tmrnm -021 -070777 -147 -128 -096 mtmmm #####fTs3] -05 -02 -15 083 -01

STM2563 103 0385 0138 -115 -013 0472 -04 -094 -076 -0330047 -03302820419 -0170622 181 118 2090726 114

STM2564 -05 -057 -134 -185 0309 -014112305810898 -052[j]72] -0890473 -06 -005 -01 067 -03 0870677 008

STM2565 079 0344 -051 -146 -04 -028 -083 -128 -112 -066 -066 -09601390229 0240586 171 113 1520502 106

STM2566 -02 -028 -143 -12 I -147 -077 -117 -073 -084 -095 -039 037 -06 069 -037 005

STM2567 -01 0252 -027 -099 -05

-0790119 -074 -026 -0190078 -007 087005 1690448 034

STM2568 091 0547 -052 -132 -021 03210161 -119 -123 -089 -045 -022 068031402941003 25054 1740657 058

STM2569 065 0723 -05 -138 0392 0151 -031 -121 -086 -046 -064 -0350139 -031 054 077 171 053 1610321 034

STM2570 064 0372 -061 -092 -086 0074 -001 -0970015 -037 -029 -026 -00203040533 139 225084 212 001 035

STM2571 -03 0381 -054 -043 -013 -034036201570287 -1

-12 -116 -056[TeT) -035 -11

STM2572 006 1946 0703 0419 2379 03722060148 -007 - -031 -034 -1070488 -023 073

STM2573 023 0235 0408 0428 0524 0753021408780308 0361028 -0210.276053400580594 033

STM2574 -07 -061 -028 0043 0397 -021 -059 -084 -117 -0371227 -039 -035 -081 -0020219

021

STM2575 -12 -056 -057 016 0103 0079 -044 -039 -044 -029 -148 -08602140153 -021 -034 -1 001 233 -127 -06

STM2576 015 -026 -015 052 0227 0402770307 -078 -03 -044 -019 -065 -066 -097 -041 -0 -01 -1 -124 -11

STM2577 053 0155 0161 [-A 54 -037 0484 -0670249[^~-1j5ij#####0138 -1030257 -04501080461 14089 150293 049

STM2578 037 -017 -054 -145 -062 -027 -086 -117 -013 -046 -044 -069 0250649 0080405 144088 2080409 089

STM2579 -01 -04 0276 -069 009 0255 -0160344 -013 008 -0770611 -005 -0760622 -064 -01 -03 01 -036 068

STM2580 088 0349 -026 -078 0132 0331 -05 -105 -01 -053 -049 -024 001060908650783 166069 1791047 093

STM2581 07 0336 -07 -14 -058 006 -022 -074 -111 -092 -048 -09502090632 -030705 16 116 2040373 012

STM2582 057 031 -019 _-1jS1 -036 03 -O48J2i_7Ϊl -076 -103 -05601520629 041 -0130883 22 142 2130871 099

STM2583 064 0468 -058 -004 -071 -001 -116 -087L7J55] -084 -098 -0460783 -031 -0010519 071 078 150808 101

STM2584 -05 -039 •021 0342 -013 0608 -004 -068 -05 ##### -007 -067 -0550681 -034 -055 -11 -06 -15 -143 -09

STM2585 -04 -06 -138 -06 -069 -033 -045 -114 -109 -101 -048 -082064207620367 -024 -0006 039 -123 -02

STM2587 -06 -015 -033 -003 034 -029 -014 -023 -021 ##### 0484 -112 -0050463 -002 -067 -14 -01^2810157 -03

STM2589 -06 -005 -096 0115 -044 -005 -024 -017 -122 -042 -018 -083 -074 -039 081 -088 -12 -13| -2 βj -042 063

STM2590 -04 0231 -026 0101 -O -019 -012 -058 -049##### -03603780256 -00604161013 -02028 013 -043 -0

STM2591 -01 0286 -01 0014 -003 -0430134 -011 -017 -022 -00088 -015 -02705191274 -05 -0 041 -006 012

STM2592 -03 0586 0376 -005 -033 -03204730366 -0070081 0080799 -05 -078 083 -071 -08019 -06 058 064

STM2593 -04 0643 1393 -078 -005 0861 -00306470332 013013813880114 -031 0313 -134 -1 -06 -08 -069 032 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2601 0550483 -016 -101 -0570437 -012 -07 -099 -072 -013 -067 044 -00502590448 158 078 1870399 079

STM2602 -030854 -0350378100500260381 03260204 -021 0273 -048 -0190425 -007 114 -05031 -13| -169J 017

STM2603 0260273 -0070044 -0020094 -051 -067 -045 -0140199 -006 -135 036 -014 -004 -04 005 1640124 001

STM2604 1350207 -0651031 0446 -0050741 0574 1763 -0550397 -062 -0060384 -0291386 -06 028 -120465 072

STM2605 -030141 062601090009 -02 -054 -109| -16β] -0150178 -067 -08 -04 -011 -016 181 -01 -11 0183 -01

STM2606 08903030071 0431 0218 -035 -015 -046 -029 -102 -0050506 -0080875 -034 -056 -01 -0 -06 -074 -02

STM2607 0970672 -02 -139 -091 0299 001 0611 -053 -13 -057 -0470575053805570541 134 113 135 -003 094

STM26O8 0230832 041 -001 00930281 0151 02981055310231780269 -056 -03500380297 -03 -02 -1 g| 1729 003

STM2609 034070904720018 -011 -004 -01 0198 -058 -0160715 -066 -013 -143 -045 -092 -02 -05 -12 -144 -06

STM2610 -04 -002 -076 -027 046 -0450361 -085 -011 0048 -022 -123 [TK)] -081 -072 -053 -07 -07 -09 -066 -07

STM2611 S -050041 0723015302720515 -0270519 -062 -07056703940416 -094 -0140445 -05 008 -04 -099 -02

STM2613 0052E-04 -011 -021 -0720039 -035 -044 -029 -0230196 -063 -0921625 -029 -027 -02 -05 -02 008 023

STM2616 034 -0090009 -12 -04602670298 -111 -008 -0471237 -0660447 -028 -0140324 121 053 1320376 06

STM2617 028 -014 -0050418019206220191 06250766 -097§3 -°⁷⁴ -°^{01 0047} ° ^{14 ^033} ~°⁴ "°⁵ -2s[ -007 04

STM2618 024 -017 -091 0874 -00108 -05300070.2120362 -030437 -014 -0220729 -022 293 -01 082 -007 042

STM2619 1170543 -00503550237 -01 -017 -052 -009 ##### 0805 -014 -083 -1220477 -01 01 -06 021 0003 039

STM2621 -0 -04900450297 053 -0030131 0051 0454 -026 -082 -042 -04 -015 -052 -002 -07 -04 -11 0129 -11

STM2623 093 098 -019 -027 -10702790027 -016 -005 ##### -043 -018 -053009504461287 186 1 161174 135

STM2624 23329430245 -078 142400350828 -012 [^2.29] 06 -001 10751404 148807731414 104 122 081 3014 07

STM2625 06603431221 13076E-O4 -002 -0360971 0157 ##### 1201 0835 -023 -022 -041 0644 -06 -08 -07 -038 -06

STM2626 -02 -015019504950308 -01300950221 0347 -0221025 -05600550791 -0180787 -14 -06 0675 -04

STM2627 0170131 02590109 -011 -089 -00602840011 -0470954 -071 -096 -019 -086 059 -03 -03 -16

STM2628 0590013 -021 -095 -050187 -021 -092 -044 -084 -053 -0470415 -021 0071 0765 187 109 1491018 035

STM2630 019 -005 -002 -0320177 -006 -0080483 -0290427 -007 -044 -027 -012 -001 -012 -02 -02 028 -013 02

STM2631 -03 -071 -03 -011 0127 -0360016 -028 -006 036 -066 -104 -04 -067 -029 -022 -04 08J _-V7J -017 -07

STM2632 0680412042605170546 055044203650602 -0133364 1248 -0031041 0562 201 -06 029 -020491 06

STM2635 0170467 0664E-040259 032 -00307770646 -017063604781164 -039 -0062039 -13047 0170222 -01

STM2636 031 033504440557037902469E-04014406630631 -045 -045 -0030029 -001 -011 -1 002 ~^39]θ648 -02

STM2637 -11 03680851 -113pMa7| -119 -064 -1150088 -064 011 046 -05 -096 037

STM2638 004 -0490749

-07536540171 -007 -023 -0050391 -0 045 031953 -06

STM2639 034 -0470468 -081 -121 0566 -1320466 -144 -006226704520156079504320521 037 087 0772146 02

STM2640 0990254 -067 -103 -018 -015 -061 -092 -062 -104 -093 -0591066061900531251 184 158 1850455 031

STM2641 101 121 040407840115 -051 -057066702521152 -08208840988[-1[9If 1551 0235 416 -0 194 -001 147

STM2642 0440708 -033| -173] -051 -0180473 -079 -03##### -013 -01805980103 -0060641 195 119 2440427 053

STM2643 0230882 -11902780424 -104074500770071 -0450396 -1290659§-V72j -0890509 -13061 -03! -175 ^ -12

STM2644 0380007 0120921 -10800140234 -023 1350132 -126 -00700240057 037 -038 -04 055 -16 3188 035

STM2645 197030803790262 -012 -042 -005 -00503470118 D4060816073808781405 -05 -01 -0 084 -076 114

STM2646 11606630087 -084 -004 -066 -1160274 -0180346 -073 -008120021 05740986 245 186 2650868 099

STM2647 0603840459 -022 -0460025 030966082403460461 -01 -1 VtfTsϊ] -086 -138 -03 -03 -07[ -251J -06

STM2648 01703540787 -073 -0470121 0161 07740683 -0530671 0521 -0690483 040196 041 093 114 -001 069

STM2649 -01 -02900890208 -0020441 0534017515220065 -082 -0170.2690141 -002 -001 -01 099 2250093 -0

STM2650 0540279 -0090373 -019 -008 -041 -087 -132 -1170019 -046 -094 -019 -0680324 017 -03 -05 -074 -08

STM2651 -03005904580531 -011 0643 -035 0450321 018^-1 TOJ -033 -053 -087 -0620771 -14 -06 p26] -127 -07

STM2652 0730545 -016 -052 -06905990429 -0630929 -0820193 -040626059404872455 213093 242 161 104 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2667 0180156 0.1450824 -0094E-040031 01490874 ##### 0254 -057 -042 -12 -064 -147 -1 011 -17[1712 -09 STM2668 040249 0602011500450331 040900850451 -015 -004 -028077732891023 -037 -11 036 064 -054 075 STM2669 0260265 -0370192 -077 023006400150372 -044 -102 -004 -041 -019 -04 -O07 059016 0670293 014 STM2670 058 -019 -0980651 -061 -03 -035 -0020149 -029 -131 0036024705990149 -028 075 -02 -040347 009 STM2671 -030025 0267 126904330358 058 -05409081964 -06 -028 -067 -085 -017 -095 -15 -04 -11 0761 -04 STM2672 013 -004 055600430153 -0430303 -030643 -003 -021 0994 -10805180126 -136 -09 -06 -130908 -02 STM2673 001 0627 0011 -0250858 -0550648 -071 05831062 -1181809 -006 -068 -040362 099004 009 -071 -04 STM2674 1090747 -04 -078 -0660053 -017 -074 -08 -076 -01 -0230334045408650986 184 128 2 1.266 062 STM2675 0420404 012 -075 -037 -0240668 -098 -096 #####[-156] -012018310070502 162 216 109 258 058 044 STM2676 1630506 -038 -103 -1020332 -053 -061 -064 -053 -124 -11308320151 -0010614 227 102 2230067 028 STM2677 0790386 -046 -08 -006 0360559 -004 -051 -037 -057 -0640613006706640412 141 048 126 015 015 STM2678 GiH -⁰⁵⁸ -034 -136 -Z12 -156 -1460701 -1881 (^35I -142 -11pT62 257] 0748 -14 -13 -2.2 -053 -14 STM2679 -01 -002 -0240171 0442 -0661377 015 049 -O34fϊ-1'84] -0730697 -097 -046 -099 -08 -09 -IJj -02 -04 STM2680 023 -008 -08902930842 -0590146 -0920673##### -096 -01308290548 -051 0098 -01 -04 -00129 -05 STM2681 -0 -009 -13903240573 -096 103 -1170.25518Oβ£3f5ϊ] -065 -0440744 -1140147 -0 -05 -02L-I₁SiJ -1 STM2683 003 -025 -037 -1090251 0158 -0320846 -06 -121 -094 -0030138125503160306 108 015 1520239 082 STM2684 0120307 0127 -0501050705 -055011817970096 -002 053 -067 -11512272363 -09 -01 1323406 106 STM2685 -01 -026 -115[^~T52j 015 -042 -012 -0_^34 £5720066 [^B] 0247 006 -042 -0350051 165 078 174 -01 073 STM2686 0260299 -039 -094 -053 -04 -048F-18 -18?, -033 -046 -016 -0290949 -0150172 073 072 2530282 033 STM2687 0030237 -121 (2TeIi] -094 -021 -019[-1JS -144##### -069 -049 -011 -00901121078 142038 1840548 -01 STM2688 -06 -064 -061 -066 -04 -006 -127 -112 -23 »4j -09700780303 -035 -001 -069 -057 -04 003 -0 -102 016 STM2690 -010063 00530706 -031 -041 03450107080611431041 -082 -102 ########## -062 -13 027 -04 -007 -0 STM2691 -02 -005 -017 -078 -114 -033071507261279 -065 -0950546 -031 -01 0341 0068 093 056 116 1036 08 STM2692 -060623 0547 -0160017 -112 -001 -033 -1350069 -0023989 -062 -083 -138 -127 -15 -01 163 -053 -1 STM2694 040295 0171 fyjϊβj -062 -001 -088 -077 -047 -056 -057 -068 -04 -00503240816 166 109 1981118 079 STM2695 1310613 011 -126 -1 01940207 -0471202 -052 -071 03550681 02650121 0727 213 05 1950595 154 STM2696 0790582 0017 -094 -093 -01401450609 061 -087 -058 -056066806490796 053 195 13 Z061328 058 STM2697 0930071 -016 -131 -05900820258 -075 -046##### -0280191 0936079300980179 134 093 1920737 014 STM2698 1320212 -044^207! -016 -002 -038 -097 -058 ##### 0005 -030366013303060242 219 111 251 1264 065 STM2699 079 046 -005 -12 -0450168 -07 -093 -074 -06900840052 07 -04502870976 224 143 2020518 035 STM2700 096 008 -023 -107 -06 -0070065 -02 -031 -072 -031 -07408790271 0091 0947 212 116 1470745 034 STM2701 0-74 041 -111 -095 -0090245 -066 -118 -019 -089 -043 -0240451 019806330931 185087 1970192 105 STM2702 0780438 -096 -101 00390257 -034 -101 -06##### -035 -091 0717 ##### 02271021 232 104 1220267 126 STM2703 0970421 0.013 [ -15fj] -035 035 -063 -04 -014 ##### -089 011 05370786 -0160716 183 08 264 046 162 STM2704 030482 -075 -143 -1060421 -028 -069 -055##### -111 -005 111908950136 1115 22 12 2.090156 025 STM2705 -08 -101 -038 -01 -015 -027 -066 -022 -126 -042329 143 -060109 -087 -07 -09 -0i[ J-2JJJ -117 -13 STM2706 033 -044 -032 -028 -0220602 -009 -03 -006 -017 -068 -0410414 -02301330012 034071 009 -007 005 STM2707 0490775 -076 -138 -03900480073 -04 -07 -106 -101 -0040.212 -001560853 229124 150248 075 STM2708 0920217 -004 -137 -095 -004 -056 -077 -038 -083 -024 -03701890105 -032 154 146 121 1090505 068 STM2709 030351 -063 -064 -063 -011 -097 -078 -064 -084 -043 -0820675093207150411 162 156 190745 075 STM2710 078 -015 -033 -132 -031 08050254 -083 -042 ##### -001 0413 038028307890184 227 11 1820389 05 STM2711 0620909 -02δ[T65t -12805190044 -0520297 -0580052 -051 0057097204830684 197007 188 018 08 STM2712 1080774 -057 -096 -0830033 -083 -07 -072##### -039 -0020782 -017 -06 1484 266 098 2240576 032 STM2713 081 -005 -009 -094 -0760255 -061 -098 -066 -034 -103 -067 068 -00402370735 242095 2280462 046 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2722 089 0896 0106 -115 -118 05360112 -0320017 -053 026 -0290687106600760507 158116 2030557 053

STM2723 028 078 -01 -011 0184 -028[jjS9J -098' -1θ| -0660316 043 0100380788 276 166 232 -021 062

STM2724 -01 0035 039 -103 -106 0263 -037 -039 -121 ##### -044 -0270747 04902471077 235 136 1960077 085

STM2726 071 0227 -119 -175 -019 0575 -001 -092 -079 -146 -05 -0610423 03605920586 148 119 1670971 038

STM2727 024 0182 -029 -106 -038 0618 -009 -114 -05 -131 -048 -0540738050704210643 188 176 281 079 132

STM2728 134 0303 -054 -12 -001 0212 -075J -1 β| -047 -105 -045 -070499028902631374 206036 2380822 059

STM2729 021 0537 0022 -188 -016 052 -023 -059 -033##### -06104240273092603070853 178088 3250598 139

STM2730 1 1044 0658 -138 -007 0858 -011 -082 -047 -07 -067 -0250347016207241126 2 143 2070554 109

STM2731 127 0519 -02 -12 -108 0472 -057 -055 -O57##### -049 -003 -0210695 -0070902 202 142 218 043 098

STM2732 073 0357 -036 -119 -09 -02 -011 -066 -07 -1.2 -072 -0210282019800950535 198032 2791037 031

STM2733 068 -001 -042 -179 -039 00550029 -093 -044 -115 -045 -083 -004046707981113 22 168 2030575 056

STM2734 058 -015 -027 -13 -032 02 -042 -098 -082 -117 -009 -0730236040401410652 211 114 1870996 138

STM2735 065 0644 -047 -123 -095 05730166 -067 -08 -082 -118 -04303020189 -0310576 172172 2160916 064

STM2736 032 084 0185 -177 -062 -0240288 -0920086 -095 -03 -0760595 015 -034 077 183 179 1991164 037

STM2737 095 0449 -017 -171 017 -002 -056 -082 -03 -076 -107 -040578 -008 -0481029 188096 2340477 173

STM2738 048 0598 0244 -165 -026 0168 -022 -143 -054##### -131 0450101 ########## 092 161 084 212 111 086

STM2739 151 0284 -021 -093 -057 06720408 -040419 -113 -031 -06403250748 -0131435 2095 298 044 061

STM2740 -07 0786 -013 0412 0949 -034 -001 04 -0530871 -12207640376 -0160061 -01 -1 028 -06 -098 055

STM27401I 117 0081 012 0075 0567 -03801350507 -12 -024174106640619 -021 1393 189 137 180459 074

STM2741 -07 -092 -119 -044 -031 -053 -092 -007 -087 -084 -045 -047 -101 -095 -012 -069 -03 -11 -0_3J -171 j -1

STM2742 -15 -061 -058 -035 -015 -031 -048 -041 -10952 -05 -101 -124 -108 -057 -125[TiJ -13[~Tδ -2.02| -05

STM2743 016 -037 -093 -138 -024 -007 -032 -098 -141 ##### -065 -08904110617 -0010057 088083 1560528 042

STM2744 053 0286 -02 -072 -041 0329017200510253 -045 -032 -044 02301730726 034 174068 1940831 056

STM2745 -12 -048 ^rT97 -087 0127 -077022100450662 -0921547 -114J -16g| -049 -135 014 -02[TT] -12 -124 -09

STM2746 02 0199 0077 -16 -016 0132 -049 -062 -075W8WW -021 -0061143072507141021 172091 1740709 064

STM2747 I -114 0259 0477 -025 -018 -108[TSJ] -109 -1340001 -138J-1.7->] -116 -14^25 -21 -33 -2.48 -2i|

STM2748 -12 -121 -138 -152 -054 -08 -147 -052 TM9[T»] 1388 [TKS] -1210059 -13 -036 -07 -06 -04 -1 -1

STM2749 -05 1308 1573 -052 -003 0152 -02 -028 -001002528180124 -108 -133 -031 -074 -08032 305 -026 047

STM2750 07 -039 -182 0245 -162 -097 -0870606 Q24J 2653 -133

-037 -15 -11 -04 -132 021

STM2751 052 -001 -009 -187 -041 0530616 -126 -083 -107 -074 -030247 -01604061023 178 163 1760645 024

STM2752 034 0777 0217 -032 0352 111713221612 [T53] 092721820621 019057912530407 029 333 0432741 186

STM2753 -03 0504 042 -076 -03405940419081800241542 -101 1445 -04 -088 -1141384 -04 036 021 1012 -02

STM2764 -13 -087 -101 -036 -086 -042 -096 -114[^2] -112 -126JT75] -036 -107| -19J-098 -12 -06 _JMDJ87f_£[5|

STM2755 -13 -047 -08 -031 -005 -041 -027 -058 -123 ##### 0155 -0760025 -124 1 -062 -11 075 -25 -167] -09

STM2756 -02 -041 -094 -103 -111 -053 -072 -053 -081 mm -02 -02202060268 -0710233 174006 2.121065 173

STM2757 096 0029 0132 -17 -055 -056 -031 -127 -08 -068 -05608290695005800540379 177 112 241 1175 068

STM2758 -01 0607 1304 -029 01160216 -022 -015 -0380876057911332538 -02904050923 003 108 -02673 -0

STM2759 066 0456 -153 -105 1403 -0470014 -0730501 0460953 -0330465 -11 0321501 088 151 1090445 109

STM2760 029 0069 -003 0459 -036 -00902830123 -0171425 -0830043 -03300160045 -036[TT]OOI 096 -053004

STM2761 041 0098 -025 -107 0012 -024 -008 -092 -012 -123 -011 -048 -012 -00503150685 18 108 173 102 053

STM2762 064 -019 -045 ^-179 -1010313 -119 -143 -149 -135 -077 -0860269 -035 -0210538 185 03 088 1 012

STM2765 003 -019 -016 -135 -072 -031 -124 -O93I-I62I -08 -02 -03502231889 -0510478 125042 1810933 032

STM2766 -04 -028 -022 -071 0585 0830156 -099 -018 -129 -116 -057 -062 -004 -041 -042 -05 -02 -051188 -05

STM2767 -07 -072 -047 0004 04420014 -05 -07 -01905670611 -024 -0890576 -095 -038 -14025 -23 -155 -13 TABLEJ - Raw Microarray Fitness Data for Engineered Salmonella

STM2777 -04 -034 -056 -069[-162J -084 -07 019 -059 -059 -131 0138 -1340379 -035 -131 -07 -06 -07[ -17i) 028

STM2780 -06 -004 -013 0421 0208 002 -0.20128 -03 -068 -04 -04606380178 -004 -075 -14 -03MeJ 1228 -03

STM2781 -03 0212 0336 03030398 106300520325 -031 -057 -026 -0580393015702080313 -14 -06 -060049 031

STM2782 -01 0157 0003 040801830481 040701260266 ##### -014 -025 -0360033 -0840714| - -a233| --00 -05 -09

STM27Θ3 -03 -023 -034 0051 0357 -088 -028 -083 -108 198 -099 -147 -1132318 -086 -129 -15

-11

STM2784 012 0345 0331 -086 -05045505020584 -0120023 113 -031 0303 -071 -032 -049 546 15 087 1382 -04

STM2785 023 0689 -085 -109 -082 -0390009 -071 1801 -008 -007 -1270332 047 -035 -006 205374 1280305 053

STM2786 013 -023 -002 -091 -015042204250919 -0151759 -0381024 -01 -0250434 -034 052001 072 -064 165

STM2787 -08 -107 -052 -061 -023 -085 -077 [TΪB] -114 -1.2 -0330004 -104 -131 -OβQΪT] -1 -11 -030048 -09

STM2788 024 -014 -019 -037 -0550584 -024 -02 -105 -076 -044 -1 -035 -081 -055 -003 063 035 058 -009 025

STM2788 -02 -018 -01 -063 -0420143 -059 -054 -11 ##### -071 -095 -005 -101 -036 -012 073033 092 -001 033

STM2789 065 0376 -057 -13 -047001402520131 -097 -1490055 -035 032 -0370971 -005 104 024 172 -005 129

STM2790 -05 -006 -011 -093 -108 -098 -024 -017 -0630135 -058 -108 -077 -105 -003 -036 -08056 -050854 -08

STM2791 065 0422 -016 I -1 S2J -0340074 -001 -079 -056 -0570119 -0280613 -03 -0041053 175 108 2031188 001

STM2791 045 0412 -066 -07901940186 -004 -103 -056 -0280376 -0750206 -031 05120175 102041 1140205 104

STM2792 -1 -O07J -178 ] -012 -077 -107 -016 -074 -05##### -111 -052 -128 -117 -123 -111 -11 -05 -070285 -1

STM2794 -02 -012 -033 -012 -068 -072 -013 -088 -046 -028 -031 -0820324 -043 -03 -029 089 016 0930174 064

STM2795 -05 -051 -074 19740145 017 -038 -025 [Tw] -073 -131 -113 -128 -02 -047 -136 109 -08 -11 -099 -08

STM2796 043 0389 0069 p1~54~] -080177 -04 -117 -086 -038 -079 -071 0251 077708230666 259 08 2780147 062

STM2797 016 0463 -049 -146 -0360362 -006 -051 -148 ##### 1006 -0550907084305020728 153 087 2.24 021 02

STM2798 -04 -008 -098 -143 -072 -0290107037908740182 -014 -004 -042 -078 -025 -008 087 -01 060852 02

STM2799 -08 -13 -073 -0J8 -0890137 -035 -0370101 -03503360344 -031 -126 -065 -044 -01 -06 003 -072 -05

STM2800 099 0183 -03 19?| -0090244 -043 -06 -044 -101 -032 -02099401090121 0888 186 085 2430679 07

STM2801 076 0477 0084 -2.09] 003 066 0020382 -086 -075 -051 -0470388112504760826 19 074 205 073 062

STM2802 004 0174 -022 0087 -073 -084 -039 -061 -01 -06 -006 -052 -136 [ -198ι -105 -052 023 -1 002 -097 -08

STM2803 05 0311 -05 -022 -012 -034 -02 -094 -014 -052^019 -0120583 -061 -0280128 111 109 051 072 005

STM2804 -09 -11 -034 0224 -05901320668 041 -043 -092^-15^ -122 -072 -031 -050399 -0 -1 047 -111 045

STM28041ι 097 0529 -018 -207I -021 -001 -098 -005 -063 -114 -034 -05704230576 0141452 249 139 1940772 072

STM2805 11 0912 063 -0500150158 -014 1285 -106 -008 -038 -025 0.2 088 -0321229 173 122 2230691 083

STM2806 019 -009 0553 0971 0491 0555 -013 106 094 -0060543 -114 -0270386 -101 -006 -03 O19Qy]θO42 -07

STM2807 059 0067 0768 0959 ########## 0093 107611870195 088 -052 ############### 033 -04 044 -120163 -04

STM2808 025 -014 -033 -018 -1140143 -042 -053 -066 -029 -088 03028502930658 -009 07 015 1440376 067

STM2809 071 0025 0314 093703620724 -0090221 0601 076215940588 -02 052 018 -022 -01 0 iQTδ]θ756 018

STM2810 108 0463 -049 035 091 0868 -005 -043 -005 -0490141 02580242 -0300391277 08 01 436 051 035

STM2811 096 059 -019 -0780197 -0680615 0130373 -0520129 -061 0874 ##### 07 1316 219099 2.281356 076

STM2812 099 0364 0985 -005 01 -02 -01 -0190055 -0343420027026709860162 -024 122 133 0420129 053

STM2813 05 0105 0508 -069 -0890088061310870838 0122885 02 052102907090322 045 088 1140143 048

STM2814 143 -014 -02 086 -012 -060274 -077 -001 -0280651 011 0335 -0270519 085 069 -04 -09 -019 06

STM2815 063 0772 12250733020904220362 1187026502350213004206590393 -020868 -05063 -081574 038

STM2816 025 -012 -031 111 0013 -0930143 -053 -021 0411 09390761 -009 -058 068 -023 -04 -02 -13 -015 019

STM2817 082 0846 -025 -11 0251 01090006 -029 -069 -093 -048 -0090348 -01403450225 188 07 2330074 086

STM2818 -01 -049 0026 -075 -0760159 -052 -098 -0420085 -0810135 -063 -08409490115 144 -02 124 -008 026

STM2819 086 -005 -035 -106 -0640083 -029 -098 -064##### -045 -0450626005303990379 228 084 2070682 086

STM2820 05 0359 -017 -044 -05303170351 -0170021 0446 -007 -0.270588 -014 1041 -0 153 116 1430442 131 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2834 068 0523 -0.29[3j3] -027 0120139 -06 -053 -119 -0 -0560682 -01103161116 203 117 1790414 007

STM2835 034 026 0068 -094 -028 -039 -044 -007 -09 -102 -097 -0740105 -02201120291 118051 1750624 054

STM2836 -01 -025 -019 -08 -070453 -007 -054 -03 -102 -009 -0230179 -0430444 -014 113015 1280251 015

STM2837 -0 -051 -093^21 -192 -003| -178 -196 -225j##### 0_271 -089 -015 -0230188 -059 063033 073 -02 OA

STM2838S 01 -017 -0304480137 -1 01760092 -018 -0 Θ^JKϊ] -1291482 -079 -069 -038 0041 -080657 -03

STM2839 285 1142 02881066137911551238 0771504 -045 043 112 0761971 11650916 038 165 1152053 197

STM2840 -01 -011 049 -106 -0540152 -0410174 -108 -075 -029 -0950497 -08 0050136 074024 104 -099049

STM2841 -07 -002 -05 0060449 -044 -016 -1020117 -027 -139 -03 001 19210867 -051 -08 -05 -01 -082 06

STM2842 -02 -011 -067 -016 -067 -123 -016 -059 -063 -066 -116 -076 -0671562 -057

07[ TaI] -104 -05

STM2B43 0 0528 -001 -107 -0350376 -04900340009 -056 -13 -0780086 -036 -1150025 -02018 -01 -049 -02

STM2844 06 0538 -034 -045 -05 -043 -0150108 -09 -003 -076 -110732015709520355 215 103 160978074

STM2845 -01 -07 -005 -141 -015 -040137 -087 -038 -072 -022^158] -105 -128 -01 -078 -05 -08 -051004 -09

STM2846 088 0586 -131 -0510402 -0370621 11981215 -0811658 -01110460182 -0310412 -03158 204 -039 06

STM2847 088 028 -128 -0310406 -0440887 -0270433 -068120601820563 -032 -051 006 -02 136 179 -087024

STM2848 021 -011 0054 -047 -0184E-04 -06 05 -019 -004 -064 -051 -077 -039 -0010691 -01 049 09 025032

STM2849 04 0375 1183 0040303088501990527QTM] 2029364130212768 -074 -0130285 -0 -02 122 -054 -07

STM2850 043 074 0323 -133 -072 -054 -018 -069 -0730708 -015 -011 -001027802810206 073084 1380386 113

STM2851 087 0032 -045 JJH39 -11800450113 -075 -14 -051 -01 -0151205 -04307550475 125036 0810499 153

STM2852 064 -001 ⁰¹⁵³LL⁷JU "^{042 0065} "°^{26 ~102} "°¹⁹ "¹¹⁸ "°¹² "°²⁷ "°^4β -00501411049 171085 180798 -02

STM2852 026 0052 -079 -108 -089 -0390083 -0670595 -051 -0501520057036508320694 135062 1291359 13

STM2853 115 002 01030409 -014 -017 -046 -055 -056 -031 -0470619 -003fiJ9O6281988 -09 -09 407 -062 089

STM2854 065 -011 0108 -145 -060052 -055 -029 -043 -049 -08 -0450886032500820916 202086 2171292 114

STM2855 045 00430523 -004 -017 -083017206980604 -058 009 -024 -081 -0130511 007 09

STM2856 -05 -079 -0230019 -0270558020608820628 -066 -245 -198 -092 -159j -017

-024 04

STM2857 005 0623 -111 -031 -028002704220146 0961116 -205 13 071 -0850966 -022 06 -12 -11 1353 043

STM2858 106 0511 -024 -076 -043 -054 -049 -057 -107 -0150135 -032038103270651 1097 195 157 1720993 1

STM2859 048 0318 -036 -036 -108 -002

-004 -109 -02101820404 0651316 189077 Z170698 052

STM2860 115 0239 -02β[2lj5i] -102 -025 -037 -055 -034##### -01 -013 -00303580408 028 2 114 2951229 091

STM2861 062 0255 -0090744 -064 -039 -0203540082 03216650219 -059[-1JMIO 163 -026 002003

STM2862 079 -033 1647 -03 -0981629 -1021235^59] 01520454 -0670228 -103 -043 037 185 -09 487 153 -06

STM2863 06 -029 -078 -009 -083 -0210267 -008098103150363 -0660017 -09603241005 074004 128 0571 055

STM2864 024 0539 0042 -077 mmmnmm -01 -041 -007016608721326 mmmtmtmmmm 0442 132 O68 412 1054 095

STM2865 017 -02 -022037102630397 -023 -0390109 -0020738 067 -038 -022 -01 -033 -08 -04 329 0158 -01

STM2866 -09 -077 -034 -01302670033 -058 -0.26 -064 -02 05902260891 0180305 -043 -1 -06 378 0017 -03

STM2867 -02 0112 -0520017 -003 -014 -102 -126 -0580623037730331001051600720429 089037 023 2732 078

STM2868 -09 -0230484 -01104160568 -044 -0040077 -142 -035 -064 -03 -074 -029 -01θ|Λ -2J -Oδf --2222 -2.4 -04

STM2869 048 -058 0093 039 -043 -0070298 -0020533 -092 -121 -034 -026 017 -026 -058 -08007 000044 --009933 -1

STM2870 063 -01 01550612 -012 -01 -0240109 -053 -0 -012 -052 -0071451 -089 -041 -11 -04 -1 -047 -09

STM2871 -0 -055 00210163 -11 -051 -093 -092J -15i| -0061118 -02 -001 -023 -073 113 078 -05 0390891 -06

STM2872 008 ■003 0248 -0940109 021 -089 -036 -106 -03104590349 -021 -02 -001 -045 059088 0770228009

STM2873 008 -06 -0040394 -0420042 -051 -0.210188 -0181308 -01 -016 -071 015 -086 -1 168 -06 -087 -02

STM2874 -01 -064 -039 016 -03 -027 -039 -003 -087 -024 -092 -013 -015 -031 -01041β[-i]r] -0i[ ^"^e] -055 -04

STM2875 -03 0643 -069 -0061517 -0170555 -049 -05604720291 11491702246108190006 -12028 -110637 073

STM2876 -01 -045 -0320309 -017 -085 -073 -063 -072 ##### 0289 -032 -046 -099 -018 -032 -09

-04 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2886 -1.1 -0.92 0.207 0.063 0.037 0.139 -0.29 -0.1 -0.85 0.809 -0.57 -1 -0.4 1.21 0.354 -0.47 -1.8| -0.4 -2.4 0.087 -0.3

STM2887 -0.5 -0.12 -0.68 -0.05 0.066 -0.2 -0.59 -1.15 -0.6 Ufflftfli -0.18 -0.53 0.99 -0.78 -0.72 -0.93 -0.3 -0.7 ^" -Z03 -0.7

STM2888 -0.1 0.118 •0.43 0.305 -0.05 -0.58 0.042 -0.44 -0.05 0.051 0.245 1.085 -0.31 -0.85 -0.26 -0.37 -1 -0.9 -3.6 -1.87 -0.6

STM2889 -0.3 -0.22 0.135 -0.49 0.034 0.185 -0.62 -0.56 -0.91 mmm -0.28 0.6 0.362 -0.13 0.516 -0.2 0.15 -06 0.96 -0.1 0 16

STM2890 -0 -0.33 0.177 0.632 -0.06 0.392 -0.32 0.041 0.27 ##### 0.826 0.407 0.189 1 865 033 -0.08 -0.6 -⁰¹Lz? -0.31 003

STM2891 -0.1 -0.33 0.02 0.44 0.055 0.449 -0.47 -0.21 -1 11 mmm 0.397 0.17 0.724 0.571 -0.12 -0.29 -0.6 0.17 -0.7 -0.13 -0.4

STM2892 0.02 -0.91 -0.27 0.712 -0.38 -0.69 -0.76 -0.7 -0.39 -0.6 -0.84 -0.67 -0.26 0.686 -0.34 -0.54 0.03 -0.5

STM2893 -0.6 -0.85 -0.61 0.013 -0.65 -1.12 -0.96 -0.78 -0.34 -0.72 -0.87 -1.37 -0.91 -0.3 -0.31 -0.95 -1.3 -0.3

STM2894 0.6 -0.28 0.061 0.818 0.555 0.363 -0.03 0.086 0.153 0.046 -1.64 0.122 0.342 0.269 -0.89 -0.29 -1.1

-1

STM2895 0.11 -0.11 0.106 -0.25 0.23 0.197 -0.61 -0.53 -0.63 -0.29 -0.6 0.557 1.591 -042 -0.67 -0.83 -1.1 -02 -1.2 0.872 -08

STM2896 -0.5 -1.07 -0.02 -0.15 -0.53 -0.22 -0.87 -0.6 -1.18 -0.08 -0.07 -0 -0.6 -0.82 -0.29 -0.6

STM2897 -0.2 -0.54 -0.36 0.18 -0.34 0.137 -0.33 -0.55 -0.79 mmm -0.96 -0.98 0.467 -0.2 -0.92 -1.1

STM2898 -0.2 -0.95 -0.62 0.566 0.092 -0.6 -0.12 -0.39 0.115 -0.8 -0.79 -0.16 -0.78 -0.1 0.325 0 13

STM2899 0.02 -0.65 0.224 0.034 -0.01 0.542 -0.16 0.565 -1.27 0004 -1.44 -0.8 -0.86 1.47 -0.53 -0.2

STM2900 -1.1 -0.84 -1.1 0.314 -0.19 -0.51 -0.63 -1.25 -0.57 -1 -1.07 -1.08 0.046 -0.81 -0.58 -1.4

STM2901 -1.4 0.328 -0.07 0.523 0.137 0.82 0.228 -0.12 -0.69 -1.17 0.137 0.416 0.219 0.331

0.31

STM2902 0.14 -0.42 0.043 -0.78 -0.53 0.122 -1.03 -0.83 -0.07 -0.22 -0.14 0.347 -0.1 -0.14 0.08 0.5 -03 0.84 -0.31 -0.2

STM2903 0.64 0.694 -0.65 -2.28 -0.86 0.855 0.204 -0.89 -082 -0.84 -0.69 -0.96 0687 0025 0313 0.311 208 098 2.14 0485 095

STM2904 -0.2 -0.57 -0.6 -1.12 -0 15 -0.55 -0.14 ^-1.57| -0 13 -0.87 -0.45 -0.85 0.353 -0.27 0.002 0.459 1.52 004 1.54 0.031 -0.3

STM2905 -0.4 0522 -044 0.246 -0.34 -0.33 -0.25 -065 0949 -0.56 0.394 0.192 -0.68 0.215 -0.57 -0.85 0.35 -0.4 -1.2 -0.78 -0.4

STM2907 -03 -0.39 -0.69 0.624 -0.08 0.184 -0.71 -1.01 -0.06 -0.77 -0.29 [-r61_j -0.92 JM 0.813 -0.32 -1 -0 5 -2.2 -0.26 0.62

STM2908 -0.4 -0.2 -0.67 -0.26 0031 0.529 -0.57 -0.18 -0.29 -0.49 -0.78 -1 03 0.248 0.006 0.847 -0.4 -0.1 -0.1 -0.3 -1.14 0.53

STM2909 -1 .1.36 -1.63 ■0.13 -0.52 -0.5 -0.22 -0.99 -0.23 -1.48 -0.53 -1.75 -0.12 -1.2 -0 -0.8 0.04 -1.42 -0.5

STM2910 1.17 1.502 •0.73 -1.47 -1 34 -0.17 -0.45 -1.13 -0.71 -0.73 -0.78 -0.5 -0.24 -0.52 -0.39 0.528 07 0.34 1 0.48 -0

STM2911 0.56 -0 17 -077 -0.07 0.38 -0.26 0.1 -028 0296 0.018 0.554 0.082 -0.61 1.17 -0.01 -0.3 0.27 -0.1 -0.26 1.06

STM2912 -0 0.319 0.314 1.204 1.454 0.193 0.355 0.523 0.635 -0.52 -0.02 1.567 0.318 -1.08 1.284 -0 -0.2 -0 -0.7 -0.02 1.42

STM2914 0.36 -0.02 -0.01 0.052 0.173 0.064 0.358 0.476 0281 -0.31 2 -0.77 -1.19 -0.96 -1.33 0.667 0.22 0.32 -1.4 -1.12 -0 5

STM2915 0.74 0.204 0.01 -0.96 -0.38 0.014 0.004 -1.11 0.006 -0.21 -0.24 0.02 0.028 0.516 0.147 1.199 1.76 0.87 1.86 1.401 06

STM2916 0.71 0.775 -0.21 -1.29 -0.57 -0.51 -0.34 -0.4 -0.63 -0.23 -1 04 0.402 0.814 0.915 0.504 2.1 1.13 1.99 1.031 0.45

STM2917 0.91 -0.15 -007 1.291 1.195 0.806 3.065 2.04 -0.97 0.269 -081 -0.31 -0.03 -O.08 0.048 064 0.25 1.41 0.039 0.62

STM2918 0.13 1.101 0.964 -0.2 -0.1 0.748 0.543 1.191 -0.52 -0.86 -0.93 0653 -0.21 -089 1.542 0.329 0.14 0.19 0.72 0.955 1.62

STM2919 -0.4 -0.37 0.361 0.601 0.011 1.066 -0.15 0.7 -0.05 -0.72 -0.84 -0.83 1.404 -0.79 -0.88 1.309 -0.2 -1 -0.2 0.086 0.05

STM2920 0.88 0.12 -021 -1.33 0.115 0.183 -0.21 -1 16 -075 -1 16 -075 -0 11 0911 -048 0009 1 078 1 <W 1 58 1 96 037 1 08

STM2921 -0.1 0.448 -0.12 0.84 -0.31 0.563 0.304 0.686 0.504 0.628 0.034 -0.16 -0.4 0.178 -0.98 0.382 -0.2 2.2 0.09 1.806 0.07

STM2922 -0.1 0 151 -066 -1 ?fi -053 -036 0525 -1 23 034 -08 -082 -05 -045 0 183 0436 0754 ? 1? 1 08 1 69 0458 0.49

STM2923 0.96 0.971 1.146 0.219 0718 0769 0.251 0.273 0.471 -0.31 D.506 0.243 3.261 -0.2 1.733 0.94 1.42 1.66 0.83 1.167 1.57

STM2924 0.85 0.594 Z746 0865 -0.01 0.825 -0.18 -0.27 0.183 1.651 2.615 -0.26 0.271 0.5 1.551 0.712 -0.7 0.23 2.69 0.829 1.91

STM2925 1.7 1.319 2.683 1.559 0.322 0.664 -0.08 0.849 -0.86 0.468 -0.78 -0.12 0.113 0.782 0.29 0.377 -1.3

-0.55 0.1

STM2926 097 1 401 -067 059 0298 -022 0805 -0 15 0038 0093 -0 13 -067 -0.26 0.966 0.25 0.077 -0.4 0.7 -0.3 -0.8 0.27

STM2927 0.53 0.227 -0.11 -1.17 -0.57 -0.08 0.087 0.079 -02 0.781 0.003 0.032 0.61 -0.15 0.127 0.981 2.01 1.28 2.11 0525 -0.1

STM2928 0.2 0.426 -0 "i -064 -078 0935 0 115 -076 -054 -072 0089 0573 0 161 0061 0.194 1.253 2.17 1.21 2.11 1.409 0.24

STM2929 1.51 0.539 -0.18 -1.59 -0.58 0.354 0.039 -1.46 -0.84 -0.72 -0.48 -0.68 1.266 0.768 -0.04 1.292 1.46 0.75 2.39 0.281 0.95

STM2930 0.93 0.16 -0.23 -1.25 -0.53 0.262 -0.53 -1.15 -0.36 -0.1 -0.74 -0.97 0.19 0.726 0.911 1.144 2.37 1.48 1.78 1.098 0.91

STM2931 0.37 -007 0.268 -1.07 -0.36 -0 1 0383 -0.42 -0.45 -0.54 -0.54 0.035 0.692 -0.21 0.377 1.174 1.74 1 1.62 0.217 0.3 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM2940 17 -002 0464 -048 -023 -041 01180495 -0230294 -058 -063 -013 -121 -1140217 093 -02 048 -06 -07

STM2941 -02 0511 1098 0354 051600050404023500920541 1590322 -086[7ό40207

-06 -120215 -0

STM2942 017 0708 0403 0087 0496 -016 -026 -013 084 -09 -09 -06 -068 045

STM2943 -06 -028 -108 0341 0335 -0240103 -01 -116 -1 -06 -120526 -04

STM2944 -02 -001 -005 0417 -064 -028 -064 -035

-134 -1 i[-16j -13 -096 016

STM2945 -07 -096 -085 -029 0009 0391 -062 -102 -065 -015 -074 -1030534 -026 -055 -037 -12 -08 -02 -052 -03

STM2946 02 0201 -007 -021 -005 -016 -012 -0320336 -0390052 -118 -03 -065 -0980081 -01 047 -08 -12 -06

STM2947 011 094 0506 1134 -058 02280643 -062 -063 -0762456 067 0610387 -0150566 077061 1140569 111

STM2947 117 0414 0035 -056 -045 06150007 -098 -089 #####0437 -017 035060402041123 17 125 2750935 072

STM2948 006 -004 0618 0428 -045 -039 -032 -001 04880422 -057 -073 -138 -107f^"-15tl] -035 -05 -04 -08prέβ] -1

STM2949 -03 0491 0405 -051 -063 -065 -071 -103 -064 -0060063 0050441 -082 -068 -068 076 -02 08 -055 025'

STM2950 046 -057 -04 -09 -126 -039 -0350601 -02 -07 -087 -124 1043 -014 -081 043 026 -04 018 -034 026

STM2951 -02 -057 -093 -053 -013 -03 -012 -084 -06 -087 -0150181 -0070027 -043 -039 -13 -03] ^24MJe] -06

STM2952 003 -031 0048 -112 -038 0547 -018 -083 -066 -099 -042 -038049302230541 0938 181 059 2630678 071

STM2953 063 062 -018 -103 -066 01550074 -124 -05 -111 -072 -064 031 0091 0538 1035 222 108 Z691022 052

STM2954 022 0923 0186 -099 0391 0724 -028 -118 |_-ϊTj -062 -0081338 -0321023 -031 047 042 015 048 -074 004

STM29541ι -01 -074 -146 -025 0984 0129 -013 -198 0312 -01 -0780624 -02401620784 -003 -03 -05 018 -084 05

STM2955S 092 0165 -023 -086 -04 0175 -03F --1186 -06 -137 -006 -002 -002 -036 -O 120387 228 18 166 025 059

STM2956 019 0551 047 -051 0344 0377 047 -00886 -002 -061 -0064903820515 093 144 087 1350757 046

STM2957 -02 0045 -032 -043 -055 -038 -055 -029 0632479330512940423105701050901 066012 0430582 056

STM2958 043 -01 0531 0039 -043 076 -00405970211 2505290821942258 1969 16950988 -11 068 -151392 111

STM2959 081 0057 0493 -026 025 13420322 1346 -014 -01703091194 -022 -0340666 -011 097 06 105 2.07 059

STM2960 119 0208 -014 0966 -01 -012 -047 -001 04560489 -067 -028 -014 -0440376 -032 016 051 032 -122 061

STM2962 -03 -058 -026 0673 -021 -011 02390135 053 -081 -049[^206] -101 01521811 -085 -09 073 15[-154J 156

STM2963 049 0194 0259 ⁰JL⁹Jl -06 -0280318 -0530065 -0780503 -091 0249 -0940338 -09 -01 021 02[_-21β[ 003

STM2964 154 0536 -027 [-1531 -037 -019 -04 -078 -059 -O 65 -013 -001 0444015207460959 175 101 Z260899 109

STM2965 062 0739 -067 -115 -047 0222 -017 -075 -01 -048 -068 -00307690373 -0331057 192 112 211 084 068

STM2967 -01 0111 1025 -041 -017 0546 -073 -007 -127 -027166915760202 -028 -024 069 -03 143 049 -07 -09

STM2968 076 0433 -009 -099 -083 -06 -087 -061 -078 -005 -0380007 021 1131 06050887 04 176 1280949 073

STM2969 007 0586 -021 -03 -011 02460801 107608270131 -084 1181 -13 -146 0130258 -06 -07 -061042 044

STM2970 081 0312 -004 -034 -004 -018 -0420223 -035 ##### -070555 067064304632828 171 081 2080688 071

STM2971 091 0251 0871 0129 -016 0431 04780489 061 -001011206960182113502290057 -11 078 048 -031 036

STM2972 158 119 0184 1006 0656 -0161031 001 1275 -067 -004 096 -057 -080814 221 088 091 065 -027 103

STM2973 039 0322 0494 0564 -004 07804921168 -0191021 -109 -09312509551364 -14 -06 -05 -15 -053 241

STM2974 -02 0363 -079 0089 -104 -007410501 037 ##### -135 -11 1 O52[-1j58] -055 -037 -11 -03 [Ti] -026 -08

STM2976 087 035 0932 0606 0281 0457 0250002 -070342 -0830493030601090357 -064 -04 -02 319 -07 063

STM2977 044 0131 -053 -107 -08 -075 -0320011 -057 -041 -059 OM∑fTδϊ] -108 -0761536 1 -03 014 1059 -01

STM297Θ 117 0591 -042 DLU -028 03980257 -063 -003 -023 -056 -020463002403460708 183 18 160559 088

STM2979 081 0866 0095 -138 -041 0619 -1350395 0930183 -028 -03 -052093301420127 -05 021 -021047 012

STM2980 024 0219 1026 0406 -038 -02 -044 -1140971 1278 D8830782 -045 -01603740362 -09 106 145 -067 058

STM2981 109 0258 -047 0658 -022 -062 0350054 078 -055 -0780605 -127 -077 -015 -07 -01 002 1171881 026

STM2982 -03 -045 0021 0011 -067 -033 -043 -002 -034 -103 -128 -105 -121 -075 -011 -015 -08 -08 113 -051 002

STM2983 022 0776 -046 -116 -068 03340032 -072 -109 -061 D 11400851117 -03301270968 172 126 171 0554 106 - Raw Microarray Fitness Data for Engineered Salmonella

STM2995 -0.57 -0.49 -0.56 0.228 -0.71 -0.51 IJjjH -0.34|-2|l§] 0.338 -0.69 0.99 0.04 -1

STM2996 -0.25 -0.23 -1.13 -0.95 ##### -0.3 0.106 0.332 -0.19 0.422 1.034 1.84 1.01 1.68

STM2997 -0.37 -0.52 -1.02 -1.04 -0.41 -0.72 -1.31 -0.07 -0.66 -0.44 -0.47 0.19 -0.3 0.71

STM2998 -1.28 -0.91 -0.85 -0.72 -052 0.82 -0.5 0.43

STM2999 !5M 0225 0.389 1 053 -0.36 0.85 0.54 0.45

STM3000 -0.14 0.512 1.007 0.396 3.067 1.1 2.5 -0

STM3001

-0.93 -0.05 0.835 0.035 0.203 0.824 1.34 1.45 1.71

STM3002 -0.22 -0.3 -0.54 -0.83 -0.61 -0.15 -0.39 0.407 0.076 -0.04 0.791 1.28 0.73 0.99

STM3003 0.336 -0.05 0.412 -0.55 ##### -0.96 -0.24 -0.2 0.605 -0.45 0.573 1.73 1.19 2.21

STM3004 -0 0.395 -0.1 0.594 ##### -0.71 -025 0.479 0.41 0.082 0.692 1.59 0.93 1.46

STM3004.1i -0.09 -0.08 -0.89 -0.89 mm -306 0.17 0.364 -0.07 0.133 1.464 2.07 1.36 1.82

STM3005 0.794 -0.66 -1.13 -0.79 ##### -0 0.19 0.579 1.417 049 1.302 1.75 0.7 1.99

STM3006 -0.24 -0.1 -0.42 0.598 -0.68 -0.05 jj -0.29 -fl.38 1.029 0.511 0.08 3.43 1.41

STM3007

-035 -043 0.111 0.246 WttmSM -0.78 -0.67Bp] -002 0.61 -1.4 0.33 -1.2!

STM3008 1.129 0.472 0.481 -0.66 ##### -0.27 4.244 0.639 1.58 1.127 0.577 0.4 0.94 1.22

STM3009 -0.07 0.027 0.668 -0.94 -0.76 -0.83 -0.59 0.128 -0.37 2.572 -0.01 0.48 0.11 0.4

STM3010 -0.2 -0.15 -0.12 -0.66 -0.41 -0.82 -0.65 -0.34 -1.08 -0.19 0.276 0.45 0.22 1.04

STM3011 -0.28 -0.23 -0.91 -1.5 -0.17 -0.62 -0.21 -0.13 -036 0.875 035 0.88 0.51 3.71 i

STM3012 -0 15 0.85 -0.19 1 592 -0.26 0.252 -0.7 0.067 -0.34 -0.27 0.303 1.18 0.85 1.3

STM3013 0.737 -0.1 0.232 0042 -0.37 -0.32 -0.75 -0.11 -0.31 -0.46 -0 0.71 2.06 0.85

STM3014 -0.15 0.606 -0.6 -0.19 -0.45 -0.11 -0.54 0.273 0.612 -0.11 1.55 1.62 0.95 1.77

STM3015 -0.01 -0.59 -0.04 1.2 0.47 1.11 I

STM3016 0.653 -0.42 -0.14 -2

STM3017 -0.35 -0.09 -1.26 -2

STM3018 -05 0.338 -1.9

STM3019 -1.22 0.196

-0.93 -0.7 -0.6 -0.5

STM3020 0.204 0.58 0.384 0.781 -0.42 -0.72 -0.75 0.127 0.005 -0.38 0.83 -0.7 0.27 -0.2

STM3021 -0.23 -0.16 0.275 -0.12 -0.59 -0.65 -1.23 -0.61 -1.17 -0.96

STM3022 -0.3 -0.73 -1.29 -0.6 -0.41 -1.07 -O5 -0.74 -0.46 -0.75

STM3023 -0.24 -0.12 -0.62 -1.3 -0.69 1.025[-1.5i] -0.4 -0.55 -0.93

STM3024

-0.61 0.225 -0.54 -1.12 -1.4 -1.12 2.475 0.486 0.093 1.141

STM3025 -0.12 -0.43 0.123 -1.1 0.303 -0.18 -0.3 0.023 0.31 0.496

STM3025.1I 0.338 -0.16 _

STM3026 0.084 -0.72 -1.39 ¹ I^S⁰ 2"!;³0"7" -1.32 ^ m S S AW>^" *] -1.1 05 -0.9 -0.24 -0.14 -1.48 -1.3 -0.9LjJBj

STM3027 .0.54 -1.44 -0.01 ψ:st -0.91 0.045 -0.4 -0.66 -0.47 -0.041 -1.811 -1 0.3 -0.2

STM3028 -0 39 0.256 -0.8 -0.4 1.35 -0.3 -1.11 -0.82 0.415 1.024 -0.33 -0.3 -0.3 0.06

STM3029.S -0.12 0.526 0.811 0.203 -0.83 -1.18 -0.06 0.09 0.338 -0.04 0.181 1.37 0.72 1.34

STM3030 0029 -0.22 -0.22 -1.41

__ri .1 4 ._V13 -o.δF-rβi -2.9I -1.1 -o.eϊ

STM3031 0.02 -0.15 -0.47 f ,-)JBjmtm -0.54 -071 -0.83 -0.25 -0.97 -0.38 -0.9

STM3033 -0.26 0.291 -1.02 -067 -1.12 -1 2 -0.84 0.024 -0.36 -0 3 1.339 -04 -1.2 -0

STM3034 0.105 -0.02 -1.32 -1.16 -0.88 -0.45 -0.27 0.473 0319 0.06 1.293 1.25 0.48 1.69

STM3036 -0 18 0.176 -0.28 -0.64 0.057 0.326 0.825 -0.53 0.12 -0.37 0.014 -0.8 -0.6 -0.8

STM3038 -0.07 -0.1 0.097 0.358 0.374 0.028 0695 0.845 0.156 1.783 -0.85 -0.2

054 -1 Data for Engineered Salmonella

STM3048 0380558 0353 -0440612017302540333 107 03 219 038 04

STM3049 1150167 -085 -051 0793008205170305 176 104 4830652 079

STM3050 019 -006 -058010401080548 -009 046002 612 -103 008

STM3051 047 046 2195 -009 1018 -101 0948 -052 099 -01 -050009 029

STM3052 048 009 -0071107 1073 -049 0140328 -07 033 -09 -005 016

STM3053 041 -041 ##### -095 -027 -02 -06 -059 -06 006 011 057 -017 -01

STM3054 1170553 -003 -0160709 -0140783 125 177 124 231 1079 029

STM3055 -05 -037 1018 -107 -039 -098 -088 -052 -05 001 -02 -108 -07

STM3056 -06 -111

-104 -048 -0150588 -095 -112 -0 -09 119 -036 -01

STM3O57 092 054 016 -116 -026 0064 -061 -098 -098 -0690011 -0140689017702470925 197 112 2120674 089

STM3058 06305850345 -071 -066 0671 -18 -268 -261 -046 D 571 -UM 0157 -02609550493 12 070810747064

STM3059S 028 -099 -122 -107 -044 Ti6Tθ42] -185 -155 mm -131 P-15βl -058 -1080124 -063 13 -040460321 -03

STM3060 113 063 -031 -124 -067 0858 -0150655 -054 -092 -065 -01705930073 0470691 218 086 20262049

STM3061 06606090358 -0130679 008507850299 -0140079 -081 0541 -011 -032 -059 025 146 03 076 -007 -03

STM3062 -03 -026 -0470568 -077 -0020135 -1241079 -018 -0 -05 -041 -0690235 -026 016078 041 -059 021

STM3083 0660044 0810102 -054 -011 00490386 -0 ##### -017 -081 033 -037 -030907 129063 179 066 072

STM3064 126095802760402 -003 -0620732 -036 -0820466 -04900250892 -0171374 -066 391 009 -0 1434 131

STM3065 1 1305059205960618 0081 077301721033 -0181119 -001 080808781336 -002 001 157

STM3066 072 -072 -00906130228 -0190198 0720803 -03202590474 -081 0256 -092289 -03 021

STM3067 036 -015037604130399 0567 -0460178 -143 ##### -051 -002038906480276 -005 -08

-01

STM3068 022 -042 -022 -0440746 00880224 -0.250539 -07 -022 -03802520256 0320395 077 014 1340499 047

STM3069 061 0041 -035 -093 -063 -031 -014 -053 -068 -054 -017 -0160568012302980607 176 069 2340779 -0

STM3070 057 -059 -112 -096 -13 -0450189 -01253 ##### 1338 014 -0681151 -0530106 038 048 027 1761 -04

STM3071 10710590955 -0860105 0571 0238 -06508470528 -016 -1 025816050211 1411 128 012 147 1023 073

STM3072 0771258110800630561 091807160112 085 071 -0070115025924351763 092 053 035 1250897 167

STM3073 11712231391 0061 0486 073801291117197204840969 0670592051530291951 016 335 101 -0 22

STM3074 05801740033 -063 -073 0262 -109 -042 -123 -0380494 -051 0439 #########» 0637 118 118 1680269 062

STM3075 041055 -081 -069 -029 -011 -005 -074 -053 -063 -035 -01204670251 05160628 17 084 2140329 041

STM3076 075 -033 -026 -097 -024 0659 -055 -001 0822 -129 -089 -065 -020352 -0090636 17 145 2450972 031

STM3077 0820541 -O 44 -122 -084 0362 -032 -109 -041 -073 -068 -075 022 0630681 0936 139 167 2250429 029

STM3078 0730212 -00408770589 -0170349 -1 0482 -028 -135 097 -04800240803 -063 -04 -03 053 -016 099

STM3079 S 1030242 -008 ;-Ϊ84J 0057 0089 -025 -055 -0520375 -03 -02202990511 05440319 211 079 1981282 111

STM3080 -02 -058 003 -121 -018 -001 -137 -149 -1480267 -096 -0570102 -075 -04 -026 -04 -08 029 -079 -03

STM3081 -01 0987066906490616 08201170534 -013 -02920060159 -007 068 -0350574 -05 -05 -091611 026

STM3082 0230413 -0220471 -011 0091 -009 -064 -046 -09806550224 -05 -003 -0150462 -01 -0 -11 -06 -04

STM3083 -00121 0413 -015 059 0302052606870019 #####00932132 021 -026 -048 -01 -04 -08

STM3084S -13 -058 -099 -056 -036 -089 -076 -083 -037 -05J -182| -04 -0120481 -123 [ -1 ^"s3| -11 -14

STM3085 -02 -03303240725 -01 0036 -022 -032 -015 -05104330587 1542 -063 -0630353 -1 -03

STM3086 -08 -085 -0640289 -039 -032 -024 -012 -02##S## -07 -081 0121 -127 -0640499 -14

-01

STM3087 060277 -012 .142 -144 0127 -047 -106 -075 -027 -066 -068 019 03602330781 148 128 190638 038

STM3089 0590324 -017 -111 -044 0103 -018 -127 -0940102 -057 -06 -016 -00204761191 187 113 1920475 105

STM3090 042 02 -023] ^~Ξ]--] -⁰³⁶ 05230468 -049 -026 -075 -069 -069022300150655 053 18 135 251 0461 114

STM3091 041 -061 -036 -046 -069 01570432 -026 -037 -118 -094 -12303550813 -052 -007 001 -01 082 -057 -0 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3101 0.6 0.205 -0.21 -0.95 -0.44 -0.01 -0.41 ^131 -0.21 -0.86 -0.56 -0.74 0.17 -0.07 0.043 0.243 1.03 0.31 3.7 0.125 0.66 STM3102 -0.2 -0.6^1.52 -1.771 -0.61 -0.8 -0.11 [-jjδβi -0.3β -0.92 -1.19 -1.01 0.093 -0.58 -0.46 -0.61 0.4 -0.4 0.53 -0.69 -0.1 STM3103 1.36 0.446 -0.34 -1.13 ########## -0.26 -0.08 -1 -0.81 1.182 -0.34 ############### 0.533 1.35 1.04 2.06 0.989 0.37 STM3104 0.01 0.458 0.115 -0.42 -0.04 0.071 -0.01 0.361 0.791 0.402 -0.74 -1.33 -0.61 -0.52 -0.05 0.162 0 11 0.23 0.53 0.21 0.39 STM3105 0.09 -0.8 -0.72 0.23 -0.27 -0.04 -0.15 -0.19 0.093 -0.18 -1.08 -1.29 -0.57 0.217 0.666 -0.51 -1.3 0.85 2.83 -0.29 1.05 STM3106 0.33 099 0.403 -0.3 -0.1 0.442 0.362 -0.48 -0 0.881 -0.23 0.019 -0.18 0.884 0.623 0.534 0.29 0.46 0.23 0.859 0.45 STM3107 -0.2 -0.64 0.303 0.785 -0.53 0.319 -0.79 -0.73 0.024 0.059J -1.6δ| 0.317 -0.73 -1.06 -0.96 -0.01 -0.5 -0.6 -0.2 0.761 -0.3 STM3108 0.5 0.476 -0.39 -1.48 -0.86 -0.2 -0.06 -1.01 -0.48 ##### 0.138 -0.16 1.216 0.247 0.431 0.858 2.07 1.21 1.78 0.201 1.32 STM3109 -1.2 -0.16 -0.25 -0.06 0.031 -0.15 0.981 0.501 0.438 -0.63 -1.25 -0.72 -0.32 2.897 0.523 -0.35] -2-β| 0.13) -2.θ| -1.4 0.39 STM3110 -0.6 0.203 -1.22 -0.66 -0.51 0.154 0.121 -0.82 -0.69 ##### 0.973 -0.91 -0.47 0.723 0808 -0.4 0.98 0.1 1.16 1.392 0.3 STM3111 0.78 0.632 -0.2BpUJIJ -0.28 -0.15 -0.31 -1.24 -0.03 ##### -1.49 -0.22 0.209 0.086 0.284 0.123 1.71 0.55 2.11 0.177 0.14 STM3112 -0.8 -0.36 -0.15 0.208 -0.59 -0.26 -0.23 0.14 0.473 -0.04 -1.22 -0.77 -0.44 putt] 0.007 0.09a[ -1.5| -1 2 [jLs] -1.41 -0.6 STM3113 0.62 0.07 -0.15 -1.07 -0.82 0.368 -0.27 -0.75 0.023 -0.66 -022 -0.49 0.319 -0.51 0.112 0.376 0.91 0.1 0.97 -0.27 0.88 STM3114 2.052 -0.19 D.079 -0.09 -0.04 1.195 0.395 5.434 -0.4 -0.3 -0.1 1.838 1.91 STM3115 0.449 0.362 0.589pJl»] -0.53 -0.03 -0.98 -0.07 -0.27 [_-!§] -0.6 [ -3J -0.57 0.26 STM3117 -0.14 -0.65 -0.21 0.281 0.435 0.635 0.284 1.37 0.61 2.72 0.197 0.34 STM3118 -3.351 1.064 -1.02 -0.09 -0.25 -0.62 -0.5 -0.48 I J-V -0.4 -0.7 -1.1 -0.9 STM3119 --11..4499 00..228822 --00..2288 --11 2266 --11 4499 11..221144 --003311 -1 -0.4 -0.6 -081 0.81 STM3120 -0.6 2.083 -0.37 -0.36 0.3 0.39 0.08 0.276 -0.3 STM3121

-2.77 0.199 1.565 -0.03 -1.05 -0.39 -0.18 -1.4 -1 -0.7 -0.7 -0.81 -0.8 STM3122 0.41 -0.06 0.283 0.626 0.132 0.028 0.174 -0.53 0.809 -0.24 -0.43 -0.63 -0.7 0 19 -0.39 -0.2 -0.9 -0.1 -1.2 -0.8 -0.4 STM3123 0.62 0.064 0.174 1.102 0.484 0.261 0.048 0.298 0.341 -0.51 -0.23 0.791 1.618 -0.77 -0.08 0.369 [ -1Uj] -0 STM3124 0.08 -0.09 -0.24 0.578 -0.01 -0.01 0.211 0.109 0.517 -0.69 -0.64 -0.61 -0.09 1.096 -0.36 -0.27 -1.4 0.09 STM3125 0.05 -0.02 0.057 0.622 0.547 0.527 -0.2 -0.13 0.266 ##### -0.72 -0.4 -0.28 -0.18 0.124 -0.23 -1.2 0.05 STM3126 -0 1 0 166 0.482 0.894 -0.54 0.528 -025 0841 0 176 -0.03 -0.84 0.083 0.394 1.202 0.366 -0 1 -0.9

0.61 STM3127 021 -0 11 0.039 -1 04 -0.18 0.037 0.573 0.607 1.223 ##### -0.92 -0.49 -0.35 0.576 0.12 -0.15 0.71 0.57 O86 -0.21 0.35 STM3128 0.84 0.276 0.028 1 046 -0.45 0.072 0.029 0.306 0.943 -057 -0.36 -0.29 -0.1 -O63 -02 0.352 -0 -0.5 j -1.!JiJ)₁SB -0.5 STM3129 -0.5 0.06 0.984 0061 -0.36 0.699 -0.8 0.295 0.058 -0.16 0.369 0.413 -0.07[VlLKJ 1.54 0.529 -0.6 -0.2; -2 -1.9βJ 1.62 STM3130 0.26 -0.52 0.308 -1.05 -1.26 -0.6 -0.39 -0.25 -0.97 0.784 -0.37 -072 0.209 2.206 -0.02 0.106 096 0.11 0.84 -O4 -0.1 STM3131 -1.2 -1.24 0.363 -0.56 -0.21 -0.25 -0.92 -1.07 -0.39 ##### -0.63 -0.23 -1 03 0.383 -0.36 -0.47 -0.7 -0.2 STM3132 -0.5 -0.31 0.062 -0.5 STM3133 0.43 0.255 0.713 1.143 0.819 1.03 1.255 1.055 1.296 0.031 1.919 0463 1.389 0.897 0.604 0.461 2.23 0.74 STM3134 -0 0.028 0.464 0.874 -0.38 1.028 -0.25 0.975 0.36 -0.05 -1.45 -0.7 1.301 -0.94 -0.31 0.165 -0.6 -0.4 STM3135 0.19 -0.16 -011 -0.27 -0.02 -0.8 0.152 0.072 -0.3 #####) -1.91 j -1.18 -0.9

[ ,^ϊ!e] -0.38 1.172 -1.2 -0.9 1.39 -1.4 -0.4 STM3136 0.98 0.249 -0.04 -0.58 -0.54 -0.17 0.357 0.095 0.619 -0.36 -1.07 1.018 -0.16 -0.27 0.199 1.519 0.66 0.8 0.46 -0.11 0.34 STM3137 0.67 0.168 0.468 -0.91 0535 0444 0.509 -0.17 -0.16 0.882 -0.13 0.181 -0.51 -0.32 0.665 -0.32 0.46 -0.5 3.77 0.97 0.51 STM3138 -0.2 0.063 -0.23 0.866 0.342 -0.06 -0.17 -0.25 -0.04 -0.06 0.099 -0.12 -0.14 -0.55 -0.49 -0.38 -1 -OJHΪJB] -1.3 -0.8 STM3139 0.21 -0.92 -0.45 0.521 -0.05 0.163 0.327 -0.08 0.058 -0.55 -0.68 -0.88 0.071 -0.64 0.865 -0.37 -0.6 1.73L-ZIJ -0.78 0.43 STM3140 0.24 0.477 0.542 -0.97 -0.38 -0.09 -0.04 -0.27 -0.49 0.032 -1.05 -0.57 0.454 0.164 0.416 0.85 1.64 1.37 1.77 0.472 0.65 STM3141 0.83 0.079 -0.05 -1.1 0.355 0.326 0.041 -0.92 2.809 -0.59 -039 -0.26 0.623 0.523 1.359 1.186 2.32 1.02 2.19 077 084 STM3142 0.11 0 134 0.377 0.264 0.441 0.171 -0.64 -1.01 0.674 -0.62 -0.9 -0.05 0.038 -0.22 -0.11 -0.46 -0.9 1.06 0.95 -0.69 -0.2 STM3143 0.5 0.112 -0.43 -1.12 -07 -0.07 -0.52 0.124 -0.72 -0.97 -0j>7 -0.08 1.058 0.338 0.349 0.313 2.24 0.96 1.8 0.243 0.75 STM3144 -0.2 -0.06 0.245 -0.8 -0.79 0.203 -0.36 0618 -0.92 0.168p1 55l -0.91 0.353 -0.87 0.188 -0.45 046 0.07 0.61 -0.78 -04 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3164 -04 -092 -04900590006 -0410182 -0.210302 -097 -021 -029 -1010007 -035 -04 -11 -0β[ -16 -2-31J -06

STM3155 -080056 -04804630261 0105 -028 -047 -015 -05706781477 -015 -006 -0190452 -07 -08 -11 -015 -05

STM3156 -05 -005 -104 -006 -036 -04 -014 -111 -086 -074 -059 -091 -079 -054 -102 -04 025 -08 02 -047 -09

STM3157 -01 -0150352 -077 -047 -055 -0160835 -0350434 -053 -045 -034 -O75QT9] -12 "⁰⁵GlIE ^{^05}

STM315Θ 0680871 0497 -097 -045 0203

-048^74] -02S| -173J -024 -0470396 018 -0230632 151 106 211 1123 087

STM3159 0790549 -023 -005 -05 -035 -039 -126 -086 mm -033 -0170.284 -007 0180499 13047 1990335 036

STM3160 0540355 -043[ -1 Sβ] -022 0467 -06 -064 -068 -119 -072 -0070884034301161276 127 125 229 -023 138

STM3161 -Oβ 0081 04650465 021 -038 013 -01 -0580531 -041 0848 014 -0040036 -096 -04 018 -093033 -0

STM3162 041 00930241 -027 -026 107022403970501 0963 -11 2418 -067047502360204 -03029 141 Z78 048

STM3163 081005216170641 1316 1064 -098 -031 -1

-0940377 -044 -08145 -06 -117 -01

STM3164 062 O 454 -016 012 -033 -02103280435

-0 -148 -04101790517 -01 -03 -1 -081 -01

STM3165 0680475 -O 99 O 369 -013 01871347 -0120398023600880634 -105 011 -047 074 069017 1031309 105

STM3166S 151 06 05520848 -094 06 -0040357 -062 -033 -10603381475 -11707040059 -15 -0 -132401 048

STM3167 -06 -03 -0740442 -012 0025 -0 -0930445 -061 -1440655 -091 -019 -005 -089 -07 -01 -03 006 027

STM3168 -O 201270088 -0530395 -081 -006 -009 -002#a#tf#[T57J -053 -084 -127 -004 -065 -08 -06 -03 -064 -02

STM3169 -01 -05804530195 -034 0458 -058 -007 -021 0157 -04801660649 -008 -029 -045 -01 -07 0290103 -0

STM3170 O 65 O 371 06330443 009 0101 -0295E-040091 0126100503820211 01880211 0312 -09 -02 -23 -072 008

STM3171 -01 -031 018300040332 0213 -007052604730571 -051 0013 -06801630112 -029 -08 -02 .-24 -023 -0

STM3172 1330852 091 1320294 0178020901360152 -005 10203132882 1978 12450529 109071 -060385 148

STM3173 034 001 -018 -1030022 -032 -06 -10307780737 -088 -0350331 023203760397 12082 193 034 045

STM3174 0590447 -02i[T5Tl -078 -031 -058 -068 -103 -099 -03 -0480651 021402351336 256 11 243 064 042

STM3175 036 O 759 1428 O 244 O 523 -037 -013 -001 0861 041 101 0791 -041 -05718070768 065 -01 1240146 136

STM3176 13408951961 -O 5 -O 38 01840177 0060189 -008 -0040168 1316149214160575 169 213 1950687 197

STM3177 070306 -04 009 -043 02730177 -149 -034«WflW> -049 -0440321 033800790236 163 165 20079 077

STM3178 07606960062pT58J -036 0664 -063 -111 -094 -073 -001 -054 -013007202280294 182 072 1490495 007

STM3179 13203150581 -097 -017 0004 -OβipTfβj -003####» 081 -061 0276 -04311580834 078081 1470625 05

STM3180 -01 -065 -025 -115 -05 -045 -053 -063 -072 -07 -115 -112 -06 -014 -0230506 157 024 1620877 029

STM3181 011 0106 0235 -108 -039 0719 -04 -101 0528 -012 -08 -027011802970551 0933 189 129 1850885 04

STM3182 037 -0080153 -1 0123 0575 -031 0014 -048 -03 -04 -017 -001 -00606851026 217 103 1760533 05

STM3183 1931156 1001 19741492 074906520133 -0031048 -0170585086604791325 -033 036 106 128 273 093

STM3184 021 -039 -O 79 -133 -O 65 -0320198 -091 -12 -042 -017 -114 -047 -00401 051 082 035 1770005 017

STM3185 -O 073 -043 -12 -054 -082 -103 j -166j -1090241 -029 -0460132 -046 -035 -028 073013 1390645 053

STM3186 059 -026 -001 -091 -08305640195 -07 -066 -03 -0240197056207320724 1469 21 157 2.321015 071

STM3187 05 -016 -0191153 -0030315 -0040561 0488##### -072 -061 0447 021 0752 -009 -0802θ| 3iZJ0583032

STM3188 066 -02203610215 -038065100070566 068 -03 -043361600660.2980127 -036 057 013 0860323 04

STM3189 0205870892 -1 -03504520801 10531442 ##### 053815280978 08200650543 -07 172 1350556 037

STM3190 0241084 -O 38 -O 57 O 8290096 -1070531 12161481 -0290705 151 148308830525 327 154 0840298 076

STM3191 -030059 O 039 O 196 O 02900250127 -00503 -0280166 -01 00270156 -068 -084[ -16[ -09 0240372 -06

STM3192 061030400670537071803580146 0181101 -031 1483 -0230121 -0560171 0606 -06 091 -120844 034

STM3193 059 -0520384092401170111 02870371 0744 -047 -121 2422033706770448 -071 206 191 -i| -166| -05

STM3194 -06 -07 -O 42 O 144 -O 47 -111 -032 -075037708751631 -098 -0854279 -078 -092 -1 -12 -0 -14 -08

STM3195 O 66 O 01 -05 -145 -O 59 -013 -036 -049 -089 -032 -038 -0640173 -01302040985 2.52 103 202 077086

STM3196S 024 -023 O 03 O 086 -O 670068 -018 -016 -084 -04100610651 -06SpTeI] 0916 -O94[J2L7] -1 -1 1806 051 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3206 103 0044 -003 -104 -037 05530246 -0090747 ##### -049 0080061 -009 03 083 21 093 2020885 085

STM3207 084 0978 -035 0443 038 -109 -012 -06306572175 -06 -0570146 -051 0782[TTTJ -05 -03 5251418 076

STM3208 004 0862 -024 0793 -026 01460664[JJi] -09 -038 -062 -02704920201 -0220683 166 147 1320747 074

STM3209 039 0221 -088 -13 -096 -032 -062 -061 -097 -091 -003 -0840669007701430684 186 143 223 027 063

STM3210 061 -017 0116 -118 -013 07404770785 f-1921 001 -068 -0480316 07908440863 239 117 2471127 103

STM3211 S 061 0558 -008 -121 0024 05960013 -1 -034 -0180004 -021 0575111900860598 186 099 181 1256 071

STM3212 075 046 -005 -056 -043 -016 -045 -072 -074 -085 -007 -059 100401750431 0799 203 1 2010916 1

STM3214 051 -076 1441 -011 -082 -121 1311 058900550445 -107 -016 -044 -1 -0082121 -04 -06 0040173 -03

STM3215 -01 0359 -004 -132 -027 -001 -0630661 1688 -022 -04 0930832162200040275 123 162 1310059 -02

STM3216 -0 -018 -092 -039 -06 -01 -065 -0850023 -041 -076 -0761181 006404020436 132 024 055 -031 048

STM3217 087 -055 0335 -007 0143 0113 -00308670333 #####03230323 -05 -025 -055 -01 -13 -07 0542519 -04

STM3218 197 0808 -062 3211 0596 -009 -015 -03105490338 -139 -086 -055 -084 -0030004 -11 -06 186 j -1δ] 044

STM3219 -01 -03 -032 -093 -054 -052 -031 0612 158 -109 -099 -031 -044 -072 -052 -029 049093 0444236 -02

STM3220 036 0188 0084 -107 0319 0392 -045 -08 -06901550447 007 1055044308390952 17 077 1840902 085

STM3221 031 1012 -004 -101 -034 0031 -046 -041 -138 -0320321 0082 01 036611420805 24 105 2.260311 103

STM3222 019 0751 1552 -035 -053 -028 -024 -107 -038 -06IpTUI -09 -056 -0780009 -007 055061 064 -045 001

STM3223 078 0336 0845 0547 0.222 10240121 -039 -052 -058 -0060026 -049 -09208870364 -06 035 003 -025 069

STM3224 -0 0171 0022 0087 -019 -095007300350191 03030081 -026 -042 -121 0093 -015 -11 -0β[^5| -112 -0

STM3225 036 059 0919 1116 0034 -0 -049 -03604440736 -13 -0161682 -042 021 0505 -1 116 -07 -007 018

STM3226 028 0064 -089 -143 -103 -00014 -1170302 -085 -085 -05 016 -009 0080059 039015 0872921 004

STM3227 055 -015 003 -131 -122 0240404 -0860341 -124 -014 -0130297 -0190091 -001 151 088 151 0135 038

STM3228 057 0505 -085 -134 -046 0599 -008 -1370058 -045 -097 02304170257 -0060481 164 093 2060488 081

STM3229 042 -034 -053 -001 006 -079 -03 -0440736 -008 -082 [5jβ] -0730487 -016 -065 -02 -03 249 -111 -06

STM3230 067 -058 0058 0778 -006 -0440438 -079 174 -006 -0110348 -008 -0240138 -072 -07 096 303 -155 -03

STM3231 -02 -026 -052 -003 0559 0183098407420865074SpHg] 00390098 -0830053 -057 -06 -05 -1 -161 -0

STM3232 066 0392 -031 -093 -022 06240025 -086 -07 -114 -029001902450627 -0770852 183 103 2.321317 083

STM3233 031 -038 -028 -035 0946 0329 -051 -12302390212 -109 -073 -032 -0650202 -001 -02 -08 -01464 -01

STM3234 064 -027 -055 -058 02 0162 -044 -047 -002 -082 -1250332 -039 -017 -032 -017 005 -05 053 -093 -02

STM3235 032 -023 0009 0188 -096 -029018401950821 -0360969 -1272586 -106 0270459 -14 006 -030056 023

STM3236 062 0042 174 1382 068 079205371371 1121 #####221407721445083702650942 -04 146 0861025 059

STM3237 098 0446 -023 -119 -031 -046 -048 -051 -034##### -06 -023 09 -002 016 1167 178 046 225 1014 005

STM3238 057 0253 -005 0045 0321 -061 080382 -069 -014 -028 -08 -053[^"-Ts] 0417 019 -12 -07 -12 -08 -01

STM3239 006 0189 0274 0616 0335 0075 008 -0270141 0674 -083 -008 -0590064 -01 -01 -09 -03 065 -053 033

STM3240 103 -018 0467 -014 -047 -015028405880526 -0270491 06509880113 -0830847 069075 282 -033 -02

STM3241 012 -053 0486 -041 0171 0275 -038 -002 -0460116 -0290283077203340193 -018 071 037 1 0433 039

STM3242 -06 -031 0606 -046 0111 0668 -0130544 071 -0280465 -072715 -0120236 -018 -07 -01 -06 1595 -04

STM3243 019 0302 -039 -022 0575 -004035404050212 -08000328490426 -022 -046 1333 -03 094 -09 -088 -05

STM3244 -02 -039 0129 0029 0096 0049 -024 -0 1171 -025 -082 -078 -027 -033 -02 -063 -01 028 -060385 001

STM3245 -03 -047 0577 0456 0022 0002 -0130053 -0091673 09 -11 -014 -0521417 -026 -14 -04| -2J 1556 117

STM3247 01 0915 075 -033 0542 0355097308030652 -0291303047402820381 08420269 113064 1020754 122

STM3248 164 125 0082 -073 -014 -021023 041 -0320169 -027 -048 -027 -01503440958 161 118 081 0425 069

STM3249 -09 0419 0524 -051 0171 -051 -093 -06 -105268916340642 -01 -0160095 -04 -05 -06 -01 -132 -0

STM3250 -01 0703 0494 -073 -005 0106 -108 026 -039 -012 -094 -101 -084064706260139 001 -02 063 117 052 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3260 043 094 -133 -146 -08905720329 -057 -061 -117 -048 -12707380159 096 2020173 051

STM3261 -09 -02 -013 -047 -046 -106 -046 -111 -12 ##### 2169 -080139 -149

-13

STM3262 -04 -001 -053 -077 -02500410032 -0360056 -116 -076 -08 -00101060496 -014 099105 1190212 019

STM3263 012 -040818 -074 0830997 0460586 -024 -105 -122 018 037 -01800850874 016 17 172 1636 048

STM3264 02100970184 -1170345 -0 -028 -073 -079 -05 -118029305280174 0040469 165068 1930706 105

STM3265 081131 -0461 -15β| -076 -068 -032 -063 -067 -04 -039 -04 -02 -03807330667 21 14 2150584 112

STM3266 0170369 -009 -109 -094 -051 -037J-158J -08##### -085 -0030052 -00102990623 205 13 1940228 028

STM3267 -11 -077 -04 -144 -064 -07309540724 -017 -0921 -1521 -112

-1 is[ -24J -0 β| -2| -079| -17]

STM3268 0650627 -044| -15β{ -0830512 -028 -106 -005 -077 -076 -036 007 -01509210045 191 097 170652 101

STM3269 -04 -058 -044 -074090101980027 -01 -085 -082 -095 -129 0162892 -0220224 051 -0 1113788 -03

STM3270 0730686 -033 -132 -06702970015 -056 -103 -0180004 -040433007502550995 172085 1760346 113

STM3271 0640623 -01 -0950042 -021 -039 -0810115##### -041 -0480392 -01203060497 191 1 130118 023

STM3272 06 -081 -1170078 -082 -059 -092 -057 -0770408 -051 -063 -037 -1 -039 -044 084 133 074 -007 -01

STM3273 -16 -169 -193 -169 -025 -16β[ -117pj^~87J -076#####

-15pT81 -198J -0 θj -18] -14 -036 J ^I

STM3274 0090246 -111 -067 -0280118 -095 -065 -149 -118 -079 -079 -055 -041 -02 -1 -01 -009 -08

STM3275 S 005 -012 079 0545 -1250105] -17θj -04408682035 -071030307311463 055 -04 107 -037 -0

STM3276 032 0330658 0780223 -077027408420001 -0520047 -1070606 -059 002 -05 082369 017

STM3277 -0902570107 0268017701920421 -089 -098 -006 -023 -060475 -036 -14 -11 -¹LiZiI -°¹

STM3278 013 -0250442 0147 -008 -11 -083 -05702410055 -050126 -0330459 QTδ] 028 -11 -105 -06

STM3279 05907020873 -010593 -041 _j£52 ####≠£jjϊ?j -1460603 -13606350052 -09 -07 -15QTeT] 085

STM3280S 0990199 -022 0182 -119 -07^-2 OS] -064 -023 -0150059027308270082 046065 1450754 055

STM3281 0330147 -051 0137 -0240016 -044##### -037 -038 MMU MUM ##### 1075 182085 17 136 076

STM3282 052 -0020228 0088 -065 -109[j204J -106 -095 -019 ##### -00306610159 165083 1650915 12

STM3283 0450504 -008 0114 -042 -046 -005 -119 -082 -061 013040206081427 195 125 222 -011 114

STM3284 0460416 -089 04440142029604260142 -01100920594pTraj -012 004 -01 02 0450071 -06

STM3285 03106070702 0706 -005 -084 -067 -0810092 -0030891 -0108390543 189207 214 09 039

STM3286 0410337 -034 -028 -008 -109 -046 -057 -01600070138001404750739 192 111 1591391 073

STM3287 07403090091 -0770142 -104 -065##### -032 -0480647051203361006 176086 2180776 109

STM3288 1010002 -041 0358 -021 -085 -096 ##### -09 -026 044 05505550263 173098 1950265 097

STM3290S 033 -039 -055 -0540261 -029^296) -027 176 -0320408 -093 -042 -041 -02 -06 -04 -0 -02

STM3291 -010396 -077 02890022 -023 -036##### -125 -061 -036 -06 -0130181 082 -04 051 -021 -03

STM3293 048 -0030229 -056 -08 -078 -127 -131 -081 -0390204 -060012 -01 138 102 15 027 -02

STM3294 -09 -039 -038 -021 0193 -055 -102 -1 -134 -084 -034 -05 -1 -01 004 -062 -08

STM3295 -09 -0650322 -209 -054 -052 01 -O3PT7I -I

-039 -073 -108 -028 -05022 -02 -051 -1

STM3296 0640292 -031 -153 -043 -041 0461 -03 -114 -056 -048 0180477104208130903 201 041 Z690927 083

STM3297 0030649 -047 -037 -049 -111 -065 -045 -065 -011 1151 015906470893 213 146 2021203 084

STM3298S 0380764 -007 -019 -051 (-155J -103 -134 -029 -09802670132 -00889 191 09 1440425 046

STM3299 036 005 -026 -0670004 -123L-Z19J -122 -07 -029 -001 -01703770407 168037 1690664 039

STM3300 -06 -009 -063 -0581721 -04 -032 -0781391 0671 -04 -030197 -089 -06 -03 -02 -098 058

STM3301 0230564 -027 -209 -017 0506 -009 -13 -032 -087 -11 -1050828 -01201030057 223073 1660985 015

STM3303 1150087 -057 -151-094 01590251 -038 -053 -043 -115 -0360049 -01 03750665 156 146 2420512 039

STM3304 1380806 -014 -143 -086 -024 -059 -039 -087 #####0048 -049 0860204 -01 0295 155 099 1610358 115

STM3305 05902590438 -137 -074 0164 -119 -056 -133 -068 -016 -0150316 -0404820928 176 132 143 094 -01 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3315 0.62 0.102 -0.65 -1.36 -0.25 0.106 -0.31 -0.63 -0.76 -0.79 -0.43 -1 0.242 0.462 0.48 0.765 1.7 0.85 1.51 -0.23 0.83 STM3316 0.43 0.144 -0.14 -0.84 -0.98 0.289 -0.05 -1.06 -0.72 -1.31 -0.81 -1.28 0.423 -0.04 0.177 0.634 1.76 0.88 2.24 1.041 0.84 STM3317 0.59 0.176 -0.5 -0.82 -0.59 0.249 0.463 0.682 0.661 -0.29 -0.56 -0.64 -0 0.355 0.44 0.614 1.65 0.71 1.26 0.512 0 STM3318 0.56 ■0 -0.65 -1.43 -0.49 -0.28 -0.76 -0.79 -0.7 mtffitn -0.43 -0.18 0.498 0.093 -0.09 0.855 1.68 1.26 2.15 -0.01 1.14 STM3319 0.43 0.392 -0.44 [jjβ] -1.12 0.208 -0.28 -0.6 -0.44 -0.89 -0.81 -0.21 0.151 0.284 0.614 0.782 2.16 1.16 1.73 1.835 1.33 STM3320 0 0.128 -0.35 -0.87 -0.55 -0.6 -0.2 -1.25 -0.74 -0.59 -0.63 -0.25 0.52 0.156 0.99 1.043 2.02 0.83 2.03 0.959 0.75 STM3321 0.25 0.747 -0.34 -0.77 -0.42 -0.36 -0.2 -0.35 -0.63 -0.62 -0.84 -0.67 -0.48 0.663 0.339 1.099 1.62 0.92 1.5 0.18 0.39 STM3322 -0.1 -0.5 -1.2SpTeT] -0.63 -0.78 -1.35 -0.68 -0.78 0.148 -0.26 0.374 -0.68 1.45 0.08 1.35 0.357 0.88 STM3323 0.48 0.307 -0.35 -1.03 -0.37 0.175 -0.96 -0.73 -0.28 0.391 0.043 0.703 0.911 2.01 1.05 1.7 1.253 0.8 STM3324 0.58 -0.48 -0.71 [TpTj -0.8 -0.6

-1.08 -0.62 0.51 0.695 -0.04 0.798 0.681 1.32 0.66 2.08 0.403 -0.1 STM3325 0.35 0.062 -0.24 -0.39 -0.24 -0.31 -0.15 -0.31 -0.14 -0.88 0.664 0.117 0.256 0.339 0.025 0.382 0.63 0.71 1.07 0.662 0.37 STM3326 0.06 0.533 0.263 0.775 0.185 0.573 0.505 0.489 0.315 -0.19 0.271 0.798 0.81 0.079 -0.01 0.056 -0 0.67 0.59 1.897 0.33 STM3327 -0.2 -0.39 -0.58 -1.27 -0.97 -0.47 -0.11 -0.12 -1.27 -0.36 -0.44 -0.15 -0.07 -0.05 0.098 0.062 1.38 -0 1.6 0.72 1.27 STM3328 -0.7 -1.3 •0.26 -0.6[ -1.7β| -0.77 -0.62 0.4351 -2.45| -1.42J --ZZ0( 7 ,,-1.87 -0.99 -1 -0.9 -0.89 0.13 -0.5 -0.1 -0.63 -0.8 STM3329 -0.4 -0.09 0.166 0.389 -0.35 -0.26 0.364 -1.07 -0.12 -0.76 -0.05 0.804 0.185 3.281 -0.75 0.53 0.07 -0.3 1.45 -0.17 -0.4 STM3330 0.45 0.946 -0.79 0.545 1.164 0.42 -0.17 -0.88 -0.8 -1.38 0.068 -1.48 -0.79 -0.81 -0.84 -0.28 0.02 0.43 -0.4 -0.31 -0.8 STM3331 -0.9 -0.71 -0.34 -0.89 -0.75 0.446 8E-04 -0.31 -1.2 -0.69 -O47 -0.37 -0.86 -1.08 -0.64 -0.96 -1.4 -1.2 -1.1 -1.43 -0.7 STM3332 -0.4 -0.75 0.218 25 -0.7 -0.62 -0.38 -0.54 -0.43 #*###f-1.92] -1.46 -0.54 -0.22 -0.99 -0.43 -0.4 -1.1 -0.1 -0.74 -0.3 STM3333 -0.1 -1.11

0.156 -0.21 -0.71 0.378 -0.42 -1.16 -0.65 -0.19 -1.19 1.131 -0.3 -0.1 0.35 0.69 -0.61 0.8 STM3334 -0.8 -0.03 -0.53 -0.69 -0.03 -0.38 0.303 -0.36 -0.43 -1.1 -0.63 0.108 -0.63 -0.92 -0.4 -0.78 pTsl -1.3] J³A-IlSl] -°⁸ STM3335 0.75 0.361 0.046 -1.51 -1.53 0.021 -0.51 -1.18 -.1.52 -0.31 -0.77 -0.88 0.483 0.732 -0.17 0.868 2.3 1.41 2.32 -0.08 -0.3 STM3336 -0.2 0.169 -0.12 -1.39 -0.23 00..441144 --00..5599 --00..5577 F: 2-2::2266 --11..0033 --00..5566 00..4477 00..005588 00..6699 00..332288 00..000055 11..0066 00..9955 1.03 0.154 0.32 STM3336 -0.8 -0.23 -1.14 -1.42 -0.7 0.34 -0.67 -0.67 ψn -0.7 -0.14 -0.21 -0.14 0.012 -0.09 0.94 0.93 0.8 0.272 0.22 STM3337 0.54 -0.27 ■0.87 -1.22 -0.68 0.049 -0.57 Qi .72 -2:ϊβj##### -0.58 -0.56 0.003 0.137 -0.2 0.456 1.47 0.48 2.05 0.476 0.6 STM3338 -1.2 -0.29 -0.43 -0.45 -0.48 -0.77 -0.25 -0.39 -0.7 ■0.9 -1.11 -0.6 -0.79 0.233 0.134 -0.53 -0.8 -0.2 -0.7 0.2 STM3339 -1 -0.12 -0.65 -0.63 -0.9 -1.19 -0.72 -1.05 -1.43 -0.78 -0.03 -1.01 -1.4 -1.34 -0.54 -0.75 -0.7 -0.6 0.06 -1.35 -0.9 STM3340 -0.9 -0.35 1.017 -0.55 -0.33 -0.08 0.806 -0.51 [l^δ -1.15 -1.28 -1.03 -0.72 -0.71 -0.5 -0.17 0.88 -0.3 1.13 -0.18 -0.1 STM3342 0.09 -0.74 0.273 9E-04 -1.11 0.133 -1.24 2.223 -0.92 -0.41 1.846 -0.89 -1 0.179 0.161 -0.53 -0 0.28 0.05 -0.69 -0.4 STM3343 -0.7 -0.16 -1.22 -0.19 0.525 0.221 0.588 -0.14 0.433 -1.09^-2.46 -2.11 -0.68 0.372 -0.1 0.676 0.06_. 0.15 4.41 -0.45 -0 STM3344 0.54 0.385 -0.82 -1 -0.8 -0.25 -0.67 -0.88 -084 -086 -055 -021 0242 0018 -086 1 103 1 93 1 ?3 1.71 -0.51 -0.2 STM3345 0.75 0.149 -0.17 -1.42 -0.84 0.237 0.125 -0.98 -0.87 -0.73 -0.56 0.058 0.233 0.242 0.049 0.124 2.33 0.95 2.65 0.581 0.89 STM3346 -0.6 -0.7 JΪU -0.76 -0.84 -0.5 -0.03 -1.33 0.657 -1.21 -1.21 -1.71 0.092 -0.36 -0.3 -0.6 0.2 -0.62 -0.6 STM3347 -0.2 -0.39 -1.21 -1.31 -0.31 -0.68 0.172 -0.72 0.188 ##### -0.27 -0.74 0.275 -1.18 -0.77 -0.41 0.49 -0.9 0.7 -0.74 -0.9 STM3348 0.23 0.609 0.21 -0.81 -0.7 0.779 0.051 0.505 0.165 -0.56 -0.5 1.766 -0.01 0.783 0.211 0.064 1.03 0.69 2.52 1.281 0.96 STM3349 0.4 0.196 -0.42 -1.86 -0.8 0.209 -0.25 -1.21 -0.83 ##### -0.57 -0.39 0.253 0.189 0.839 0.414 1.62 0.78 1.73 1.034 0.59 STM3350 1.26 0.165 -0.14 -0.59 0.043 0.133 -0.27 -0.85 -0.41 -0.42 -0.83 -0.06 0.136 -0.23 0.17 3.43 0.92 1.84 0.728 0.59 STM3354 -0.5 0.005 -0.3 -0.47 0.549 -0.43 -0.51 -0.78 -0.92 -0.51 -0.72 -1.07 -1.46 0.486 -0.38 0.155 -1.1 0.05 -0.4 1.358 -0.2 STM3355 -0.9 -0.6 -0.1 -0.15 -0.04 -0.66 -0.32 -0.64 -2.36 -0.5 0.847 -1.07 -0.71 4.881 0.116 0.457 -1 -0.2 -1.721 0.68 STM3356 -0.9 -0.39 -0.07 -0.32 -0.03 -0.71 -0.04 -0.51 -0.79 -0.72 0.095 -1.11 -0.37 -0.73 0.357 -1.45 -1.2 -1.5 STM3357 -0.39 -1.62 -0.79

-1.4J -1.8 0.42| -2.91 STM3358 -0.5 -1.94]

-0.2 0.54 0.24 0.76 0.045 -0.4 STM3359 0.32

-1.18 0.564 -1.1 -0.92 -0.57 -0.15 0.284 0.61 -0.02 0.87 0.8 1.4 0.485 0.56 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3370 -020478 -042 -081 -127 033 -049 056 STM3371 I -1 ej -131 -039 -064 -127

-04 -066 -0 STM3372 0820341 0276 -05 -018 0472 -00603010195 ##### -033 -0440275 -024 -0140874 184096 1040027 104 STM3373 045 02 -016| -1 S2J -061 0152 -021 -072 -06 ##### -07903960898059907560791 209 117 1980837 077 STM3374 -00253 -025 -130107 037 -015 -12 -059 -068 -063 -05204860524 -0260511 17 123 2020481 108 STM3374 1t 058 -049 -OO2I-I52I -019 03580129 -122 -099 -105 -0390068041904060398 041 159089 2530772 081 STM3374 1(033 026 0044 -123 -118 -0430044 -141 -075 -055 -014 -0380641 -039 -0130447 174 148 2720545 069 STM3375 -04 -034 -14 -063 -111 -090691 -004 -003 -112 -085 -0960186 -014 -071 -029 14 -02 091 -054 -02 STM3376 0520185 0117 0020215 -06705710306 -011 -033 -086 -054 -056 -0820921 -062 -14 124 088 -105 074 STM3377 -09 -101 0383 -124 -032 -082 -09 -082 -028 #####[T_5j] -032 -0610252 01 -052 -05 -1 211 -046 007 STM3378 -03 -047 -O 31 -116 -072 -03 -092^-154] -086##### -056 -0410304 -056 -029 -02 094 -04 062 -028 -0 STM3379 0830598 -013I-I 89J -061 0668 -03 -098 -075 -033 -024 -0550235 -03903221124 223102 2130869 034 STM3380 0230104 -025 -109 -056 -015 -031 -1 -06 -07 -01 -0330267004503141291 158 14 1970274 09 STM3381 0520293 -077 -1 -072 0018 -088^-17β| -118##### -077 -060521026904861182 145135 119 072 074 STM3382 040484 -027 -116 -035 -057 -077 -126 -0920488 -077 -036 -0330279 -0730042 014042 067 175 042 STM3383 091 0381 -0220085 -126 -009 -062 -031 -077057704721461 1024 157 119 1990817 125 STM3384 -04 -128 -059[TM] -071 -105059401190929 -004011710910196 -11 013 -06 -04 072 STM3385 -08 -134

-117 -119 -122 -081 -058 -0421914 -043 -003 -022 -051 -08 -1 048 -057 -02 STM3386 -020198 -007 -009 -0090614 -038 -07[^"T&B| -031 -088 -004 -027JTIj 005f Tβ] -076 028 STM3387 0570396 -⁰⁴⁸GHI -⁰⁵² 0192 -OI3QT53J -089mm -022 -0070396013201681013 264 137 2.42 -002 006 STM3388 017 -015 062 -010605 -02 -05 -126 -028 -006031900170008 -04601290508 068 102 090775 062 STM3389 -020569 1017 -084 -01 063502420617 -047 -055 -035 -013 034090803350399 105 089 1470171 081 STM3390 0200630111 -05 -021 015 -0190168 -0620258 -109 -028 1102 024 043 -054 026 -01 0130371 04 STM3391 0320435 -031 -0040547 -033 -023 -04603020131 0172 -016 -038 -00426480497 05 001 10041 244 STM3392 078045304080737 -045 0121 0395 1689 015 ##### -011 0650576 1522 107 -02 -0 019 13 -014 116 STM3399 19039909830409 071 04990564 164 -021 ##### -118 054 1203 -05 -021 0223 032 062 0180561 1 STM3400 077 -0420778 -0460492 045300890555 -122 -038 -111 -054 1066 -026 -0660591 049037 0161 -173 -04 STM3401 039 -118 -056 -032 -046 -112 -045 -102 -0130248 -0160586010612040238 -025 -17 -16 -25 -Z76 02 STM3402 0580288 0029 -103 -093 0502 -076 -029 -072 -056 -048 -013 -003067902221054 189082 2390366 088 STM3403 0570416 -045 -147 -053 -004 -Oi|Tjl9Jθ159##### -048 -03904380457 -001 05 183 112 2060479 109 STM3404 -01 -056 1184 -057 -071 -0420347 -141 -064 -0140008 -1170002 -078 -12 -102 -1 -09 -12^-226] -1 STM3405 12101330926115500560837 -024 -025 -1303511118 -045 0310746 060793 -03093[ -Z4| -017 052 STM3406 0620313 -053 -148 -0790104 -051 -119 -061 -071 -036 -0550169 -0211170778 146 123 1961304 106 STM3407 053 -006 -018 -0640471 0174 -132 -27{_-08 -019 -047 0210275 00204580552 149088 1770887 025 STM3408 -01 -045 -033 -085 -126 -031 -051 -191 -IU4] -092 -039 -058 -054 -0680674 -026 128 -04 115 -039 042 STM3409 027 -025 -003 -083 -067 -009 -042 -115 -031 -05 -037 -0460406 -0307550646 17046 1940877 084 STM3410 040606028801070435 01740459 -0040716 -053 -0861292 065 -0300350124 -02021 -03 -088 -02 STM3411 0590354 041 0089 052 00680111 -0060366 -048 -079 -066 -035 -045 -0370162 032 03 -03 -056 -04 STM3412 -01 -038 -046 -075 -014 0336 -022 -075 -038 -0850516 -106 -015 -013 -059 -025 114 -0 164 -03 -02 STM3413 -11 0011 1230306 026 1095 -031 079[TjWJ -08 009 -113060201441438 -038 -1 064 -14 -124 096 STM3414 011 0555 -015 -0980334 0420054 -00301872141 -054 -0390801052607230778 224084 2120374 11 STM3415 0860049 -022 -099 -06 -071 -039 -072 -085 ##### -03900340725071802520713 192 134 1830785 075 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3426 0.8 0.877 -0.23 -1.39 -0.16 0.261 -0.65 -0.66 -0.45 ##### -0.55 -0.12 0.66 -0.18 0.556 0.951 1.81 1.05 2.29 0.403 0.61

STM3427.S 0.46 0.209 -0.34 -1.16 -0.96 0.206 0.031 -0.87 -0.48 -1.14 -0.38 -0.37 0.898 0.111 0.102 0.411 2.1 1.56 1.85 0.322 0.71

STM3428 0.37 0.127 -0.69[-174] -0.41 -0.16 -0.28 -1.4 -0.8 -0.77 -0.35 0.38 0.602 0.162 0.604 0.743 2.04 2.03 2.54 0.52 0.62

STM3429 0.63 0.201 0.081 -1.43 -0.32 -0.01 -0.28 -0.82 -1.04 -0.67 -0.57 -0.91 0.838 0.331 0.256 0.976 2.08 1.03 1.88 0.795 1.18

STM3430 0.82 0.198 ■0.54 -1.46 -0.83 -0.04 -0.53 -0.25 -1.09 S#### -0.54 -0.61 0.776 0.186 -0.02 0.537 2.19 1.58 2.53 0.331 1.03

STM3431 1 0.395 -0.56| -1.78[ -0.17 0.143 -0.49 -0.97 -0.79 ##### -0.54 0.071 0.227 0.256 0.02 0.724 1.93 0.83 1.9 0.733 1.1

STM3432 0.99 0.54 0.385 -1.36 -0.4 -0.57 -0.08 -0.46 -0.76 -0.13 -0.67 -0.05 0.229 0.136 0.617 0.879 1.8 0.62 2.62 0.299 0.8

STM3433 0.68 -0.19 0.108 -0.85 -0.67 -0.26 -0.05 -0.66 -0.6 -0.8 -0.56 -0.61 0.194 0.57 0.833 0.843 2.03 1.23 1.87 0.779 0.56

STM3434 1.14 0.642 -0.79 -1.09 -0.45 -0.35 -0.1 -1.14 -0.59 -0.65 -0.49 -0.22 1.171 -0.66 1.046 1.169 2.38 1.3 2.5 0.652 0.84

STM3435 0.41 0.283 -0.53 -1.44 -0.44 0.231 -0.27 -1.22 -0.56 mm 0.141 -0.35 -0.5 0.032 0.378 1.408 2.17 0.9 2.42 -0.43 0.09

STM3436 0.68 0.081 -0.58 -0.03 -0.37 -0.57 -0.8 -0.68 -0.82 -0.1 0.922 0.766 0.396 1.379 1.64 1.09 2.4 0.267 1.06

STM3437 0.39 0.296 -0.29 0.562 0.579 -0.2 -0.49 ##### -0.55 -0.24 0.15 0.463 1.138 1.014 1.74 1.7 1.96 0.203 0.88

STM3438 0.95 0.773 -0.69 -0.27 -0.18 -1.01 -0.93 -0.6 0.023 0.22 0.43 -0.15 0.289 0.565 1.53 0.55 2.61 0.551 0.11

STM3439 0.52 0.314

-0.13 -0.16 -0.26 0.49 -0.86 mm -0.45 -0.24 0.676 -0.19 0.557 0.408 1.97 1.09 1.7 1.114 0.66

STM3440 0.65 0.352 -0.4 -1.32 -0.05 0.147 -0.27 -1.11 -0.17 ##### -0.16 -0.16 0.41 0.214 0.598 1.255 2.13 1.29 2.21 1.182 1.26

STM3441 0.8 1.221 0.324 -0.27 0.071 0.06 0.432 -0.11 -0.63 ##### -0.54 0.178 0.395 0.39 0.882 1.154 2 1.48 4.31 1.04 0.96

STM3442 0.4 -0.19 0.139 -1.21 -0.68 0.68 -0.48 -1.2 -0.26 -0.9 -0.53 -0.77 0.772 0.059 0.028 0.255 2.25 1.5 2.21 0.287 0.52

STM3443 0.54 0.179 0.959 -1.61 -0.69 0.952 -0.6 0.919 0.803 -0.19 -0.4 -0.32 0.577 0.317 0.386 0.275 1.19 1.2 1.67 0.102 0.84

STM3444 0.34 -0.23 0.064 XIL92 -1.26 0.638 0.305 1.076 0.309 -1.29 -0.62 0.132 0.29 0.878 0.205 0.474 1.61 1.09 1.85 0.307 1.48

STM3445 -1 -0.79 -0.33 -1.63 -1.86 -1.23 -2.53 -3.41 ##### -1.41 -0.32 -1.33 -0.76 -1.28 -1.25 -0.4 -0.9 0.17 -0.71 -0.1

STM3446 0.17 0.227 -0.39 -1.43 -0.99 -0.24 -0.14 -1.11 -0.53 -0.95 -0.36 0.209 -0.26 -0.01 0.097 1.049 1.88 1.16 2.44 0.669 0.19

STM3447 1.18 0.63 -0.12 [JΛ] -1.18 -0.07 -0.24 -0.51 -0.51 -0.14 -0.65 -0.38 0.695 0.042 -0.02 0.641 2.37 0.83 2.2 0.563 0.64

STM3448 0.35 0.279 0.154 -1.28 -0.86 0.204 -0.35 -1.01 -0.18 ##### 0.403 -0.2 -0.1 0.09 -0.01 1.398 1.53 1.35 2.6 0.56 0.97

STM3449 0.53 0.465 -0.04 -0.83 -0.94 0.317 -0.41 -0.65 -1.02 ##### 0.092 -0.08 0.337 -0.01 0.224 0.649 2.23 1.14 2.07 0.28 0.67

STM3450 0.25 0.821 -0.35 -rO5 -0.33 0.139 -0.43 -1 03 -085 -1.01 -0.45 -0.25 0.596 0.014 0.517 0.799 2.62 1.23 2.28 0.563 0.7

STM3451 -0.1 0.233 0.009[ -169l -0.05 -0.28 -0.97 -0.96 -0.47 ##### -0.12 -0.55 0.12 0.245 -0.25 1.39 2.08 1.02 1.87 0.162 0.41

STM3452 -0.7 0.042 0.337 -0.58 -0.04 0.071 -0.12 0.779 0.022 -0.44 0.323 0.068 -0 -0.15 -0.17 -0.03 0.24 0.43 0.1 -0.83 0.35

STM3453 -0.3 -0.57 -0.7 -0.36 -0.29 -0.35 -0.66 -0.75 -0.53 -1.47pf79J -1 -0.2 -0.83 -0.16 -0.57 -0.6 -0.6 0.55 0.423 -0.2

STM3454 -0.4 0.269 0.725 -1 -0.39 0.619 -0.84 0.645 -0.97 -0.59J -1.67J -0.51 -1 -0.98 -0.93 -1.17 0.22 -0.9 0.08[jjj4J -0.4

STM3455 -0.7 -1.08 -0.32 0.513 0.243 -0.52 -0.12 -0.04 1.262 0.118 0.287 -0.05 -0.12 0.034 0.157 -0.19 1.42 -0 0.72 0.104 0.75

STM3456 -0.5 -1 2 /1.62] -0.73 -0.26 -0.56 -0.27 -0.08 0.508 ##### -0.99 -1.05 -0.16 -0.11 0.003 0.013 0.8 0.7 1.05 0.141 0.35

STM3457 1.27 0.587 0.86 0.574 0.089 0.338 0.418 0.954 0.792 1.122 -0.36 -0.02 1.023 1.458 0.621 0.825 -0.8 0.65 [ 5] 0.496 1.09

STM3458 0.91 1.117 1.221 0.749 0.217 0.142 0.855 0.232 -0.34 1.948 -1.39 -0.85 0.242 1.119 -0.49 0.059 0.78 0.32 0.68 0.027 -0.2

STM3459 0.87 0.822 0.999 0.649 -1.24 1.197 0.28 1.366 0.517 -0.33 -0.05 1.003 0.266 -0.19 0.323 -0.97 -0.5 -1.21 1.07

STM3461 -0.6 -0.81 -O.29I -I.64! -1.37 -1.3 -1.17 ,-2.43 ^' ;-1.β] -0.77 [vlΛβ] -1.43g§fpz| --i.24ψiM^:$-€ώ}

0-52 -1.27 -0.9

STM3462 0.73 0.964 0.173 -0.93 -0.52 -0.26 0.153 -0.57 0.614 -0.1 -0.19 -0.51 0.257 0.367 0.929 0.092 0.53 0.17 1.49 0.648 0.83

STM3463 0.95 0.332 -0.1β| .,-2.i| -1.43 0.287 -0.09 -0.78 -0.74 -0.78 -0.61 -0.21 -0.46 0.328 0.197 0.553 2.88 0.59 1.62 0.419 0.79

STM3464 1.07 0.284 0.338 0.534 0.907 0.578 0.934 0.833 1.517 0.459 -0.06 0.691 0.711 0.148 0.248 0.169 0.08 1.83 -0.1 0.796 0.32

STM3465 0.56 0.442 -0.74 -0.51 0.224 -0.49 0.132 -0.91 0.036 -0.96 -0.82 0.151 -0.29 -0.64 -0.65 1.195 1.04 0.53 5.27 0.356 0.11

STM3466 -0.1 0.107 -0.43 -0.95 -0.49 0.213 1.064 1.625 1.864 ##### -0.89 -0.24 0.031 -0.09 0.514 0.891 1.01 0.82 1.59 0.795 0.95

STM3467 -0.1 0.623 -0.67 -0.13 -0 -0.52 0.006 -0.48 -0.21 -0.05 0.635 0.271 -0.4 -0.67 0.336 -0.1 -0.2 -0.1 [^tθ] -0.18 0.39

STM3468 0.53 0.067 0.531 0.101 -0.05 -0.53 0.029 0.961 0.823 0.28 -0.09 -0.23 -0.73 -0.96 0.229 0.547 0.53 0.44 0.46 0.243 0.55 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3478 -04 0307 -045 026 -02034403030411 -008 ##### -06907790444 1180481 043 -0 044 056 -022 066

STM3480 087 0107 -015 -122 -034 -032 -018 -079 -117 ##### -114 -0830272030300050624 222 102 187 108 101

STM3481 019 -036 -045 -102 -105 -069 -054 -0390151 -131 0864 -0750166004800250177 117 021 114 -002 -03

STM3482 01 0606 -083 -117 -0380088 -0020825 -077 -057 -125 -0640114024900190964 198 104 210859 033

STM3483 029 0061 -066 -096 -07 -013 -059 -125 -08 -126 -078 -0590073 -002 -00486 152 148 2450681 113

STM3484 003 -024 -004 -111 (-1SJt] -068 -105[T77J -116 [TK] -124 -129 -00402310397 -02 032 -04 1340041 037

STM3485 017 0267 -086|-184|^0270091 -034 -135 -101 -103 -064 -061 0646053600090814 177 078 1840316 049

STM3486 -0 0246 -084 -121 -0870154 -035[TjS4) -108 -074 -071 -0570142 -028 -0410373 095033 1910557 065

STM3487 079 0066 -003[Ta-] -041 -013 -056 -1 -096 -046005700021025092802220722 163 099 1550399 068

STM3488 -03 -021 -0150119 -002 -0680674083801960144 -044 -0520054 -0090382 -033 074 -02 1030719 051

STM3489 -03 -013 -077 -042 -0060371 -086 ΓTΞ -069 -0403350591 11290931 05 -032 133019 242203 192

STM3490 06 0439 -02 -080032060300270624 -143 ##### -031 0529 -01604460481 0118 087039 1372752 072

STM3491 036 0663 -058 -1,78] -041 0092 -038 -081 -0.29 -097 -0190121 0446019702260704 166 122 1990567 073

STM3492 -04 1133 -192 -0540745 -0670965 -0780973 -084 -022 -147 -03 -023 -015 124 439 -0₂[

STM3493 018 0599 062407190088 -038065306180435 -0470152 -036 -089 -052 -071 -031 -12 078 ^"1-0131--0¹³8⁵8 -0°³5

STM3494S 074 027 -024 [^22] -066 -004 -041 -0680031 -08 -0360173023603140411 0653 222 174 1921011 092

STM3495 068 0089 -025 -047 -025 -016 -001 -073 -068 -087 -051 -001 0273021507140837 203 126 2150947 025

STM3496 062 0387 0917017210080639 -056 -12 -135 -093 D 573 -0592685 -0650833 -068 003035 250137 119

STM3497 048 -007 0079 -111 -082 -012 -016 -092 -057 <#### 0108 -0550699 -04901580398 199 112 2280355 066

STM3498 02 032 -016 -141 -035 -024 -057 -149 -055 -062 -074 -091 -002 -002 -0330308 176 04 ^71 087 072

STM3499 -05 0564 -0150393 -009 -061 -005 -0080241 -022 -088 -086 -101 -05 -059 -119 -1 -08 _Tβ] -142 -05

STM3500 013 0329 05480112 -0330553 -009 -091 -062 -077 -088 1591 0440799 -0230165 009 04 025 003 028

STM3501 072 033 -001 -107 -00076 -0950124[TM] -013055304270742094304181485 122 127 217 1896 111

STM3502 068 0459 -054 -08 -0.24 -0290065 -058 -113 -082 -037 -030637010505631186 182 109 2070537 105

STM3503 014 0102 0156 -044 -05 017 -001 -0970873 -076 -086 068 045078904590325 167 068 1250775 111

STM3504 -05 -009 -059 -031 -0290336 -011 -041 0158 -086 -025 -058 -003 -021 -002 -089 -08 -06 -05 -039 006

STM3505 041 0341 0129 -099 -02 -017 -013 -018 -134 -098 -088 -07206560221 0481 0378 077 079 2070273 137

STM3506 -13 -083 "⁰⁶⁸L^yL-"!**?] "¹²⁵ '¹ ^ ^{^008} "°³⁷ -073139502641858 -141 092 -045 -06047 -032047 143

STM3507 015 1142 0151 -09 -0480355 -02 -075 -009##### -103 -0650143 073 021 0786 285 091 2270552 044

STM3508 008 0312 -0290043 005 -0120165 016 -004 -08 -071 -027 -07442760266 015 -06 088 16 -054 08

STM3509 -11 -046 -065 -114 -0.29 -1_040275 -016 -041 -111 -07[TJT] -041 -08 -103 -034 241 -08^ -32 -214] -13

STM3510 -03 0005 -084 -14 -05i[_-1_5β] 0260293_^ -126 -0630201 -118 -0660108 -105 -069 684 029 -211 -137 -09

STM3511 023 -08 -098[T76] -076 -082 -082[Tjκj -04 -028 -102 058 -0540261 -049 -026 039 -01 056 -053 -05

STM3511 001 -025 -⁰⁸LLU?] -⁰⁹⁸ -06 -053 -134 -05 -029 -071 0506 -0580515 -058 -036 084 -01 068 -026 -01

STM3512 -09 -046 -096 -132 -003 -067 -067 -015[TUT] -039 181 \ -1 SsJ -12 -088 024 -08 -06 -09 -04 -051 -08

STM3513 034 0568 -028 -08814190391 -026 -1340002 -006 -006 0160122 -07205430028 168045 1490357 055

STM3514 -04 -039 -051 -069 -0580215 -066 -025 -068 -029 -077 -095 -132064 -022 -128 -06 -06 -09 -043 -08

STM3515 -07 -105 -088 -052 -02 -06 -024 -055 -007##### -088 -049 -077 -056 -044 -136 -05 -06 -00011 021

STM3516 -06 0098 0364 -096 -0480025 -066 -044| -1731 -041 -171 -132 -00701150297 -02 -02 -0 045 -037 08

STM3517 -13 -051 -0280256 -0020466 -073 -017 -099 -048 -16 -074 -121 -107 -055 -057| -1 e] -01 -11 -09 -01

STM3518 059 0241 -023 -114 -0630924 -032 -118 -056 -053 -014 -020575046311510938 183 103 2160821 078

STM3519 -04 -009 1004 -079 -04 -09102661054 -034 -084 -1011-161] -058 -0240312 -112 009 -02 003 06 018 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3532 -02 -041 -005 01810062 -028 -0170035 -028 -0080118 -062 041 -05 -071 -09 -11 -06 -01 -075 -08

STM3533 001 0126 -062 -046 -097 -028 -108 -0220471 -1140258 -068 -052 -037 -020187 047 -0 128 -002 001

STM3534 -08 -111 -047 -041 -043 -144 -076(^289] -092 -037J -163] 2273 -133 [T∞] -0620344 -07 -11 -05 -033 -0

STM3535 -051178 -011 -0420652 -040855 -0330478 -0140048 -051 -09 -1380251 -073 035 -09 024 -041 014

STM3536 -06 -017 -06 -019 -025 -020075 -0220126 -037 -013 -042 -064 -054 -005 -01 -08

-04

STM3537 -007460533 -0880128 -0480008 -012 074 -018098501820205 -0420049 047 101 014 0470093 049

STM3538 -0 -048 -088 jsraj -116 -078 -027 -0740759 -0760039 -111 -088 -108 -076 -081 02 -05 1590262 -01

STM3539 0450689 -052 -097 -051 -001 -005 -127 -086 mm -019 -0270426 -01804020693 249 144 151391 108

STM3541 021 014606360454 1141 0248079603950321 -033 -021 0974057911080555 -027 085 188 0550523 089

STM3542 014 -014 -043 -143 -041 0006 -04 -016 -074 ###*# -089 -094 028038406180868 201 135 157 099 069

STM3543 -03 -121 023 -O83f?57j -058 -097 -003 -117 -094 -091 -124 -124 -106} -176J -084 002 -1 -09 -006 -13

STM3544 0891057 -019 -075 -059 0316 -006 -03303630355 015 -00800120544 -004 -034 116 105 1550355 064

STM3545 0120001 0121 09380212 -031 -0250703 -004 ##### -028 -099 -074 -0891618 -116 -12034 137( -1781163

STM3546 -03 -0070846 -0090425 04800260043 -023 -02 -0290031 -125 -1370645 -033 234 -06 -17 -159 06

STM3547 Si -07 -025 -04202830449 0223 -045 -062 -064 -027 -064 -041 -017 -01 -001 -086 -14 -07 -33 -074 -04

STM3S48 -02 -002013303460324 -007 -01 -057 -037 -021 -0217250217 05 -042 -029 -08 -04 -19 -094 -04

STM3549 -03 -072 -0090228 -0270107 -054 -044 -038 -040319 -04 -042 -037 -012

-04 -172252 -03

STM3550 0820521 -005 -126 -057 0474 -017 -029 -0 -1030003 -0520747016304940405 194 107 167 057 083

STM3551 0130543 -018 -0390049 061902820418 -012 -026 127 -0.20494 -0270556 -018 286 118 3130308 071

STM3552 080122 -043 -089 -062 -008 -021 -0850549 -09 -01 -0720384019500540179 184 032 Z09 088 062

STM3553 070481 -091 -033 -089 -054 -027 -0130126 -057 -021 03170476 -017 -0650623 09 134 016 -074 -08

STM3554 -02^ -iai| -ioi[ -19! -071 0305 0512690602 ##### -136 -075 062 -0660191 -147 -02 143 -1 -018 097

STM3555 0340698 -015 0412 -036 -124 -088 -12900570372 074 -00903180958 193 081 2 1103 066

STM3556 0450557 -038 0479 -018 -020158 -014 -03 -0180196168703840872 195 132 185 073 036

STM3557 02403860039 -0470407 -03803980729 -028 -067 -072 ########## 0317 -02 -05 -00886 -11

STM3558 058 -002 056 -047 -006 -114 -019 -05507790193 -068 -0180118 -049 -06 -04 -01 -105 -04

STM3559 07900850748 0009 -0970308 -125 -056 -092 -051 -075 -004650412 083052 -0 -077 -06

STM3560 -02 0330435 -016 -039 -032 -028 -089 -07 -023070801690321 0739 201 168 1790908 111

STM3561 017 -015092δ[ 0126 -04 1178 -0320891 -072 -054 -0252596 -0440087 104 05 086 1846 021

STM3562 01204960266 0090763 -0550431 ##### -047 -005 004037904980579 158 132 1790848 066

STM3563 -00457 -067 -0140666 -093 -082 -098 -027 -0150739098602140427 267 114 207 1554 083

STM3564 04209320191 0026 -03403931877 -001 0528 -134 -062 -032 -0092324 -02 007 -041391 039

STM3565 10901830424 0645 -011 -121 -07 -093 -058 -01 0270391 -0231162 195 098 2.190799 115

STM3566 0650412 -0β[ -024 -041 -045 -042##### -08 -012 -008030804630825 279 04 221 0742 018

STM3567 0780258 -01 -012 00602040564 -045 -059 -0480909056407620208 -06 -0 -050408 08

STM3568 0160087 -013 0052 -022 -05 -064##### -041 -0250545 -00802891168 238 135 101 0727 075

STM3569 0920379 -043 -008 -014 -068 -053 -043 -05 -0040854 -04903121109 205 131 191 1296 128

STM3570 1050607 -O 21 [ 0401 -051 -065 -075 -1040364 -0490559 -03814770459 17 09 20684 05

STM3571 0280534 -018 -029 -101 -121 -006 -007 -059 040415060504231097 186 091 260833 128

STM3572 0680069 -019 056308590401 066##### -026 -0680411 034507830944 222 128 2030604 086

STM3573 090706 -O 44 -006 -077 -052 -149 -089 -036 -031 0558 -0050311 0865 175 064 211 0312 111

STM3574 -0102730385 -033 -106 -051 f -182]«***» -109 -006 017088305260861 083065 139 -003 074 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3585 -07 -012 -057 -054 -028 -09 -01 -089 -034 0089 -058 -006 -086 0508 -052 -057 -13 111 -08 -105 -05

STM3586S -11 0771 0405 -034 -008 -038 069 0415 015 -049 -11 -078 -041 -151 -042 -077 -08 014 -13 0609 02

STM3587 051 0501 -059 -129 -082 07 -006 -062 -067 -056 0691 -051 0603 -014 0033 0435 128 022 195 0675 033

STM3588 093 -026 -038 -098 -041 0261 -025 -101 -153 -044 0155 -019 0882 051 0721 1092 199 111 175 1045 121

STM3589 0Θ9 0518 -075 -183 -028 0193 -011 0958 -077 iltifUlll -035 -056 0741 0072 0344 0799 192 12 216 1138 091

STM3590 065 1012 -024 -169 1021 1323 0254 1951 -127 0529 -128 ■024 0775 -088 2075 0769 105 179 194 0058 138

STM3591 -06 -051 -115 -111 -08 -066 0206 0148 -06 -078 -1 -062 -038 -052 -055 -03 088 02 054 -091 -03

STM3592 -18 -021 -078 -053 -01 -081 -009 -084 -097##### -069 -188 -14« -217 0008 0167 I -23 -13 -18 -2^3 -05

STM3593 054 0055 0179 -104 0012 0463 -013 -126 -071 -053 -045 -004 0202 -003 0118 1033 185 114 236 1132 105

STM3593 085 0753 -02 -087 -025 0135 -014 -1 -047 -084 -051 -04 0783 0734 0062 0519 209 167 242 072 -0

STM3594 -05 -004 -128 -121 -137 -149 -013 -103 009 -089 -091 -059 -091 -108 -071 -085 -04 -04 097 -051 -01

STM3595 07 0325 0114 -089 -056 -013 0107 -032 -05 -107 -085 -026 0117 -037 0453 079 179 084 173 0892 058

STM3596 03 -014 0002 -067 -048 -072 0465 1253 1099 -038 -098 -01 -074 0225 0081 0716 095 052 178 0357 059

STM3597 -07 -125 -139 -016 -064 -143 -178 -261 0726 141 -03 -033 -074 -03 -127 -04 -09 03 -038 -02

STM3598 028 -03 -097 -113 0267 0256 -02 -017 -033 -08 -054 -013 -015 1265 0699 -036 -03 027 089 -002 046

STM3599 -05 0009 -009 -001 009 -031 -021 -051 -085 -036 -03 -073 -044 0336 0089

STM3600 -1 -005 -033 0046 -013 -005 -02 -004 -052 -038 -065 -063 -043 -039 -002

STM3601 -08 -086 -062 -171 -136 -138 -053 -002 -145 -062 -109 089 -073 0601 -124 -065 -04 -09 -07 -12 -15

STM3602 074 -015 -043 -128 -037 0246 AR -094 ttmm -044 -0.21 0266 0226 036 0481 238 081 185 1168 088

STM3603 087 0387 -084 0481 0893 0207 0253 -055 -059 0984 0521 -051 0515 112 0295 2016 098 058 13 0451 046

STM3604 03 0437 -082 -031 0278 0406 0108 -076 -105 -057 -09 -019 0258 0007 0762 0426 104 062 152 0118 107

STM3605 -08 -06 -024 0085 -018 -054 -031 -04 -028 -05 1

-!» -077 -128 -087 0237 -123 -09 -1 - 2808 035

STM3606 -12 -044 011 -057 -036 -103 -002 -013 -109 -099 -119 -123 -025 -03 -13 -17 -06 0043 -08

STM3607 051 0196 -123 -02 0083 0012 -002 -07 -01 -1111 -189 -009 0654 1016 -13 -04 04 -08 -04 -074 -15

STM3608 -02 -002 -043 -064 -012 -007 -033 -092 -132 -105 -077 -2.08 AIL _-079 1038 0469 -1 021 -06 -163 026

STM3609 -11 -063 -045 -12 -036 0223 -021 -076 it It U H H -028 -168 -211 -157 -047 -135 081 -08 -13 -2.16 -15

STM3609 -11 •053 -01 -077 -143 -002 0119 -026 -071 -065 -02 -116 -146 -148 -006 -13 106 -03 -02 -125 -05

STM3610 :ij] -13δ[2[68 -082 -104 -073 -06 -065 -11 -126 -116 -228 0627 -173 0111 -076 -17 -12 -18 -052 003

STM3611 039 -021 -042 -179 -127 -003 -035 -116 -05 -028 -032 -029 -029 0043 0515 0422 209 077 187 0945 -0

STM3612 -02 0565 1027 -088 -051 -037 -02 0189 -109 -012 -034 -011 0068 0032 2017 -024 071 -03 044 1265 205

STM3613 028 0289 -05 -019 -047 0735 0329 -027 -012##### -096 -061 118 -051 0398 0193 072 047 147 0566 126

STM3614 035 0378 -063 -061 -098 -007 -012 0266 -014 0646 0413 0996 -024 225 102 174 0049 093

STM3615 -09 -005 -123 -108 011 -01 0045

-079 -059 -Ijjθj -068 0396 -09 -1 -11 -04 -075 077

STM3616 -06 -026 0238 -177 -127 1396 0552 0097 -04 -007 -121 -099 -085 -126 0017 -056 -02 -11 101 -048 055

STM3617 004 0876 -027 -124 -075 -003 -092 -048 -094 -096 -084 -077 0416 -016 1144 0627 237 066 146 0718 071

STM3618 082 0712 -013 -078 -067 0107 -056 -088 -057 tWtfttfl 0234 -033 0044 0856 037 0725 224 103 271 0332 119

STM3619 -05 0104 -03 -011 0331 0407 0478 0414 0738 -032 0226 -05 -06 -109 -028 -042 -12 -02 -02 -075 017

STM3620 089 0476 0377 -123 0215 -011 0619 0652 0334 -079 -042 -081 0357 0219 -008 0329 157 096 168 167 102

STM3621 019 0629 -04 -142 -044 0151 -078 -134 -077 -024 -02 -005 0198 -024 -025 0489 16 127 223 0612 031

STM3622 -02 -044 1399 -074 005 0972 0476 1281 -02 IWIItItI -026 -029 0669 -083 0184 -004 -09 -05 -07 164 004

STM3623 025 0261 0126 -152 -01 -019 0458 -008 0337 -11 -003 0293 0478 0459 0574 0433 099 104 147 0896 077

STM3624 -03 0951 -043 -029 1162 -027 1754 -078 057 0164 -046 -091 -093 -039 0492 0053 -08 008 -04 0628 013 TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3632 112 0245 1253 0366 0234 166802751381 -073052312151142 -103 -07706851342 -05083 [^"Tβ] 0588 13

STM3633 056 0015 -042 [ -164 I -04 -043 -042 -092 -041 -083 -057 -0540402023204130324 222 128 181 0409 126

STM3635 034 -048 0046 1208 -043 -07 -0580023 -111 -0081501 -009 -046 -028 -005 -011 -03 -02 -09 -149 -03

STM3636 -12 -094 -009 -032 -077 -029 -0550179 -083 -087[ -15θ[ -126 -083 -067 -002 -062 -0 -1 -09 -024 -07

STM3637 013 -019 0112 0474 0499 0232 -037 -068 -002 -044 -051 -034 -104 -015 -054 -114 -1 -05J -3J -103 -05

STM3638 095 032 1207 0009 -021 -011 -047 -007 -016 -032 -1 -021 0467 -069 031 -017 095 061 1420843 068

STM3639 036 -005 0627 -017 0445 0344002302150423 #####00570585 108 -03202330896 -0 -01 22 015 031

STM3640 -06 -051 -072 G-LU -059 -108 -121 -07 -103 -1361304 -056 -001 -021 -125 -04 045 042 -068 015

STM3641 093 -082 -025 0714 -021 0673032700340103 0650401 08090469 -041 03430061 -11 026 -1 -121 027

STM3642 075 0289 0191 -065 -076 -002018903740373 -021 -07702060129 -02504630502 17 14 1840147 048

STM3643 014 -016 093 0154 -002 0075068405161224 -013 -0020668007201460179 -044 -05 143 -11 -042 -05

STM3644 068 0012 -038 0515 0288 00890342 -086 -0.24 -085 -011 -041 0171 0751 12020619 163037 180462 105

STM3645 003 -043 -005 0918 0119 0705018405490742 -089 -1032624 -066 -0450568 -011 -03 -0

321 048

STM3646 043 0074 055 096 -026 -021 -0060003 -022 -027 -024 -008 -08 -0161577 -036 036 021 112 -068 134

STM3647 021 -01 -015 0034 0028 0270138 -0240554 -042 -039 -053 -067Jjf jp] -132 -069 -09 -0 θ| -25 -2.7Ϊ] -12

STM3648 -02 0404 0479 -053 -019 0607 -021 -0370975 -0351215 -001 -01 -041 07890103 143 135 043 -061 089

STM3649 053 0815 -04 -109 -057 -0 -098 -098 -069##### -05 -060486 -01400420484 279 168 2950873 068

STM3650 04 -042 -01 0505 -012 -03700840288 -015 -13 -091 -046 -003 -096 -017 038 -13 -01 f -1 θj -141 -04

STM3651 -07 -059 -051 -012 -061 -062 -079 -0360036

-0540902 -003 -07 -12 -09 -1 -142 -11

STM3652 07 0772 -032 -206J -067 -048 -089 -069 -073 ##### -039 -007 -0150111 0073 1013 144 132 160065 015

STM3653 -02 0102 -006 -027 0607 -051 0186 -0560263 -0581105 -0320226 -01409540037 026 006 -1 -024 -0

STM3655 052 0606 -042 -065 -07 0319 -059 -143 -103 -046 -058 -0370642 0130361 1071 22 102 228 1389 028

STM3656 104 0567 -001 -093 0163 -03 -022 -026 -046 -033 -055 -0030021 058406751457 25 102 191 -06 078

STM3657 143 0774 -049 -022 -101 0277 043 -0150326 ##### -061 -0660437 -0381885 176 076049 1330994 167

STM3658 079 -058 -017 1013 0088 -021 -061 -061 0171 03940857 -123 -0460083 -045 -001 011 -07 -13 -064 -05

STM3659 -0 -03 0808 -013 0199 0733 -07 -001 -051 02821114 -0150391 -019 -039 -049 -1 -06[ -22J -079 011

STM3660 094 0843 0417 0687 -023 0350052089904390798 161 -102 -0290443 0230386 -04 33 -022004 057

STM3661 -04 -045 0685 0113 0214 -02700490597 -002 -0380386 -0290774 -0131365 096

STM3662 -03 -026 0452 -022 -019 0086 -028 -07 -013 -091 0369 -0780357 -0670252 002

STO3663 -05 -067 0037 -08 -001 -04406331021 0878 ###W -ZI4I -062 -126 -099 -126

-08

STM3664 047 -012 -0 -036 -051 -035 -022 -056 -115 -006 -074 166 -069 -061 10030467 026 051 123 -039 125

STM3665 -02 029 0575 -018 -01 0247 -0160138 -033 -0110514020404261271 07480878 -1 102 -140772 054

STM3666 046 0527 -076 -105 -054 -067 005 -133 -0270018 -034 -082 -02 -034 -057 -035 114 031 0820239 -02

STM3667 085 0481 -014 0238 1431 -057 -017 -028 -062##### -112 -035 -096 -148 -091 -077 028 -06 236 -059 01

STM3668 046 0591 -105 -13 -058 0648 -047PTJTJ -014 -088 -0430949 1066 -093 -025 032 08 009 142 -003 069

STM3669 -03 -042 -034 0371 -01 -009 -017 -079 -028 ##### 02831683 -04904060146 -068 -06 -01 -08 -085 005

STM3670 [TTI -005 0069 -018 08902920132 -068 -2 -11 068605540267 -129 -108 -118 098 -09| -16| 0195LUJ5;

STM3671 -1 -091 -095 -103 -0350159 -123 111 -177 -018 -022 -111 -034 1331 -003 -058 -03 -14 -05 -126 019

STM3672 -04 0118 -021 -001 -006 P 258 -0330024 -05511871769 -076 -00210030485 -07 -1 -07 -070321 012

STM3673 -1 -082 -047 -037 -131 -019 -065 -08 -108 -075 -074 -125 -045 PEIl -0380325 -06 -i| -22J -128 -02

STM3674 114 0027 -051 -123 -091 -050085 -166 -1511 -1051173 -0650136 -0040241 0076 142047 1640844 063

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3686 -1 -1.26! -1.99 -1.06 -2.16 -1.75 -0.32 -2,11 -1.88 -2.17 -1.82 -2.73 -2.3β| -0.84 -IΛHΪJHJ -i[j3 -0.1| -22 -1.8| STM3687 0.25 -0.98 -1.19 -1.45 -0.99 -0.5 -1.48 -1.59 -1.95 mm -1.32 -1.33 -⁰⁵Ll-⁵IJ -^{095 0204} -°³ °-¹⁴ 0.06 -0.09 -0.5 STM3688 0.49 0.377 -0.87J -Taj] -1.17 0.532 -1.24 -2 -2.33 -1.05 -0.73 -0.42 0.297 -0.25 0.065 0.081 1.29 0.71 1.36 0.542 0.49 STM3689 -0.2 0.873 -1.43 -0.98 -0.57 -0.94 -0.56 -0.24 0.755 ##### -1.18 -1.2 1.625 0.748 -0.43 0.556 0.36 -0.4 0.7 -0.18 0.18 STM3690 -0.5 -0.53 -0.45 0.661 -0.04 0.369 -O.βl ^Te] -1.37 -1.38 -1.33 0.756 -1.19 -092 -0.24 -0.4 -05 -1 -2.9 -1.52 -04 STM3691 -0.2 -0.57 -055 -0.82 -0.08 -0.1 -0.4 -0.44 -1.12 -0.88 -0.16 1.112 -0.38 -0.4 0.77 -0.46 0.71 0.49 1.26 0.116 0.73 STM3692 -0 0.278 0.696 -1.08 -0.64 -0.47 0.055 -0.54 0.016 -0.47| -2] -0.19 -0.21 -0.74 0.097 -1.1s[ -1,β( -0.4 0.31 pTs4] 0.43 STM3893 -0.2 0.83 0.363 0.269 0.993 0.709 -0.59 -0.07 -0.45 0.2 1.177 -0.92 -0.26 -0.41 -0.33 -0.41 -0.9 -0.4 -0.3 -1.07 -0.4 STM3694 0.29 -0.05 -0.5 -1.03 -0.18 0.034 -1.12 -0.611 -1.62J 0.109 -0.18 0.497 -0.06 0.121 0.217 0.592 0.78 0.92 0.62 1.159 0.62 STM3695 0.54 0.283 -0 -0.46 1.1 -0.59 0.06 0.556 -0.43 mttm 0.393 -0.16 0.939 -0.53 -0.85 1.033 -02 -0.4 0 -0.85 -08 STM3696 -0.8 -0.54 -0.34 -0.82 -0.37 -0.04 -0.09 1.207 0.935 -0.22 -1.08 -0.48 0.402 0.117 -0.47 0.015 -0.2 -0.8 -0.3 -0.77 -0.4 STM3697 0.18 0.669 0.839 0.356 0.68 0.648 -0.35 -0.87 -0.25 0042 0.518 1.492 0.848 0.157 1.146 1.445 -1.3 -05 1.36 -0.37 1.68 STM3698 -0.4 0062 0.205 0.518 0.273 -0.05 -0.22 -0.37 0552 -0.46 -0 -0.16 -0.08 -0.99 0069 -0.08 -1.2 -0.7 _-29J -0.34 -0 STM3699 096 0.235 -0.31 -1.25 -1.19 -001 -0.29 -0.89 -1.17 -0.57 -0.46 -0.65 0.722 0.182 -0.24 0.266 1.86 0.74 1.55 1.487 0.41 STM3700 0.57 0.274 -0.31 J -1.5J -0.36 0.921 -0.5 -1.12 -0.79 mm -0.26 0.09 0.556 0.454 0.12 0.8 1.94 0.6 1.53 0.961 1.11 STM3701 0.38 0.709 -0.45 -1.03 -0.31 0.256 -048 -1.21 -1.01 -1.04 -0.26 -0.14 1.202 -0.46 0.896 0.65 1.65 1.27 1.64 0.694 0.54 STM3702 1.35 0.792 -1.02 -1.05 -0.3 -0.17 -0.22 -0.91 -0.89 -0.7 -0.7 -0.16 0.561 1.036 -0.07 1.045 2.24 1.12 2.33 0.684 0.44 STM3703 0.16 0 124 0.006 -1.46 -0.43 -0.04 -0.99 -0.73 -1 -0.99 -0.66 -0.73 0 14 0.126 0398 0.172 1 49 1 13 1.84 0.089 1 01 STM3704 0.52 0.563 0.638 -0.15 0.788 0.087 0.144 0.047 -0.32 -0.92 0.007 -0.66 0.206 0.077 -0.18 -0.1 -0 -0.2 0.44 -0.31 0.05 STM3705 0.66 0267 -043 -1.11 -0.83 -0.2 -0.56 ( -,1.7β| -1 03 -0.41 -0.27 -0.33 -0.08 -0.98 0.129 0.173 1.31 0.53 1.92 0.29 0.53 STM3706 0.29 0.248 0.441 0.64 -0.1 0.546 -0.3 -0.69 -0.22 -0.02 -2.6 -0.691 -1.66] -i.rapTe-i] -0.01 -1.2 -0.9 f3j.8 -1.86] -0.8 STM3707 -0.4 -0.29 0.003 0.25 0.278 0.043 -0.05 -0.12 0.16 1.251 -1.54 -0.6 -0.15 -0.86 -0.24 -0.15[ -JLβj -0.9 -1 0.759 -0.1 STM3708 0.13 0.203 -0.07 0.508 0.345 0.182 -1.06 -0.04 0544 1.341 -1 -0.49 0.812 -0.55 -1.08 0.13 -0.2 -0.2 0.45 -0.35 -0.8 STM3709 0.33 -0.33 0.148 0.339 0.251 0.298 -0.22 0.232 -0.48 1.613 2.109 1.42 1.531 0.044 1.088 0.2 0.12 -0.2 -0.4 0.587 1.39 STM3710 0.7 0.226 -041 -1.02 -0.49 0.323 -0.48 -1.4 -076 -0.68 -0.49 0.311 0.486 0.088 0.847 0.778 1.99 0.69 2.27 1.325 0.37 STM3711 1.34 0.714 0.132 -1 23 -0.39 0.153 -0.07 0.262 0726 -0.67 -0.98 -0.89 0.635 0.8 0.131 0.954 2.23 1 2.67 0.854 0.67 STM3712 -0.82 -0.72 -0.19 0.739 0.11 0.85 2.32 0.94 2.93 1.067 0.53 STM3713 -0.7 -1 3 -1.4 1.086 -0 8 STM3714

-1.4 -08 4ΛΪ -1.29 -0.7 STM3715 0 1 0.089 0.071 0.521 0.593 0.286 -0.14 -0.47 0.059 0868 0.444 -0.32 -0.06 -0.75 0.221 0.157 -0.4 -0.7 -0.5 0.027 0.21 STM3716 -0.93 -1.31 ##### 1.149 -06 -0.6 0.589 -0.01 -0.06 0.61 -06 0.74 -0.44 0.47 STM3717 -2.39 -1.91} -1 -1 ^'.78 ' -1.24 -09 -026 -083 1.21 -0.5 2.2 0616 -05 STM3718 -1.4j -2.01 -1.18 0.191 0.068 -0.64 OOI -0.4 0.38 -0.82 -0.7 STM3719

-2.B7] -0751 -21 -1.87 -0.54 -0.85 -1.15 -0.78 P-1.7] -O.θJ -2.5 -204 -I-Sj STM3720 0.15 0.115 -0.44 -0.57 -0.75 0.678 -0.29 -0.72 -034 ##### -0.45 -0.71 0.634 0.263 0.912 0.821 1.79 1.1 0.89 0.689 0.9 STM3721 0.75 -0.33 0.116 -1.18 -0.66 0.143J -2.37 -274 -2.24 -0.78 -0.3 -0.71 0.396 -0.45 0.599 0.925 1.57 1.02 1.82 0.03 0.04 STM3722 046 0.008 -04 -1.24 -073 0.42 -1.36 -1.2 -1.7 -0.28 -0.37 -0970.3630.2160.2340.375 1.77 07 1.91 0.659 0.73 STM3723 -1.7 -2.44 -2.43 -1.53 -0.69 -0.76 -2.8 -2.89 -3.06 -2.61 -2.2 -259 -1.56 J238] -1.4 -1.9 -1.7 -2.71 -1.9 STM3724 0.37 0.1 -0.41 -1.07 -0.38 0.028 -0.26 -0.89 -0.34 -0.44 -0.22 -0.13 0.158 0.119 0.681 1.221 1.97 0.75 2.16 1.163 0.47 STM3725 0.78 0.322 -0.02 -1.43 -0.87 0.339 0.256 -0.87 -0.51 -0.5 -0.21 -0.24 0912 0208 0.145 1.182 2.18 1.29 209 1 064 0.43 STM3726 0.41 -0.06 0.118 0.928 0.215 0.945 -0.24 0.558 -0.39 -0.1 -0.25 0.811 -0.93 -0.44 0.479 1.471 [ .-I.9] -0.2 1.14 -0.4 0.23

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3738 0.64 0.248 0.547 0.482 -0.34 0.066 0.183 0.472 1.321 -0.88 -0.16 -0.48 -1.03 -0.97 0.194 -0.02 0.01 -0.6 ^*;-2^"i -0.38 0.48

STM3739 -0.5 -0.78 -0.41 -0.41 -1.1 -2:18 -0.53 -0.16 0.31 0.278 -1.13 -0.8 -0.96 -0.42 -0.17 0.06 -0.2 -0.3 -0.5

STM3740 0.27 0.477 0.991 -0.16 0.364 0.663 0.72 0.74 0.383 M fO 0.771 -0.57 0.01 0.236 0.145 -0.02 1.46 0.18 0.85 -0.01 0.42

STM3741 0.95 0.04 -0.17 -0.96 -0.1 0.369 0.092 -1.33 -0.55 -045 0.134 0.317 -0.3 0.509 1.68 0.88 2.09 0.843 1.1

STM3742 1.14 0.157 0.071 -1.1 -0 98 -0.51 0.178 0.539 0.422 -0 69 -0.4 -0.13 0991 0.218 0.232 0.877 1.96 0.93 2.39 0.89 1 02

STM3743 088 1.254 -1.93 -0 25 1.283 -092 1 602 0864 0367 0 104 -1 05 0563 086 -066 0008 -027 1 83 06 -08 -1 01 -0

STM3744 085 O fil -0 16 -078 -006 -0.69 0.426 -0.61 -074 -066 0 103 -0 12 0.433 0447 0991 1.122 2.2 1.42 2.48 0.739 0.74

STM3745 1.1 0.675 0.512 -0.03 -0.32 0.113 0.189 0.329 1 005 -0.13 -0.11 0.193 0.516 0.947 0.763 0.768 1.72 0.88 1.61 1.226 1.01

STM3746 1 15 0738 0601 -058 -049 -0.18 -0.47 -0.34 -1 81 -0 57 1 31 2.24 0.594 0.88 -0.51 0.456 1.23 2.25 1.39 0.591 0.49

STM3747 0.89 -0.2 0.056 0.001 -0.34 -1.42 -0.1 0.132 1.183 -0.47 -0.7 -065 -0.62 -0.26 -028 -082 -1.1 -0.3 0.52 ■0.43 0.52

STM3748 0.11 0.656 1.135 -0.41 -0.64 0.161 0.441 0.127 0.653 -0.97 -069 -065 -0.21 1.029 0.172 0.34 1.85 0.42 1.39 1.157 0.37

STM3749 0.22 0.164 0.231 -0.7 -0.51 -0.18 0.225 0.04 0.459 -0.48 0.479 0.242 -0.44 0.391 0.596 -0.1 0.72 -0.2 1.06 -0.05 0.69

STM3750 066 0.72 -0.25 -0.59 -0.32 0.345 -0.57 -0.71 -0 09 tttftWU -0.42 -0.05 0.183 0.292 1 319 1.09 1.58 0.89 1.6 0.697 1 42

STM3752 -03 -0.2 0.29 0.755 0.228 0.658 005 -0.27 0.233 -0.29 •0.07 -0.68 0.471 -0.67 -1.17 -0.16 -1.2 -0.6 -2.2 0.387 -1.1

STM3753 0.74 0.398 -0.3 0.485 0.526 -0.48 0.883 0.046 0.719 -0.08 -0.11 -0.22 -0.04 0.538 1.027 1.383 -0.4 0.3 -0.8 -0.06 0.89

STM3754 -0.4 -0.54 0.657 0.59 -0.67 -0.12 -0.52 0.69 0.762 -0.85 -045 -0.15 -0.6 0.142 1.268 -0.44 -1.3 -0.5 -1 7 -1.47 0.66

STM3755 0.11 0.045 0.947 -0.31 -0.16 0.34 -0.33 0.787 0.131 ##«## 0.347 0.138 1.176 -0.61 -0.34 -0.6 -0.2 0.091 -2.9 -0.39 0.37

STM3756 0.2 -0.25 -082 -0.2 -0.78 -0.69 -1.64 -1.92 -1.53 -0.66 -0.72 -1.01 -0.3 -02 -059 -0.26 0.5 -0 0.67 -0.5 -0 1

STM3757 0 19 0.02 ■0.4 0.33 0374 -0.69 -0.22 -0.28 -1.25 ##### 0.421 -0.55 -0.7 -0.92 0.507 0.057 2.93 -0.2 0.99 0.914 -0.3

STM3758 -0.4 -1.07 0.087 -1 15 -0.81 -0.32 -0.46 0.45 -1.08 -077 -1.13 -1.19 -0.91 -0.36 -0.41 -1 18 0.03 -0.9 0.91 -0.26 -09

STM3759 S -0.3 0.145 0.056 0.064 0.28 -0.32 005 0.641 0.255 0.797 -1.26 0.111 -1.01 -0.2 -0.23 -0.25 -0.4 0.71 1.33 0.582 0.2

STM3761 0.79 -0.07 0.709 0.041 -0.36 0.086 0.078 -0.8 -0.6 mm 0.886 1 071 -0.17 -0.79 -0.61 -0.32 -0.7 -1

STM3762 -0.2 -0.71 -0.7 0.122 0.359 -0.12 0.215 0.278 0.286 ##### 0.334 -1.68 0.699 -1.4 0.539 -1.25 -1.1 0.1

STM3763 -1.43 -0.71 -1.27 0.138 -0.98 -0.97 -0.29 -0.67 0.038 -0.35 -0.2 0.214 -1.3 -0.8

STM3764

-1.41 -'.:«59J $£* IM ^v"-2.-34 -096 -0.91 -1.08 0.113 0.146 -0.81 -1.21 -1.1

-0.6

STM3765 -O 0.225 0.174 -037 -0.37 -0.34 0.037 0.194 -023 -0.84 -0.2 -0.16 -0.66 0.481 1.008 -0.48 -1 0.43 -0.2 -0.38 0.77

STM3766 -1.5 -0.65 -0.18 -1.21 -1.17 -0.59 0.186 -0.24 0 031 J -1.C6 '- ,2.47^* -0.63 -0.66 [ ^I .74' -0.87 -0.55 -0.9 -0.6 -0.8 -0.74 -0.8

STM3767 0.74 0.471 0.346 -1.35 0.258 -0.01 -0.33 3§ -1.19 -0.35 -0.33 -0.34 1.148 0.772 0.566 1.372 1.48 1.33 2.56 0.727 0.91

STM3768 0.57 0543 -0.07 -1.84 -035 0.528 0.424 0.007 -0.76 -0.52 •0.82 0 174 0.084 0.291 0.518 0.922 1 92 1.21 2.01 0.203 0.6

STM3769.S 022 -0.09 -0.56! J-TM- -1 13 -0.22 -0.22 -1.03 -1.39 -0.99 3.363 -0.47 0.279 -0.7 -0.05 0.822 1 45 -0.2 1.39 0.637 -0.2

STM3770 -0.4 0.019 -0.57 -0.99 -051 -0.55 0.938 -0.53 0.851 -0.67 -054 All -0.45 -0.71 -0.08 0.65 0.05 1.15 -0.02 0.64

STM3771 0.98 1.217 -0.33 -1.25 0.794 0.042 -0.19 0.548 -02 0.492 0.391 0.786 0.685 1 43 1.33 1.51 0.187 0 54

STM3772 0.27 0.676 -0.36 -1 2 0.154 -0.54 0.24 -0.05 -025 2.044 -0.74 -0.26 1.202 -0.75 0.947 -008 0.72 0.25 1.33 -0.43 0.69

STM3773 0.42 0.172 0.228 0.313 -0.69 0.218 0.173 0.511 0.752 0.57 1.456 0.097 -064 0.66 0.314 -007 -0.6 0.18 0.55 -0.51 0.03

STM3774 -1.4 -0.41 ⁷^ -1.31 1.277 -1.26 1.197 0.54 0.135 0.436 -1.61 -1.16 -0.12 -1.3 -0.63 0.29 0.47[ -2.2 -2.77J -09

STM3775 -06 0.224 -0.53 -0.28 0 193 -0 17 0.75 0.373 0 856 -038 -0.69 -0.43 -0.84 -0.74 0.249 -0.7 -1.1 -0.1 2.58 2.043 0.27

STM3776 0 18 -0.02 -0.02 0.189 0.283 -0.1 -0.13 -0.45 0.451 0.819 -1.25 -1.3 -0.54 -0.28 0.45 -0.31 -0.9 0.338 0.5

STM3777 -0 1.284 1.14 -0.44 -0.27 0.321 -0.48 -0.58 1.439 -049 0.538 2.137 0.016 -0.19 0.369 0.347 0.98 0.45 1.54 -0.41 0.67

STM3778 -03 -0 19 -09 -0 11 -004 -04 -068 -095 -067 -1 01 -1 58 -0.7 -0.62 -0.13 -0.39 -0.97 0.24 -04 0.35 -0.73 -0.3

STM3779 -1.3 -0.67 -1.08 0.304 0.36 0.166 0.069 0.093 0.135 -1.39 -0.89 -0.31 1.261 -0.24 0.478 -0.93 -1.4 -0.4 ²⁹⁵E -2.4TJ 0.55

STM3780 -0.4 -0.55 -0.1 0.4 0.386 0.109 -0.05 0.082 0.204 -0.54 0.423 -0.19 0.295 -0.41 -0.29 0.091 -0.8 0.15 -0.5 -0.81 -0.4

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3792 055 -0070242 1070628 -007 -00083064500981168 03600680635 -051 0229 029 058 -19 -077 -03

STM3793 0370125 05803220431 0911 -004021300581447 0070799 -008 -059 -046 -01δ| -1 β| 045 -15 -112 -06

STM3794 07206070021 -084 -0570617 -012 -08 -014 -055 -062 -029 124006606230837 212 157 2080923 104

STM3795 009 -023 -013 -094 -113 -009 -095 -142 -127 -074 -057 -058 064 105700610701 167 145 1550676 092

STM3796 -006650582 072 -01802060196024401872187 0250493 1041 3224 084 -014 045035 -070467 083

STM3796A. -0202130608 -019 -012 -0270352 -038 -071 0466 -056 -038 -085J -164) 025 -056 -15 -08 -140091 -01

STM3797 -01 05140173 03680418 -0120763 -0350585 -003 -103 -0962151 -1150217 -027 -15 -09 -35J -053 036

STM3798 021 0234 -07 -098 -11 0086016204281528 -070073 -126 -043 183 1213 -001 067 086 111 -003 106

STM3799 -01 0044 -039 -011 -037 -011 -101 -051 0941 -133 -131 -078 -0340043 -011 0181 13 02 0630219 -01

STM3800 0040123 -054 -0650087 -005 -008 -0901551052 -109 -0980181 054213570213 01 -02 071 -024 132

STM3801 08514230511 13331028 00410555 -084 -0250637PT56|θ406 -011 0304 -0030589 -04 -0 -072624 037

STM3802 0590401 025 -007 -072 -06 -0140645 _" ¹JJ⁴J -07 -097 -0520088 -081 -106 -053 0 -07 0352014 -06

STM3804 031 0749PTtStS¹10490196 ^•-175J -0 -2.260532 mtm -07 -03 1277 036 316 -045 -111 -1 B| -01 -033 257

STM3805 0580334 -048 -131 -0580114 -123 -2-25 -124 -078 -055 -0680722 -044 -0580841 116054 1890467 -01

STM3807 -0 -01 -041 008 -05 -038 -023 -1^*62i -092 -05 -058 -122 -155 -139 001 -031 -1 019 0240583 021

STM3808 S 02200240201 -114 -066 0697 -005 -101 -061 -0780555 -0370869 -004 060651 184 077 2470989 075

STM3809S 01303380618 -0970027 -0020189 -078 -143 -0831384 -0271068027409650277 117 07 131 063 202

STM3810 -06 -0630103 -001 -018 -059 -058 -087|~?Tβ3] -03J -202[ -06911990551 -1080932 -07 -05 -θ[__:2O5J -01

STM3811 0680525 -002 -108 -05 00160798' 10941018 mm -091 0240751 038205180721 145 123 194 1165 085

STM3813 04505830635 -038 -086 0290131 -068 -039 -075 -009 -05209370332 -0110567 196 13 1961159 053

STM3815 0740873 -02 -084 -028 -003 -05402470663 -093 -04 -076 -004 -01602490718 192 105 1770577 043

STM3817 123 -053 -018; -1 SJ -044 0105 -046 -131 -053 064 -018 -0030564040601020657 216 1 222 1099 001

STM3820 -030083 -023 -147 -055 -011 -051 -016 -051 -009 -04 -032 -01 -0130208 -032 094 046 155 -006 072

STM3821 -03 -041 -073 -028 -016 -017 -023 -0390324 ##### -008 -12 -018 -076 -09 -037 018 -06 262 002 022

STM3822 -01 -013 -071 -018 -108 05070201 07690153 -047 -039 -125 -061 -1090776 -016 -04 -03 -05 -144 092

STM3823 -06 -016 -036 -016 -059 -031 -033 -11 -005 -032 -047 -045 -1360614 -042 -088 -07 08 -05 -013 -04

STM3824 -05 -044 -104 -0270695 -01202580071 1136 -105 -09 -031 -0830108 -081 028 01 012 -01 0272 -06

STM3825 059 -008035304990926 -0970936095612640676J -224J -069 -101 064δ| -167 -224J -01 22 -14 -056 -09

STM3826 077 017 1567 -003 -063 0584 -079^202] -03##### -046 -04902623859 -013 -051 08 -04 1 -027 053

STM3827 0370254 -024 -143 -024 01650077 -093 -018 ##### -033 -0280348001302060762 145 105 1661382 093

STM3828 -030227 -0220183 -028 -069 -005 095035503880421 [~Tj] 1 Q43pl S8¹ -083 -045 -12 -05 -114E-04 -09

STM3829 023098606870226 061 04780628 -003 012 -008 -0930821 -02200040525 -05 082 072 -090319 091

STM3830 012 -002046407130374 0561 0025 -088 -0.2303460049 -076 -004 -0220331 0694 -02 -04 -±4 -013 -01

STM3831 -06 -144 -0840581[Tω] 0466 -078 -043 -006 -OOlfTss] -135^194~[ -115 -130096 -07001 ^r7j1243 -05

STM3832 0280145004106570189 01750312020601740796007304520291 0336 0220004 -03 -01 2.24 -039 012

STM3833 00507530129 -0280769 0338 -063 -032 -02802330805 -062 -0230081 -0180844 -01 074 0850638 045

STM3834 0990105 -0550492 -145 -112 -054005403530909 -09405430187| -17^ -135 -029 -08 -12 -092368 -09

STM3835 0480307 -034 -069 -063 0174 -043 -083 -076 -012 001 00660633 -007 -0090629 123062 1730745 086

STM3836 1420419 -106 -049 -002 -088 -043 -103 1 0178 -1151258 -057 -089 -093 -127 -02 018 -04 -121 -06

STM3837 0602050291 -113 -043 -005 029 -088 -011 ##### -073 -0040867 03406250629 18 124 2450887 127

STM3838 0350384 -072 -069 -074 0382 -089 -117 -12 mm D 033 -0050779 09405980974 249 175 2230676 1

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3851 S 0520299 0958 -045 -046 -0850046 103 -014 -037 -0090383 -0473465 -042 -057 144053 05 -034 007

STM3852 106 1410211 -0830708 0060608 -071 1139 -091 -0163891048301580619 076 17 139 2182078 138

STM3853 092 1186010404530778 165 119 2130949 041

STM3854 -1 -07 -103 -1 -1 047 -0 002 -107 -07

S7M3855 042 -046 -0231235 -119 001 028 021 -064 057

STM3856 068 043 -0190569 106 166084 1861271 033

STM3857 -02

-113 -087 -038 -13 -02 -07 06 -051 -0

STM3858 05905920606 036 -048 -048 -01 08650839 -044 -095 -037 -1490148 -0090261 -1 -05 -11 -114 -01

STM3859 0480167 066911890027 -0110187 0280502 -052 -14706650091 -06608260956 -05 -03 -060247 09

STM3860 057 -0 -1 151 021 -056 -009 -048 -034 -05 -O 19 -067 -01303481042 055 -14013[_-2.i] -O 64 05

STM3861 0540395 -021 -0880724 00670054 -066 -024 -097 -03300940318049110060904 228064 2010657 128

STM3862 114 -012 1113 -0.260557 1142 -0020253 -028 -026 -0380153 074 059 0720807 121 083 1330746 046

STM3863 0160626111701060685 093301260802[^' _i72j)7J 065 -086 229 -00701730225 -015 -02 -0 -08 -009 -03

STM3864 0730012 -O05J~3i~86] -066 -0010023 -111 -093mm -091 -067 -05074604180263 173089 241 1 127

STM3865 0420678 -079 -124 -013 -0060312 -08 -045 ##### 003202141102 -030661 107 199 142 2.481678 099

STM386B 0790774 -041 -088 059 -0420341 -092 071 -099 -00503990492062306720713 211 093 2151391 151

STM3867 -0 -015 -101 -126 -084 -054 -073 -061 -058 -098 -077 -0530465 -007 -0220399 143029 220848 153

STM3868 0780499 -07 -114 -102 -0350361 -08 -016 -067 -054 -01 041009108270498 275 1 2060849 086

STM3869 10705990032 -141 -034 -0060324 -12 -054 ttttttm -028 -0190754 -0640961 1229 239 125 2450878 118

STM3870 0780317 -041 j-ijωj -O 57 018 -032 -037 -005 -096 -056 -055015900180778 056 233 12 2290844 155

STM3871 051 -032 -001 -093 -051 -026 -01δ[-217] -086 -082 -057 -0490831020704480794 283052 2020459 145

STM3872 072 -002 -062 -14 -119 0030075 -101 -045 -113 -067 -0870813044404520891 187 123 2171052 098

STM3873 S 050804 008 -114 -074 02540057 -029 -089 -066 -045 -04400780328 0221039 207083 1930715 093

STM3873S 0440237 -054 -086 -038 -030431 -081 -067 -1140231 -054 034015703410621 211 058 1840676 097

STM3874 0510179 -02 -065 -099 -0120122 -039 -048 -0220132 -0721066049306921233 181 128 234 109 122

STM3875 025 0950856 -095 -066 01603770986 -043 -079 -114 -021 -037 -0270302 -024 14045 2160478 063

STM3876 112 -045 0589 -0290104 -015 -02 -083 0020158 -00202270084 -042 -02 -022 051 -04 -02 -0 031

STM3877 -010117 1401 -121 -057 1258 -082042100421787102358040371 10220389 107 157068 2050807 105

STM3878 S 047 -06 -0050043 -018 0253 -00264 -0390537003609660987 -01506310224 -03077^ -3J -13 062

STM3879 -03 -046 -0160291 -078 -026 -097 -014 -011 -0551104 -0280043 -07 -026 -055 -02 -04 0152525 -0

STM3880 08 -0 -099 -099 -0190053 -053 -042 -102 -057 -056 -0351687 -03206220548 22078 1620647 139

STM3881 007 -011 -083 -01 -05201880051 123 -083(S#S*# -103 -08508610483 -0420553 101 -0 105 -018 063

STM3882 120446 -0671196 -042, -IJ73] -021 -1340801 -102 -1050578 -0460381 -038 007 033 -01 011 -068 -05

STM3883 0831001081201270125 13561432084602630231040839540948 -0241164 -048 088042 3881994 082

STM3884 07102290533 -091 -0550178 -046 -009 -054 -0360335405102550323 -0090322 136033 2010429 -0

STM3885 049053105730306 -0060158 -0330434 -019 -0750128 -124 -019 -071 -11 -073 -05009

STM3886 002 -06909110038 -025 01125E-O4 -0090093| -206| -11 -085 -149 -1[ -218| -083| -16j -05

STM3887 008 -0131055028502470344012905530404 -0102650453 -11065505430245 -03

STM3888 04027603130858050501580577024706471023 -101 -003 -016 -081 -013 -078 -03055 0430159 043

STM3897 097 -014 -0080408137414190191 15161149 -04 027073 416 -046 117

STM3898 050281

-131 ##### -049 -0590066050200530834 223 129 2080634 049

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3910 038 -01 -0.2502020178 -008 -026 -0350927 -029^9i| -021 13150045 -027 -003 082004[Tβ] 248 -01 STM3911 074 -0070274 -095 -004 -015 -00403720977 -094 -072 -0700770028 190592 2 105 1760857 238 STM3912 0570499 -0421 -163] -0460148 -075 -058 -001 -054 -053 -056 053025810850918 199091 1910805 152 STM3913 077 -042 -057 -066 -014 -0170139 -03[-1Jβ7]##### -094 -0643132 -06208950262 009 -0 0110329 156 STM3914 032 -0210066 -007 -005 -0170298 -128 11 -115 -099 -078 -019 -049 -055 -04 -1 -01 O57|-168Jθ12 STM3915 r, 19 -269 -294 -171 -226| -085] -375 -406 -337 -16JT-216 -169 -119 -138 -101 -12 -1 -14 -0 βj -Z1 -17[ STM3917 061 -0390253 -135 -0640168 01800730141 -056 -046024806450864 13830644 197 092 2070892 05 STM3918 -08 -075046503540408 -068 -0930192 -064 018 -003 -073 006 005 -03 -057 -05 STM3919 _L-18| -083L-261 -Z31 -1 -14 STM3920 -07 -078 -1O3'-217 -228 -052 -059 -0050272 011 -065 -097 017 -07 065 -068 004 STM3921 -05

^{Λ 48}L -177 -173 -1671 -088 -159 -008 -062 -146 -078 -082 -06 056 087 -022 -07 STM3922 063 -050484 -0402920313 -07502591176 -0841 -235 -027 -137095411970429 -01 -05 -1 1888 079 STM3923 069 034 -084 -111 -1180218 -038 -133 -021 -026 -04 -08105940608 -002 101 172 14 1930931 057 STM3924 0590285 -012 -1691 -07903420019 -089 -078 -097 D077 -0350659 -01 -0150483 226 124 199 076 039 STM3925 -080329 -05 -199 -049 -074 -003 -075 -05908785848 -087 -118 -151 121 -061 -02 -09 17 -121 051 STM3926 0030179 -035 -061 -072 -005 -008 -107 -083 -054 -048 -001 -003 -00502920759 242 099 188 1227 084 STM3927 03 -026 -071 -142 -0830076 -044 -018 -096 -055 -054 -008102404390541 0742 173038 2140235 102 STM3928 1050598 -013pT62J -0770068 -019 -088 -049 -051 005201630164053205470883 219087 2130798 152 STM3929 0990614 -034 -101 -011 -021 0092 -0590045 -089 -00403550722003206680809 217 15 2081202 1 STM3930 04804760778 -017 -031 -026 -009 -02306650683 -008 -027 -083[-164J -045 -09 -07 -1 i| -2.2J -084 -01 STM3935 060371 0393 -06305090175 -05209271383 -053 -028 -0280522 -00405150793 176 11 172 11 073 STM3936 -08 118 -087 114 -089 -026 -060696 141 -079 -113 -006 -139 -015 -073 -045 007 033 011 -043 -04 STM3937 -03 -051 -112 pug] -085 -04702080405 065 -112 -081 -04509290381 -0330607 198018 2931692 17 STM3938 041 0061 0370889 -035 -001 -106 -054 120222 -075 -011 1854 -1360835 -038 -08 -05 037 -039 096 STM3939 0580501 -059 -056 -00523 -031 -095 -044 -055 -048 -0330223 -0050391 1958 207 129 2031999 074 STM3940 -08 -0990427 -051 -006 -002 -106 -017 -08402643475 -069 -003 -134 -017 -023 021 -03 012 -095 -0 STM3941 -04 -0621208 -093 -0560336fT5| -059 -078##### -013 -041 -01602631153 -026 048 013 103 -011 092 STM3942 022 -0250461 -02500860183 -0070595 -022 -023 -099 -033 0390557 -002 -03 056 053 11 -017 047 STM3943 -03 -032 -052 -092 -09 -01502290058 -074 -102 -05 -096 -0.25 01 -02 -059 09 033 1580237 088 STM3944 007046800060155 0.23 -066 -006002709850415 -043 -082 -035 -072 -014 -054 042 -07 041 -088 -04 STM3946 05403240067 -081 -0230179 -046 -1 -077 -072 -041 -045 -0070222 1131256 203 106 149 115 082 STM3947 040478 -021 -135031702530002 -084 -069 -076 -05 -034 -006181016 088 225 068 2341046 098 STM3948 061 0302 -046 -114 -011 0268 -009 -135 -0590609 -075082708670425 181 055 151 096 1930955 162 STM3949 011 -018 -097 -172 -06006702130088 -074 -114 1 -084 -003 018 0380117 124 013 4750733 053 STM3950 0690242 -005 -196J -055 -01602440011 -025 -116 -037 -04303180157 -0080519 167 071 181 1112 015 STM3951 -03 -043 -112 -065 -059 -092 -105 -W-I 79 -176 -369 -^] -065 -143 -082 pi 56 -1 βj -i[^~-24 -2.541 -09 STM3952 1550091 -07612050116 -0160103 -037 -15 -1153271 -0540341235516120587 055 -0 0670271 091 STM3953 -04 -096 -027 -131 -0730006 -094 -127 -082 -1030845 -133 -00504390101 -032 015 042 087 -001 -03 STM3954 -0 -033 -01 -05 1488 -0880726 -054 -066 062 -12 -081 -002 -025 -054 -076 -09 -13 -04| -202J -14 STM3955 058 04605480371 08020538027905920291 0149|T79] -0861076 -0090623 -086 -1 -05 -07 -101 061 STM3956 12708521505 -034014805690073 -0021116 -002 -033 1420271 -05 1650351 -07 031 -01 0442 151

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM3968 106 0489 -007 0399 ■012 -026 -002 -058 0079 0126 093 0238 -031 -083 -026 0885 -01 -02 149 -12 038

STM3969 024 0653 -0 -013 0364 0178 014 0524 -012 -033 -025 -015 -061 0844 0702 0346 -03 006 087 0431 059

STM3970 038 -005 -033 -117 -04 0161 -03 -058 0168 -049 -003 -023 0384 0078 0397 0856 224 097 173 124 076

STM3971 091 0285 0076 -108 -014 0282 -006 -051 -043 mmm -082 -027 0362 -06 0796 1261 182 067 214 1045 063

STM3972 083 0107 0068 -14 -046 0041 0346 -094 -045 -027 -031 -043 0577 0158 0757 0897 201 121 2.45 1484 05

STM3973 -26 -26 -252 -227 -299 -098 -326 -349 «-325 -175 -136 -271 -182 -082 -154 -134 -12 -15 -05 -188 -19

STM3974 -21 -2.82 -236 -256 -331 -224 -392 -299 -4.78 -201 -249 ,-242 -157 -176 -134 -138 -14 -19 -14 -089] -15

STM3975 -18 -188 -2.11 -22 -2.64 -198 -24 -3.28 -315 -164 -Z04 -148 -115 -151 -059 -165 -09 -17 -03 -176 -03

STM3976 S 153 0886 0965 0576 0177 0306 -119 -165 -108 -018 1416 0383 0227 1418 0243 -017 17 031 -01 1553 -03

STM3977 071 0307 -O 81 j -173 -039 -031 -038 A3* -048 -128 -053 -005 0664 0842 0254 0879 237 117 177 0796 035

STM3978 034 -044 -027 -055 -106 -053 -006 -052 -037 -132 -04 -013 -02 -025 1371 148 06 137 0716 062

STM3979 -18 -2.44 -188 4179 -291 -306 -344 -231 -156 -08 023 0027 0425 -008 -152 -002 -07 -11 -258J -13

STM3980 -06 -036 -071 0254 0263 -055 -09 -057 -09 -067 -052 -098 -017 0841 0125 -057 -07 -09 -09 -12 003

STM3981 102 0232 -002 0575 004 -083 0227 -048 0681 2542 0648 102 0606 1788 0179 029 054 078 -13 007 05

STM3982 077 1333 0002 1366 1498 -042 1205 0702 0507 131 [-159 -008 -062 -085 -032 -015 -01 096 385 -033 -01

STM3983 043 0689 0531 0264 -031 -045 0295 0498 0697 0348 -023 -043 0088 -127 -017 0057 092 056 -01 -121 -02

STM3984 008 -025 -054 0226 -009 -081 0672 0787 -024 -095 0405 -076 0366 -008 136 -064 -01 -03 015 -04 054

STM3985 048 0126 0761 0018 001 0392 0003 0471 0225 -035 -03 1456 0901 -032 0894 -047 -06 -2.6 -003 051

STM3986 -12 -114 -173 -144 -185 -088 -166 -232 -172 -12 -194 -101 -14 -122 •087 -036 003 -03 068 0119 029

STM3987 063 0906 -047 -116 -079 0539 0153 1694 0228 -081 -038 -005 0325 0713 -005 0918 235 114 2.46 0887 083

STM3993 029 0261 -013 0177 -058 -028 -037 0369 0406 -1 -104 -012 09 -095 2179 -03 -12 185 -08 -04

STM3994 025 013 -074 -066 -083 -014 -071 -137 -072 -076 -055 008 -031 0176 057 0339 112 005 144 0428 05

STM3995 -05 -141 -063 0013 -171 -018 -016 2254 -087 3 0223 -066 -021 -149 -022 -03 -04 038 -084 -11

STM3996 053 035 0825 0216 0.255 -01 0559 0571 081 134 1193 0758 -036 -043 -018 2323 -11 -04 Zⁱ] -147 -0

STM3997 042 -001 -042 -121 -06 0278 -05 -08 -003 -08 -09 -069 0081 -036 -009 019 192 089 174 101 033

STM3998 016 -023 -035 -053 0282 -05 -054 0518 0943 -025 -06 0623 0612 0282 -009 -001 083 14 108 -034 048

STM3999 088 -01 -003 -184 -041 -007 -017 -09 -076 mmm -047 -002 008 0857 -084 1045 225 132 289 1033 049

STM4001 075 0227 -018 -111 -061 -002 -044 -067 -059 -023 -086 -037 0335 0005 0598 0705 239 123 2 0755 086

STM4002 074 0253 -102 -096 -062 0253 -024 -119 -042 -103 0188 -002 0595 0226 05 0816 175 063 192 0659 086

STM4003 049 051 -017 JLH -012 0169 -049 0501 -054 -076 0504 0285 0108 0472 1196 189 101 19 0932 109

STM4004 048 001 -083 -2.41 -071 -109 0206 -197 -248 -23 -272 -152! -055 -116 0711 -04 019 -ⁱ[ -175J -08

STM4OO5 045 -032 -062 -064 -104 041 084 -046 -086 1011 -051 -036 -005 -041 1235 0268 116 065 129 0421 104

STM4006 -05 034 -149 -06 -089 -07 -104 0358 -358 -089 -071 -145 015 -035 0323 -012 -03 -04 027 -12 005

STM4007 037 -03 -048 -066 -104 -034 -137 -072 -163 -031 -083 -013 -02 0023 0696 0219 138 003 132 024 043

STM4009 083 -037 -085 0096 -184 -076 -035 -111 0389 -144 0332 -⁰⁶¹L-Ji? -i⁵^ -104 -131 -11 -06 -05 -12

STM4010 09 0388 0099 0271 0695 -004 023 -095 o 926 mmm -134 -052 0493 0987 -069 -0 012 17 -07 0735 007

STM4011 -03 -018 036 -01 0077 -066 -017 -006 1043 0559 -173 -03 -08 -004 -0 -079 -15 072 -19 1023 005

STM4012 -0 018 0136 0102 0013 -013 0195 -009 0847 078 0022 0135 -019 -015 0064 -08 -01 -03 -059 -04

STM4013S -01 -011 0303 0215 022 0284 0008 0136 0491 0158 0522 -029 0302 -093 0204 0057 -13 -06 -003 006

STM4014 007 -02 0258 -037 0164 -037 -025 -027 0636 252 -005 -07 -01 0094 027 0238 -07 -07 -i -0l 5l -025 006

STM4015 -06 -005 -04 -011 0183 -03 0046 -002 -01 -044 -035 -012 -071 -028 -025 -09 -04 -07 -2 -129 -03

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4026 059 -014 053 0195 -069 -026 -017 -0.2906130247PTTTI 0104 -017 -0210522 -032 009 -04 -04 -025 056

STM4027 -O 50753 1037 -011 -03 030901780589 -0780067 -0530386 -079 -061 1077 -067 -0 -02 -13 -002 099

STM4028 0640095 -04 -109 -023 -029 -014 -064 -053 -064013912380111 0401050399 13 053 164 -052 047

STM4029 -08 -072 -04601190023 -05034401290297 -012 -024 -008 -098 -156 -009 -1-tl -1β| -11 41i| -19β| -04

STM4030S 00701480461 -043 -038 -08803360183 -001 -001 -0540224 -098 -197 0331 0207 -08 -111 -2 -Z22j -02

STM4031 026 -0450039 -118 -058 -0221 -155 -1781 -142 -014 -017 -0420.281 -01806481658 148 085 22 104 052

STM4032 -070919 -0990609 -019 -1030938 -131 07060255 008 -068 -103 -1406660267 -07 -03 -01 -14 087

STM40322I 052 009 -011 -099 -075 05330178 -101 -081 -034 -084 -056 052018508890744 193 15 1810913 054

STM4033 0301020321 -124 -099 -055 -055 -035 -121 -081 -037 -051 052 -00302660858 229 085 1730686 102

STM4034 -01 0106049503730218 -0190231 0377067301070285 -007 -012 -0630876 -013 069 -03 0880416 078

STM4035 -0701650533 -0880138 0699 -0430984 -048 ##### 16331922 -0090171 1305 -011 -01 013 024 -041 151

STM4036 05707640449 -0330223 074306020445 -008##### 15630316 -034029201283E-O4 004 -01 030016 054

STM4037 061 0276025803670251 00490048 -015 0650258 -0560014 -061 -0871178 -076 -09

-131 095

STM4038 0350681 -029 -056 -096 -0320868 -01 -070313 -069 -070247 -052 -021 0136 024 105 075 -03 -04

STM4039 059 -060205 -009 -021 0042 -013 0020898 -014 -04905640315 014 -058 -026 -14 -01 -14 -038 -08

STM4O40 -03 -0330072 0250453 0203 -01 0271 0382 -091 0768 -058 -035 -089 -0160139 -13 -O9[ -26] -11 -03

STM4041 -04 -061 1059 -142 -117 0423 -051 0993 -095##### -111 -046 -0130168 -061 0299 -01 04 073 -014 -02

STM4042 139 -00101540143 -031 -104 -006 -0140733 -0720345 051 0412 -02410682423 051 -09 0121223 089

STM4042A 09203460058 -148 -034 0294 -012 -0830011 -068 -046 -051 0655 -030755 1202 207 07 2140659 062

STM4043 0770603 -011 -011 -015 -081 -031 -083 -035 -04014210620247 07 247 097 188 -015 076

STM4044 -02 -0180321 -082 -047 -028 -009 -040838 -026 -05801940039 -08204430014 05073 0980253 095

STM4045 1 019 -022 -073 -054 -004 1564 -066 -053 -081 0023 -019 085 00609330612 219 127 1650855 066

STM4046 032 -07206590239 -027 -041 0124 1417 059 -062 pTig] -039 -14 -0080057 051 -01 052 -05 -125 036

STM4047 05700231051 -095 -074 0117 -00211860095##### -08 -042053710291141 0422 159084 1530567 106

STM4048 -040578 0370867 -108 -055 -084 -120031 -021327 -090377 -051 0915 -02 -04 -07 -05 -059 111

STM4049 0502440949 0440076 0361 -01 0309 -0244212 -105 -00041 -0230488 -032 213 059 034 -128 035

STM4050 -0304880461 05140054 -0090193 -005 014 -04 18320412302104050151 -023 -1 -04| ^] -099 018

STM4051 0530343 09404880593 061 -01900850.221 -01 382304970191 0501 0590747 -14 094 5460191 067

STM4052 -01 -13 1490272 007 0840261 0778 -055 009061706580187 -00304390431 -07 -08 426 -042 025

STM4053 0560067 -064 -12 -09 -012 -071 -113 -07 ##### -01 -0330226073203490989 165095 2340699 09

STM4054 0290119 -035 -111 -056 0262 -059 -1 -038 ##### -057 -0070491 017704431103 184 114 191133 041

STM4055 0570174 -012 117 -0 -091 -064 -08 -021 04090916071305390619 187 038 240963 084

STM4056 S 061 -067 -015 -035 0

-083 -073 -09 -069 OI2Q217J -106 0280055 -09 04

STM4057 -01 -0150047 -129 -138 -013 -0261025 -1 -085 -04301490273 -0150742 -004 102025 151 1853 009

STM4058 -12 -019 -O 39 -148 053 0432 0046 -073 0283 -033 ,r

³L -230231 -116 [Z-1i67 -19 -193 -11 -11 -06 0985 -15

STM4059 082 0260065 -154J 0069 01860216 -014 -O 38 ##### -01102760791026502341279 171 119 246 041 067

STM4O60 -04 -03 -092 -0380098 -013 -087 -089 -078 -04418910279 -11703330461 -086 -02016 0360169 037

STM4061 08 -0740324 -022 -122 -012 -01606860883 -1 -03 -12 -11 -09

STM4062 [ -18 -2.09 -184 -211 -2.66| -116 -093 -108 -074 -⁰⁹ -175 -13

STM4063 -05 -07 -071 -084 -047 -052082606451337

-06 -11 -09 -156 -14

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4076 -04 -016 018804620258 -004 -027 -015 -0250035 -02603150277 -03806180178 395 -02 -19] -044 026

STM4077 006 015 0384043504030304 -009 -063 -01800820581 -1040064 -09205090276 032 -0 -09 -0J5 008

STM4078 -09 -07 -059 -014 -084 -065 -0220177 -129 [ -1 βθ| -129 [-1871 -09813690154 -05 -15 -13 -11_-158, -01

STM4079 S -05 -015 0211 -031 -076 -036 -026 -0680077 -076 -083 -023 -0140404 -03 -033 064 -0 104 -024 -02

STM4080 -05 -037 0163 -054 -06 020729 -106 -046 mm -01710070235 -097 -0330104 -13 -08 ^"^Z9] -133 -01

STM4081 046 0327 -008 -126 -0490156 -013 -099 -109 -058 -055 -0050549009904410405 205075 1560608 083

STM4082 027 0174 -Oeef -1 ej -120028 -051 -093 -057 -O73OO25 -O 68 O 894039609630961 233128 2130508 086

STM4083 035 0259 -023 -09 -0390026 -015 -118 -047 ##### -04900140522025803360489 267081 1430727 075

STM4084 059 0599 0147 -135 -02806160023 -145 -055 -003 -062 -045068311740508 112 14085 1450432 058

STM4085 -01 0019 0449 J) 97 -016 -0580316 -01106350206 -045 -082 -07 -1130708 -066 -06 -11 -11 [^"-Tail 02

STM4086 043 -0150061 [-2M] -049 -012 00803970266 ##### -037 -03402330103 0081292 195048 207 077 081

STM4O87 064 0297 -058 -118 -0420645 -031 -121 -02 -089 -05 -0330571080802320786 201 091 2020598 12

STM4088 023 -02 -078 [^Jrø] -0780893 -057 -062 -085 -108 -039 -0440326 -01804580355 203134 2130897 063

STM4O89 056 0221 -038 -12801620093 -003 -049 -105 -0340193 -0630737044303070458 208141 1610761 067

STM4090 -0 0193 -019 -139 -128 -139 -066 -091 -058 -083 -092 -074 -118 -053 -144 -035 356 -01 024 -097 -11

STM4091 -13 -0150154 -022 -026 -009 -078 -079 [Til] -108 -0δ|-186| -114 -084 -074 -121 [Tej -14 -14QTOT] -12

STM4092 019 0352 0242 -093 -0970222 -0580221 -024 -105 -068 -032 -017 -02602550497 145 139 1690476 051

STM4093 -08 -023 1148 -14806090057 -03605240782 -066 -068 -0270738 -057 -05 -039 -1 006 -032022 056

STM4094 -04 0422 -124 -034 -012 -02502730122 -027 -018 -11 -078 -112 -0080023 -002 -01 -03 036 337 -0

STM4095 06 0708 029 [ -167J -0440028 -035 -101 -054 -085 -077 -013037505840231 093 233134 2041308 021

STM4096 122 0244 0191 -122 -0690006 -058 -035 -043 -0820493 -0920743 -00904980921 238 189 180731 088

STM4097 -09 01830488 -01703420375032401490005 -O74QT5] -03 003 -008 025

STM4098 -14 -088 -001 -05600590325 -025 -036 -03 -0231484 -020106 -038 -04 -053 -07 -02 -19] 0078 -03

STM4099 -08 -034 -001 -0430894 -08 -002 -0620637 -082 -106 -03β [_-1 _jβ7J -041 1395 -034 003_[ ^"Tj -32^299] 128

STM4100 046 0238 -0580164 -0660139052207360321

-028 -055 005 -01 J₁VST₁I ββ] 036

STM4101 -06 -046 -073 -137 -122 -055 -049 -005 -131 -126 -096 -075 -088 -083 -075 -069 061 06

STM4102 -07 -019 0174 -01102770263 -063 -087 -066 -0170329 -024 -024 -0470422 -048 012 064

STM4103 -13 0644 0651036807141496 -0151334 -057 -071 -14 QTe-J] 0233 -0720065 -125 -14

034

STM4104 035 -012 -0110223 -03 -054 -069 -0460228 -012 -03 -12 -0730245 -0031609 046065 -040464 -03

STM4105 -05 0351 -057 -116 -063 -032 -078 Qi_6βj -126 -089 -028 -0461467 -0160244 -012 075048 049 -015 004

STM4106 -02 -03 -01 -0680027 -0850242 -1160947 -108 -040593 -022 -04701740781 001 -06 074 -078 071

STM4107 -03 -033 -083 -004 -015 -018 -067 -062 -09 -1060017 -031 -073 -02 -04 066 -043 024

STM41O8 083 0314 00980589 -0190203 -0950621 -0680349019200070604 126 1 1950746 053

STM4109 -05 0786

070403581794 _-0_25 -036 -065 -072 -055 -066 038 -067 065 -07 089 -041 02

STM4110 -09 -049 -062026502380703 Qi∞, -029 066 -023 -069 -087 -003 -081 -11 025 -093682 -04

STM4112 -02 0418 0539013402790079 -042 -028 -093 -047 -041 -08 -072352826620491 -03057 0490088 26

STM4113 025 -053 -01

-134 -120175 -01406250078 196037 -020484 058

STM4114 037 -006 1027 -04302220201 -0090676 -03612280029 -075 -047 -065 0960122 078053 0690231 09

STM4115 07 0404 0545 -087097600880518 -053 -07##### -0604290224029302660894 127 122 1890725 054

STM4116 -07 -064 03270082 ########## -147 -086 -129 -081705 -12 ############### -107 -0078 11 -032 088

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4130 048 0046 011 0606 0275 0029 -015 0440443 -03 -082 -092 -068 -0351354 -129 -1 -03[ ^1j5ji287 138

STM4131 058 0052 -092 -099 -055 0452 -018 -087 -074 -002 -069 -0450092066408371308 247 111 165 1155 108

STM4137 067 0335 -0O6[-1[56 -068 -014 -045 -091 -048 -081 -056 -021245 038 0440907 179 161 2380177 108

STM4138 055 0623 -021 -102 -089 -034 -002 -022 -0180697019202021328 235 145 204 1215 046

STM4139 -04 -017 0453 -098

-075[-259]##### 1946 -0980049026314851408 082 104 1 2445 12

STM4141 066 1132 -029 ^209 -0240028 -069 -068 -098 -017 -011 -0030325099304590652 158063 231 0561 072

STM4147 041 066 -042 -098 -0600550156 -0760126 ##### -074 -034 0402840036 092 19 112 Z1 0809 042

STM4148 058 1046 0014 -033 -04401180372 -149 -089##### -03 -00803680271 -0270739 217 123 191 0573 06

STM4149 064 0201 -056 -1 -103 -0040425 -078 -086##### -043 -0151081060307650604 135083 196 044 092

STM4150 107 0782 -026 -125 -0490219 -014 -109 -081 ##### -1 -0220527055801430423 153 119 2680455 075

STM4151 079 0463 038 -087 -046 -015 -009 -121 -057 -028 -07 -0650845056507410516 184 066 2030387 069

STM4152 02 0478 -051 -254 -1870021 -029 -074 -076 -017 -059 -0020263027603530795 189 175 201 0942 067

STM4153 054 0231 0108 -064 -05 -0350517 -001 -055 -063 -05 -095 -0420108 -0141915 145061 138 045 019

STM4154 07 0727 0235 -119 -05 -0240156 -064 -032 ##### -12301181125035205990966 238 116 2521163 087

STM4155 065 0272 -033 -127 -032 016 -017 -105 -051##### -02 -0902950391 -0220208 161 103 207 065 123

STM4156 108 1221 -031 -134 -0170226 -08 -075 -05 -085 -069 -032 -0111401310936 228 154 211 0704 115

STM4157 -09 -068 -042 0105 -03801030053 -0280181 -043 -08 -121 -02805230034 -018 004 022 -03 -083 -05

STM4158 082 051 -023 -127 -120009 -042 -04 -036 -113 -049 -017 0240216 0352084 207076 197 101 081

STM4159 094 -022 077 -024 0086 -062049715391601 -024 -0810143 -07 -004 -0191188 028087 ^Te] 0771 085

STM4160 064 055 -014 -135 -053 -01502320073 -033 -058 -026 -0740484 -0 -0531153 229097 Z310948 104

STM4161 038 064 0039 -138 -007 -00476 -01 1091 -096 -057 -050783 -0160151 1116 217 02 2430969 05

STM4162 08 0789 -037 -12 -0810254 -02 -066 -085 -088024601410711 01603470617 222 104 2270794 088

STM4163 045 0283 0295 -085 -110057 -039 -002 -126 -104 -041 -0520769053906020719 213074 1960705 102

STM4164 096 0511 1199 -029 01702870677079206810012 -084 -0101230154 -069 -018 017005 1 1934 057

STM4164 058 0825 0574 -112 00440256083104390377##### -083 -04804850076 -0210014 081 -01 111 1116 063

STM4165 133 0141 0076 Λll 0410543092407181889 -01 -10206 134 1960121 042 147083 190615 081

STM4166 035 0047 -057 -139 -0650006 -021 -0650706 -0660059 -0570164 -02703220649 172065 2.340383 -01

STM4167 106 -014 -043 -016 -049 -007 -096 -134 079 -015 -1 -034 2550653 -0470813 081 -04 037 -018 -0

STM4168 096 -008 -069 0516 -07 -015 -028 -0820917 -032 [-iO/] -13727250074 -040558 042 -03 -13 -106 02

STM4169 046 0044 -08 -091 -056 -02 -094 -136 0250831 -041 -0370249 -05 -0180258 146051 1520366 101

STM4170 -03 0052 -045 -118 -0840499 -082(2TeSlJ 0231 -02 -034 -004 -0170517 031 0291 1 -02 15 043 123

STM4171 041 0381 0298 -046 -043 -095 -044 06090908471575 -06 OOOΘ^ja) -0430681 -08 -06 -10205 003

STM4172 01 0193 -018 -003 -012 -027 02802540258 -012 -057 -0160579 -141 -04 -058 -08 -08 561 -04 -05

STM4173 007 0367 0259 -049 -032 -035060612750754 -053 -03707110665 00505090576 166032 J^28_ 101 038

STM4174 035 036 -004 0179 0101019701040809 021 #####0846 -06 -066 -071 -018 -022 -03041 ( _-2iJTrø] -02

STM4175 028 -065 0472 -105 -2180075M 851 -00θ[ -1 ffil -042 -1180146 -135 -058 -0 -01 0592447 006

STM4176 046 -03 -14 -198 -256 -074K251 -165 ^■ -3T90233 -026 -048 -098

-145 -09 -08 2190104 -03

STM4181 111 0159 -036 -137 -059 0016 -025 -099 -036 -11 -00269 -004045400080507 197 135 170667 041

STM4182 -08 -055 -013 0215 0094 0141 -01103190342 -058 -071| -197) -081 -161 0323 -009 -1 -0β[ -33 -19 -0

STM41Θ3 -03 0107 -001 1142 -02407930558 -018 -023 -0850881 -0731439 -15β| •O 24 -127 -15 -01 -15 -076 -03

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4196 -1 0178 -09303050389 -043 -025 -076 -02 -016 -134 -058 -061 -061 -023 -024 304 -11 j^~3Tβ] -088 -05

STM4197 1080036 -048 -131 -028 -0360186 -135 -085 -051 -076 -058 134057303060269 202 127 220203 005

STM4198 -03 -002 -0350166 -02 -055 -006Ki5i| -047 -093 -093 -067 -0220818 -008 -009 -11 103 -29 1473 007

STM4199 -040116 -048 -0020151 -03 -013 -052 -005 -076 -097 -057 -030977 -011 -035 -1 067 -23 154 -02

STM4200 0690082 -00306440246 -037 -025 -037 -0360256 -0680056 -096 -079 -043 -024 -12152 1250472 -04

STM4201 _-1_βj -043 -O 67 [JTw] 0106 00740019 -064 -0290412 -111 0839 007 -021 -076 -077 -1 045 -19 -169 -0

STM4202 -07 -002 025 -01 0191 0699 -013040600131134 -050119 1351 -022 -0780501 -11 -01 002 -02 -08

STM4203 -06 -03105220012 -029 0081 030400690535 ##### 066305240205 -0430975 -096 -12 -06 002 -103 08

STM4204 -14 -049 -064 -019 -001 -041 -04 -051 -064 -083 -142 -075 -106 -036 -039

-11 -0 sJTβsj -06

STM4205 -14 -06 -069 -00214 -031 -039 -044 -087 -055 -121 -027 -005 -02 015 -077 -1 -11L-25] -005 -02

STM4206 125 0040258 -141 -062 0118 -063 -089 -031 -047 -075 -0220093 -00800240118 18 158 2240531 093

STM4207 0290086 -064 -123 -06 -00403080365 -063 -059 -044 -026 -041 -03204760073 193 057 1140164 -0

STM4208 0450408 -016 -086 -004 -032 -037 -064 -017 -0110296 -0370459 -0340426 -049 -03 128 0840054 027

STM4209 0580341 0077 -11 -075 -041 -01 -042 -02 -041 -078 -01801290412 -0420787 176 09 2040705 066

STM4210 -01 0128 -149 107 -134 -003 -021 -1160358 -048 -144 -104 -004 083 -0530046 071 146 0842977 -02

STM4211 0490361 -038 -135 -06 -00216 -094 032 -098 -055 -0160023 -02800770458 134078 1590038 081

STM4212 -070382 -047 -0120004 0368 -03 -047 -061 -021 -0391777 1091 0576 052 103 -05052 0030011 019

STM4213 -01 0163 -044 -134 -012 0164 -012 -056 -1131043 155 -091 -02504620259 -01 01 045 037 -059 031

STM4214 -02 -025 -136 -103 -053 -0060305 -1260625 -045 1160013 -062018503550086 044 102 1 0663 -02

STM4215 -1 -013 -04 -0170206 -07 -018 -092 -036 -079 -069 -024 -10213440051 0317 -11 -1 -12 -097 -02

STM4216 -0201390052 -132 -023 -01 -037 -06 -074 -05 -07 -009 -001 0085 -04 -06 109054 089 -084 -05

STM4217 -02 -02 -05801070077 -084 -O01 -052 017 -039 -126 -036 -041 -059 -11

-13} -2.2 -2^~δ] -09

STM4218 0530239 -078 -115 -034 014 -024 -114 -065 -005 -09 -019 -0170105 -0150528 099 -02 166 -023 015

STM4219 S -00338 -05 -0220443 -0030292 -065 -01803120163 -0730912 -0220026 -073 -07 -03 062 -069 026

STM4220 070279 -06 -0570075 0112 -043[-179J -059 -021 -025 -068 -034 -0440589 -003 107044 124 -003 067

STM4221 056 -016 -06 -097 -106 -024 -076 -125 -103 -048 -05 -0202060021 0260364 157 059 1920659 063

STM4222S 0270762 -019 -084 -031 019 031 -029 -077 -062 -098 -026 -0030216 -035 -024 133 041 1650372 074

STM4223 084 -0040252 -073 -03 0311 -082 -076 -0740304 -031 -0460323 -016 -002 -002 026035 2.220196 044

STM4224 -03 10750187 -001 0363 -114 -013 -095 -0060149 D363 -079 -1150603 -0150803 046 026 -02 -084 009

STM4225 062 -025 -025 -024 -103 -029 -076 -023 -077 -0330028 -03 -06716750091 -008 024 001 048 -044 015

STM4226 0270107 -02207820258 081 0501 08221057 -104 -114 -0070222 -028 -037 -068 -04 049|_j27J -079 028

STM4227 -01 035 -063 -126 -037 0504 -108 -0260224 -078 -111 05580328 -1180081 -019 018 04 0281109 013

STM4228 111 031507150653 -04 -003 -012 -002 -067 -029 -066 -07 -06200370727 -057 -14 -0

-124 075

STM4229 034 1239 -02905970553 -0050259 -0291143 -021 144 -0650847 -1071231 -049 -02 -0 038 -058 068

STM4230 098096308020551 0388 -001 0531 0311 0778007405960939 -015 -070471 0384 -09 082 -140328 066

STM4231 037 -0060672 -036 -016 0654

-03 -065048402490295 -045 -037 -02 -02 -02 -045 005

STM4232 0340776 -080392 -012 0022051502340827 -042 017 -00802460416 081 035 07 023 1170309 141

STM4233 067 -02 -015 -129 -11 0019pl 73 -298 -2~4til -034 -028 -0240199043202430495 099058 1940033 08

STM4234 014 -032 -053 -07 -087 -015 -0840877 1073 -086 -126 -0130513 -006 -0570055 054 01 062 -101 -02

STM4235 08 035 -047 -089 -055 00320179 -096 -04 -01 -045 -041 04450431 -0020822 19 099 1870878 059

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4247 0.22 1.019 0.703 0.426 1.266 0.978 0.93 1.741 0.683 -0.04 -0.62 -0.96 -0.81 -1.45 0.354 -0.88 -0.3 0.1δ[ _j22\ -0.19 0.43

STM4248 -0.5 0.683 -0.07 0.569 -0.12 0.834 -0.18 0.721 0.408 ##### 0.443 1.353 0.323 -0.08 0.345 -0.77 -0.6 -0.3 0.47 0.675 0.37

STM4249 0.12 -0.65 0.521 -1.07 0.299 -0.67 -0.35 0.312 -0.26 0.757 0.314 0.029 0.522 -0.3 -0.42 -0.02 0.13 -0.1 0.49 3.582 -0.4

STM4250 0.61 0.385 -0.42 -1.18 -0.58 0.55 -0.74 -0.45 -0.23 ##### 0.132 -0.46 1.123 -0.9 0.431 0.806 1.49 0.97 1.03 0.66 0.85

STM4251 0.75 0.595 0.255 0.228 0.375 0.727 0.213 -1.33 -0.77 2.472 -0.37 0.217 -0.61 -0.7 0.08 -0.7 -1.15 0.29

STM4252 0.24 0.986 -0.83 -1.29 0.445 0.168

-0.72 0.432 2.312 -0.1 3.395 -0.39 -0.17 0.63 0.41 1.72 -0.1 0.74

STM4253 0.8 0.425 -0.54 -1.4 -0.84 0.312 -0.44 -0.55 -1.28 -1.21 -1.4 -0.42 0.922 0.179 0.419 0.717 2.6 1.21 2.09 0.769 0.38

STM4254 0.44 0.575 -0.17 -1.01 0.153 -0.16 -0.32 -0.14 1.313 -1.39 -0.23 -0.2 0.668 0.146 0.055 0.838 1.9 0.42 1.72 0.49 0.92

STM4255 0.9 0.208 0.159 -1.45 -0.31 -0.58 -0.04 -1.18 -0.66 ##» -1.03 -0.48 1.216 0.197 0.363 0.455 2.24 0.98 2.02 0.198 1.24

STM4256 0.33 0.377 -1.1 -1.34 -0.54 -0.06 -0.34 -0.98 -0.78 ##### -0.17 -0.14 6E-O4 0.181 0.231 0.167 1.97 0.92 1.58 0.314 0.9

STM4257 0.77 0.042 -0.32 | -i:sβj -0.76 -0.79 -0.81 -0.66 -0.39 -0.11 0.784 0.543 2.13 1 1.9 0.194 0.5

STM4258 -1.64 -1.66 I -0.62 -0.55

-0.81 0.802 pzU] -0.58 -0.81 -0.87 -1.24 -0.8 f-tτ] -0.5 -1.47 -1.1

STM4259 -0.1 -0.17 -0.8 -1.04 -0.56 -0.12 -0.74 -0.77 -1.44 -0.8 -0.47 -0.85 -0.13 0.938 0.341 -0.35 0.98 0.11 1.47 1.755 0.32

STM4260 0.42 0.273 -0.45 -1.12 -0.18 -0.64 0.226 -1.29 -1 -0.74 -0.32 -0.67 0.606 -0.26 0.572 0.365 JL48 1.15 2.1 0.793 0.7

STM4261 -0.84 -0.84 -0.59 -0.11 -0.19 -0.61 -0.97 -1.37 -1.01 -1.18 -0.41 -0.76 -0.83 -0.3 -0.β[_-17] -0.β| 2LJ] -0.4 -1

STM4262 -0.6 -0.7| -1.64 -iiϊ] -0.07

-0.89 -0.64 -1.21 -0.33 -0.25 -0.33 0.015 0.17 0.08 1.06 -0.81 -0.5

STM4263 0.41 0.424 0.027 -0.3 0.077 0.089 -O.07 -0.46 0.335 ##### 1.787 0.052 -0.3 -0.11 0.023 -0.59 -0.1 -0.2 -0.2 -0.7 0.47

STM4264 0.23 0.068 0.122 0.928 0.298 0.278 0.374 0.34 0.605 -0.45 D.496 -0.46 -0.68 2.128 -0.03 0.337 -0.4 0.26 0.79 -0.19 0.14

STM4265 0.21 0.146 -1.33 -0.39 -1.25 -0.93 -0.81 -1.49 -0.02 tttttm -0.81 -1.01 -0.36 -0.06 -0.85 0.16 0.94 0.43 1.45 -0.22 0.13

STM4266 0.79 0.532 -0.43 -1 21 -0.18 -0.16 -0.21 -0.83 -0.34 -0.7 0.117 -0.6 -0.21 0.077 0.296 0.844 1.51 1.1 2.26 0.695 0.25

STM4267 0.93 0.275 -0.37 -0.29 -0.48 0.196 -0.68 -0.63 ##### -0.69 -0.53 0.819 0.119 0.543 0.368 1.92 1.52 2.18 0.538 0.68

STM4268 -0 0.174 0.246 0.196 0.157 0.886 -0.16 0.292 -0.2 0.534 -0.77 -0.76 -1.15 -0.66 0.146 -1.33 2.82 -0.2 -1.3 2.823 -0

STM4269 0.44 0.098 -0.6 1.006 -0.22 -0.18 -0.2 0.244 0.877 mm -1 FSU] -0.22 -1.42 0.672 -0.04 -0.9 0.33 -0.3 1.266 0.68

STM4270 -0.4 0.301 -0.82 -0.23 0.467 -0 0.318 -0.88 1.239ΓM:74| -1.03 0.493 -0.83 [ -1.761 -1.371 -1.98] -1.3 -0.7l TJS ~Ε^\ -1.1

STM4271 0.7 -0.07 -0.05 -0.57 -0.1 0.428 -0.28 0.246 -0.04 -0.48 -1.04 -0.03 0.641 -0.28 -0.03 0.374 1 1.72 1.42 -0.08 0.76

STM4272 0.63

0.027 -0.04 0.683 0.246 1 308 0.412| -1.55 -1.5[ -0.57 0.281 -0.81 0.678 -0.1 -0 ¹ 'L1Z³J -0.8

STM4273 1.07 -0.26 0.444 0.051 -0.72 -0.14 -0.22 0.244 0.152 0.152 -0.32 -0.17 3.577 3.327 0.831 -0.31 -1 0.62 -0.2 -0.36 0.86

STM4274 -0.3 0.422 0.465 -0.04 -0.22 -0.49 -0.58 -0.81 -1.02 -0.58 -1.45 0.166 -1.06 -1.39 -0.83 -0.86QΪJB] -1.1

-1

STM4275 0.9 0.919 -0.511 -0.17 -0.22 -0.36 -0.48 -0.18 ##### -0.5 -0.8 0.698 0.926 0.254 1.094 1.45 0.94 2.8 0.263 0.29

STM4276 -0.1 0.328 -0.371 -0.51 0.694 -0.23 -1.03 -0.52 -0.98 -0.57 -0.25 0.395 0.355 -0.39 1.591 2.34 1.44 2.14 0.45 1.05

STM4277 0.02 -0.08 0.171 -1.02 -1.12 -0.5 -0.88 -0.92 -1.37 -0.31 -1.23 2.724 0.009 -0.61 0.249 0.08 1 1 0.966 0.3

STM4278.S -0.6 0.435 0.141 -0.05 -0.01 -0.37 0.458 -0.05 1.161 -0.68 0.461 -0.49 -0.32 -0.87 -1.2

-O.δQl.8] -1.44 -0.6

STM4279 -0.5 0.057 0.003 0.449 -0.31 0.225 -0.26 0.933 0.19 -0.79 -0.03 -0.07 0.182 -1.27 -1.3 -0.01 -1.2 0.8 -1.4 -1.05 -0.2

STM4280 0.14 0.619 -0.65 -0.5 -0.2 0.171 0.589 1.886 0.492 -1.02 1.671 -0.12 0.271 0.262 0.458 0.013 0.11 1.01 0.75 0.263 0.8

STM4281 0.15 0.414 -0.06 -1.21 -0.31 0.118 0.24 0.734 0.02 -0.59 -0.95 -0.22 -0.06 0.049 -0.09 0.537 1.45 0.52 1.72 0.933 0.34

STM4282 -0.5 -0.54 -0.09 -1.06 -1.24 _3.47 -0.28 -0.46 -1.37 -0.42 -0.63 -0.42 -0.48 4.22 -0 0.07 -0.65 -0.5

STM4283 0.25 -0.41 -0.68 -0.06 -0.32 -0.75

-0.03 -0.27 0.495 0.603 1.355 1.536 0.496 0.33 -0.4 0.92 0.136 2.2

STM4284 0.34 0.308 -0.31 -1.03 -0.26 -0.25 -0.48 -0.53 -1.18 2.299 0.403 0.287 1.543 0.14 -0.01 0.357 1.19 -0.1 1.07 0.177 0.08

STM4285 0.37 1.01 -0.11 0.325 0.23 -0.63 0.912 0.828 1.044 -0.09 -0.45 0.375 -0.04 0.552 0.252 -0.1 -0.6 -0.5 -1.3 0.393 0.6

STM4286 0.28 -0.66 0.059 0.018 -0.8 -0.1 0.224 -0.95 -0.44 0.088 -1.12 -0.29 0.527 -0.66 0.027 0.182 1.1 0.81 0.83 0.421 0.44

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4299 -030037 -012 -06901430543 -00306030287 -09707790033 -0831853 -008 085 -03083 -I_^ 0499 021

STM4300 016 -086 05691168 -01207890014007909850807 -079 -117 -122 -077 13 -082 -08 023[ -17 0412 102

STM4301 0220253 04740169 -067 -027 -00600130567 -077 -1390365 -031 -0504560341 016 112 044 1156 085

STM4302 0420764 0462 -018061705370322 -0302551157034612130985066700870577 149 054 06 -056 014

STM4303 -01 0624 -053 -09 -0020247 -034 -042 -014 mtmtt 06170558 ttttttmt ittttmtt tmm -001 -02 052 -090599 031

STM4304 0050378 -0040546 -03600660004 -099 -073 -0 -11 -0520859) -16β] -02144 004 11 -17 095 02

STM4305S 023 -047 -002 027 -028 -047 -0120032 -008 -056197207520017 -063 -027 -052 -04 032 -097 -04

STM4306 0240256 -005 -092 -01 -005 -0550147 -062 -032 -056 -0250526 -001 05540898 188 114 203 0971 075

STM4307 0430476 0094[-157J -050662 -039 -0630044 -029 -021 -0470276 -012 -O 0741 22 115 248 0757 065

STM4308 1031061 132301920096054609420821 1319 -01 05551418 -011 083705271166 131 093 -024 141

STM4309 -01 01 -03204340059 -0650169 -017 -079 flfl###|^?8t] -071 176['_r202] -074 -036 -02 -05 Tea] -01

STM4310 -06 -075 -0720443 -045 -079 -063 -074 045 -0551833 -051 -021 -11 -028 -045 -05 -03 -088 -03

STM4311 -04 -028 -02501570499 -00602830062 -01 -097 -053 -065 -01 0077 -025 -07 -15 -04 -1 0718 -09

STM4312 -02 -005 001800060491 02890031 -026 -025 -0320315 -0380059 -0404880163 112 065 106 0069 073

STM4313 05 047 -056 -11 -050029 -077 -018 -016 -045 -088 -079 -0420148 -0 065 075064 114 -027 -0

STM4314 058 -001 -018 -091 0160144 -05 -08 -085 -065 -072 -041 0347 01304250079 123035 131 -059 -03

STM4315 1020092 -015pT56] -060176 -012 -075 -091 -055 -11 0002 -013053702290798 167 117 145 1014 081

STM4316 0640378 -018 -107 -046 01 -053 -0150551 -023 -065 -0150132 01902690677 127 104 175 0759 046

STM4317 -04 -029 0155 -058 -114 -045 -002 -038 -051 ttmm 08320462 -031 -008 -050655 018 -02 027 0218 -02

STM4318 -050354 -05202120443 -1220058 -014 -016 -004J--272I -113 024 -069 -008 -128 -15 -12 0426 -08

STM4319 0460041 01291241 08860846052608351001 1807 -107 -020652 -011 02880052 -05052 -17 0815 052

STM4320 050356 -029 -119 1080136 -029 -087 -091 -031 -052 -0331713021404241143 227 107 197 0716 106

STM4322 091 0202 -015 -117 -03602460057 -054 -01 -049 -09 -097 0080646 -0030856 169 138 182 1161 134

STM4323 0770027 -019 -0630134 028 -044 -094 -001 -014 -07 13606750155 -015 -015 088 003 1241648 056

STM4324 070204 -067 -092 -0830279 -031 -048 -048 -064 -045 -031 06490468 -021 067 188 156 2160418 072

STM4325 054 02 -0460158 -011 -0560053 -043 051 0630161 -091 0505 -128 -094 -043 -15032 -0 -116 -0

STM4326 004 -048 059808320421 00130485 -0040602##### -0280979 -039 -117 -028 -041 -04 149 -01 099 -05

STM4326 -02 -038 082706280058 -0020589 -0080466 -052019810340126 -065 -025 -06 -03215 -07 1388 004

STM4327 101 1056 0074 -136 -03903340227 -007 1084 -079 -068 -0090356 0203970839 2.22 125 212 0416 07

STM4328 0890316 17021411 03730827 04704030726 -11608361021 0231 -07301220558 0.21 095 -1 238 108

STM4329 0940262 ~°¹⁶["li§l -0860447 -018 -072 -1 -034 -022 -03904430369 -0050277 224 079 222 0979 074

STM4330 0590381 -054 -118 -0280608 -073 -138 -072 -049 -039 -071 0302061611090885 197 087 185 0807 119

STM4331 0030234 0718 -004 -097 012 -01 -064 -105 031 -074 1383 -071 0095 -01 -088 -02 -08 -04 -064 019

STM4332 0270216 02460532 031 -022 01 -0550011 -021 052807790413 -018 083 -04 142 -02,Ts] -043 034

STM4333 -1 -024 -151J -028 -0881 -168J -Q8β[ -18 -212 mm A 172301 -103 -096 [Taj -12 -04 -12 024 -101 -11

STM4334 0060639 1186 -0903381182 -08802180608 -1560649 -102 1093 137 18920414 -03 134 048 -079 113

STM4335 -060323 1468 -041 04560681 -01305031419 -108 -022 -111 062911740925 -021 -04 084 036 -148 127

STM4336 071 -008 -003[-17TJ -047 -032 -062 -068 -079 -065 -066 -0370516086401180107 163 171 172 071 015

STM4337 -04 -013 -0470081 0285 -05204830417 -078 -051 -0040597 -044 [TeTJ 0077 -015 -12 -0 -13J -197J 013

STM4338 051 0334 -021 -052 -091 0378 -031 -057 -118 -02203270075 -03 -0530846 -008 14 062 15 1992 044

1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4351 -12 -074 -08913431.2120829 -056 -109 -0720079 -082 -059 029 -05 -05 -051 -06

STM4355S -03 -007 -099 -147 -026 -0650617 -109 -2.04 -189 -0660024 -107 -148 -06 -12 -08 -089 001

STM4356

04940474 -0030677 -095 -042 -041 0654056809030276 138 065 1 1386 162

STM4357 0 003 -06 -1 35 0501 0334 -079 0249 -142 -093 0359 -028 -0090093 0020674 193 072 1450332 065

STM4358 -1 -061 -118 -077 -016 -074 -088 0649 -147 vi'ssj 0999 -03 1406 -057 -07 -084 404 016 067 -053 -03

STM4359 075 071 -054 -1 18 -088 0374 0195 0306 -0 -049 0524 -088 13821301 -015 -017 172 0 1280701 079

STM4360 0240057 -066 -1 24 -057 0376 -031 -07 -052 -091 -04 -08 -021 -031 -0250769 143 033 247 093 078

STM4361 090109 -071 -1 62 0084 032 -041 -069 -03 -049 -041 -007 -046 -049 -031 0902 229 103 282 -012 056

STM4362 0330858 -045 -067 -037 0246 -119 -092 -061 -033 -06 2040048 066

STM4363 -12[-Z02j -14 -1 17 -074 -072 -069 -258 -174 -19βj -12 -18 -226 -08

STM4363 -12[_-2JM[ Λ -1lβ -1 05 -067 -113 -065 -077 -269 -176 -195

-12 -18 -Z29 -05

STM4364 064 015 -012 -162ι -08 -016 -062 -0120054 -039 -042 -0290165 -01 -0130673 145075 2150558 061

STM4365 0760504 -063 -128 -0320367 -027[_j-1jBiJ -094 -066 -052 -0740321 -03401930261 225 198 260777 059

STM4366 086 004 -046[ -161 j -018 -01 -048 -09 -022 -048 -052 -0230083 -020361 0792 163 097 1940983 095

STM4367 050461 -051 -065 -0540228 -066 -061 -146 ##### -0203560663086710450647 204 081 1830184 044

STM4368 0070004 002 -0150642 -019 -042 -109 -032 -13pi^"93J -128 -059 -139 -091 1073 054 -08 -02 -097 -1

STM4369 0530197 06390037 -011 -003 -02508990078 -0830406 -006 -011 -06 -009 -064 -09 -06 -02 -044 009

STM4370 -07 -048 -072 -055 -034 -095 -025 -1 -026 -081 L₁IJBiJ -087 011 -119 -077 -076 -13 -08 -14 -096 -05

STM4371 -03 -002 -072 -015 -003 -022 042 -0310057 -0440431 -017 -043 -04 -033 -073 -05 -07 JlT] -023 -07

STM4372 -02 -02 0771 -0340262 -0390013 -085 -11300871546 008 -041 -017 -101 -024 16 043 2.07 1632 -13

STM4373 -06 -005 -021 0018 -0550409 -05301420004 -0260162 05503361943 -033 -058 -11 -07 -04 -089 -02

STM4374 -070202 036 -043 -0020515 -042042301760583 -08306590025 -0181003 -022 -07 -05 -130787 069

STM4375 -01 -012 05920336 -0190224 -030142[_-1_67J##### -078 -029 -024 -079 -051 0539 -19 -14 131 -112 -07

STM4376 -02 -047 -054 -01 -087 -093 -081 -115 -046 mm 1652 -039 -126|j2_25j -143 -123 -17 -11 -09 077 013

STM4377 -00358 0387027304460228033704810161 -031 -1380824 -031 -145 -055 -063 -12 -04 052[~-213J -06

STM4378 -05 -018 0518 -066 -1 01060611 0189 029 -084 -106 -1130199 -001 -004 014 049 138 111 0017 021

STM4379 065 -017 -092 -145 -098 045 -006 -08 -033 ##### -002 -03306320079 -0680298 181 086 1840651 079

STM4380 0920508 -OI2QV7] -^14802840255 -⁰²⁷ -°²⁷ -⁰⁴⁴ -⁰³³ -^00606711126 -^{0860823 182 16} 221 0108 083

STM4381 08 -008 0192 -1070144 -013 -1060448 -1070466 -117 -0570675 -0360695 01 051 027 ⁰JL⁷JL¹⁷ '°³

STM4382 -1 021408060259 -0061204321032 -004 mm#^ΛT^[ -077 f -19 -Z9 -3 ϊβj -11

STM4383S 029 -03 0174 -006 -032 -023 -0120252 -032 -123 -048 -0581284 -125 -0761437 -16 -07 -21 -164| -01

STM4384 0540227 -097^209] -064 -0380036 -126 -021 -073 -085 -005062706750571 0847 155 132 2080816 075

STM4385 067 -009 0043 -133 -0560234 02 -027 -082 -121 -01201580167 -037 -065 -005 092027 145 015 051

STM4386 138 019 0145 -08 -045 -0 -026 -097 -082 -02 -009 -008105905740561 0576 207 106 204 1275 13

STM4387 161 0108 -0250947 -0520808^-185] 03290638 -119 -0851111 057 -04307030411 105 294 135 -019 136

STM4388 031 -011 -08 -0730674 -062 -008 -149 -059 -104 -082 -026 -0220221 0161 -002 059 -08 06 -076 008

STM4389 0440075 004 -075001705090538 1243 -131 000416040904 17034385 -031 0948 115 062 1352323 082

STM4390 -01 0325 0013 -015037806060207 -021 -09 -051 -045 -135 -001 01961E-03 -023 065 009 0540156 049

STM4391 046 -011 0098 -116 -1180136 -014 -09 -027 -062 -069034904670521 05270626 181 092 1690263 054

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4405 0.07 -0.11 1.611 0.298 -0.04 -0.4 0.014 0.327 0.61 -0.12 0.438 -0.11 -1.02 -0.22 -0.44 -0.61 -0.4 1.11 -0.1 -0.81 -0.5

STM4406.S 0.54 0.593 0.407 0.355 0.237 0.355 0.185 -0.85 0.752 -0.48 -0.04 1.242 -0.08 0.073 0.268 0.129 1.07 1.71 1.38 0.68 0.67

STM4407 0.02 -O.3| »"-1.62 -0.13 -0.34 -2.15J 1.015 0.486 1.067 0.516 -0.06 -0.56 2.46 0.777 0.067 -0.091 -1.6| θ.44 -1 0.911 0.01

STM4408 -0.3 0.042 0.103 -0.39 -0.27 -0.72 0.34 0.367 -0.33 -0.09 0.205 -052 -0.91 -1.36 0.309 -0.88 -0.6 -0.7 -1.2 1.151 -0.4

STM4409 -0.7 -0.79 -0.57 -0.24 -0.26 -0.67 -1.1 -0.97 -0.87 -0.3 1.08 -0.02 -0.68 -072 0.032 -0.02 -0.2 -0.2 [ -1.7] 0.39 -02

STM4410 0.26 -0.12 -0.44 -0.69 -0.16 -0.56 0.16 -0.2 0.004 -0.33 -0.7 -0.51 -0.19 -0.61 0.297 0.072 0.9 0.22 1.08 -0.09 1.17

STM4411 -1 -0.34 0.356 -0.85 -0.76 -0.75 -0.58 -1.09 -0.47 ##### -0.21 -1.16 -1.21 -1.44 -1.39 -0.09 0.39 0.36 0.05 -0.98 -1.1

STM4412 -0.5 0.015 0.006 -0.3 0.195 -0.25 -0.41 -0.29 -0.83 -0.47 -0.95 -0.79 -0.25 -0.9 -0.97 -0.23 -0.9 -0.3 -1.1 0.331 -0.6

STM4413 -0.9 -0.42 -0.48 -0.23 -0.02 -0.48 -0.19 -0.53 -0.39 0.241 0.895 -0.65 -0.43 -1.42 -0.01 0.042 [_-1j}| -0.8 [j^ -0.75 0.16

STM4414 1 0.245 -0.7 [IfSr] -0.89 -0.07 -0.43 -0.56 -0.8 mmtt 0.243 -0.07 0555 0.275 0.173 0.686 2.06 1 47 2.09 0.639 0.46

STM4415 0.45 0.249 -0.79 -0.91 -0.12 0.662 -0.27 -1.3 -1.22 -1.16 0.035 -0.89 0.391 -0.24 0.494 0.218 1.81 0.73 1.44 0.736 0.62

STM4416 0.06 0.066 -0.25 -0.93 -0.51 0.247 -0.63 -0.55 -0.16 -1.38 D.005 -0.46 0.409 0.437 0.516 0.708 1 86 1.31 2.04 1.18 0.86

STM4417 -0.3 -0.27 0.575 1 949 0.939 0.632 0.254 0.107 0419 0.171 -063

0048 -079 -1 15 -0.2 0.36 0.22 -0.65 -03

STM4418 -0.6 0.067 -0.52 -0.05 -0.22 -096 -0.07 -0.98 -0.38 ##### -1.3 -0.72 -0.97 -1.3 -0.76 0.489 -1 -0.7 0.32 -0 -0.5

STM4419 -0.8 -1.09 -0.71 1.515 -1.92 0.617 -0.1 0.157 0.281 -0.85 -1.11 -0.85 0.308 -081 -0.26 -1.21 -0.4 -0.7 072 -0.35 0.12

STM4420 0.32 0.165 0.45 0.04 -0.35 0.245 -001 0.24 -0.08 -0.59 -0.37 -1.02 -02 1.319 -0.15 0.076 -0.9

1.287 -0.2

STM4421 0.58 0.294 0.021 -0.64 0.922 0.47 0.053 0.341 -1.18 -0.51 -0.76 -0.53 0.008 -0.3 -0.26 1.041 1.13 1.7 0.94 2.666 0.51

STM4423 -0.6 -0.34 -0.23 0.155 0.156 0.445 -0.47 -0.73 -1.1 -0.08 -0.91 [ :_:1.77,j -0.21 -022 0014 -042 -0.6 -0.41 -1.8 -0

STM4424.S -08 -1.03 -0.31 -0.03 -O 0.009 -0.09 -1.43 -0.6 -0.41 -0.47 0.016 -0.34 0.782 -0.07 -0.6 -0.8 -0.3 -0.3

STM4425 -0.8 -0.27 -036 -0.21 0.149 -0.13 -0.01 -0.05 -0.43 -0.8 1.89 -0.3

STM4426 pfiiil -O.99I 2u5] -1.24 -0.67 ^"SSβl 0.246 -0.76 -0.23 -0.82 -1.5| -0.6

STM4427 -1.4 -0.2 -0.61 -0.95 -0.56 -1.05 0.344 -1.01 -0.24 -1.14 -0.4 -0.1 -0.5

STM4428 -1.3 0.073 0.306 -0.57 -0.14 -0.79 0.449 0.748 -0.48 -1.88 -0.9 -0.7 -0.4

STM4433 -0.4 -0.13 0.025 0.254 -0.29 -0.07 -0 -0.32 0.474 0.152 -0.03 -0.75 0.684 -1.2 -0.48 -1.07 -1.2 0.62 0.02

STM4434 -06 0685 -004 -0.68 0.056 -0.67 0.041 -0.71 -058 -0.06 -0.5 [^1.54 1.57] -1.04HTT] 0.89 -0.8

STM4435 -0.1 -0.51 0.125 0.369 -0.14 -0.05 -0.43 -0.48

-028 -0.51 -0.49 -0.02 -0.05 -1.08 -0.07 -0.28 -1 -1 -0.3

STM4436 -0.9 -0.02 -0.5 -0.45 0.05 0.03 0.165 0.093 0592 0.261 0.491 -0.65 -0.65 -0.23 -0.12 -0.53 -1.1 -0.2 -0.4 -1.28 -0.1

STM4437 0.21 0.301 [ -0.34 -0.21 [

^7^ -1 26 ##### -1.08 -0.44

-1 29 -0.86 -1.1 -0.8HlSJ -1.49 -1

STM4438 0.6 0.566 -0.43 0.044 0.524 -0.36 0.558 -0.21 0.055 -0.37 0.396 -1.03 1.571 -1.12 -0.45 -0.67 -0.9 -0.8[ -17J -0.36 -0.9

STM4439 0.96 0.101 0.279 1.165 0.552 0.12 -0.2 -0.32 0.322 -0.07 -0.59 -0.68 -0.02 -0.76 -0.55 0.131 -1.3 -0.7 0.84 -1.42 -0.7

STM4440 0.13 0.569 -0.37 -1 03 -0.9 0.08 -0.25 -0.26 -0.35 -0.43 -0.76 -0 13 -0.14 0.199 0.221 0.554 2.12 1.07 2.07 0.501 -0.2

STM4441 0.65 1.271 0.076 0.015 1.032 -0.6 0.96 0.991 0.763 -1.27 -1 32 0 183 -059 -033 -0.2 -0.5 041 0.85 0.57 2.959 -0 3

STM4442 0.32 0.346 -0.281 53 -0.88 0.237 0.143 -1.11 -097 -0.79 -0.43 -0.21 0.529 0.444 0.28 0.889 2.26 1.27 2.2 0.428 0.68

STM4443 1.89 0.161 0.947 -0.64 -0.42 0.223 -0.19 0.138 0.172 0.26 2.636 -0.44 -0.27 -0.15 -0.16 0.385 1.16 1.43 1.94 0.423 0.21

STM4444 0.54 0.281 -0.05 0.257 -0.43 -0.4 -0.21 0.09 -1.09 -0.57 -0.53 -0.37 -0.24 -0.2 -0.7 0.293 -0.3 0.42 0.97 0.469 -0

STM4445 0.71 0.488 0.317 -1 08 0 15 -0 15 0.165 0.45 -004 -0.61 -0.08 -0.38 0.666 0.022 0.723 0.834 1.14 0.82 1.72 0.812 0.79

STM4446 007 0.181 -001 -007 0305 0.226 -0.13 0.429 -0.26 -0.86 -0.12 -0.28 -0.37 0.228 -0.7 0.1 -0.5 -0.1 -1.3 -0.51 -0.2

STM4447 -0.2 0.018 -028 0.11 -0.07 0.175 0.913 -0.42 -0.66 0.764 -0.56 -0.64 0.268 -0.36 0.245 0.357 1.3 0.22 1.49 -0 13 -0.2

STM4448 0.05 -0.2 -0.17 0.085 -0.3 0.019 0.309 0.586 0.907 3.118 0.187 -0 19 -0.74 -055 -0.1 -0.96 -1 3 -0 -1.2 0.053 0.17

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4463 049 0442 -005 -079 0164 -033 -066 -086 -068 -018J§£7i| -066 184 -0121555 012 -02 -05 0180939 106

STM4464 -01 0328 -079 0225 -067 -074 -013 -061 -062 -0261578 -074 -078 -039 -04 -022 017 -01 002 -004 013 098 -01 049 -073 -05 -056 -1 -02 ;39 -209! °¹6 -011 -1 083 191 04 049 -06 -066 -07 -119 -04 133 -11 1099 -11

-082 -037 -09 -12[_j31_ -1βi| -14

STM4472 013 -062 -001 -008 -026 0437 -032 -097 -054 -0220311 -0870315018200840485 -04 -07 052 -057 08

STM4473 -07 -073 -033 015 0057 -027 -03 -046 -018

-085 -05304390639 -047 261 -O5f5Tlθ698 038

STM4474 -01 -006 0588 0388 0629 0609 -0130177 -0570661 13906250616 -012 -0130174 -11 -01 031 -057 -03

STM4475 111 0364 -013 -066 -073 0691 0544 -05900170341 019 -0520274076507161562 228 125 231 0853 117

STM4476 S 068 0196 -002 -126 0121 0218 -006 -092 -058##### -0560261 01870035 -0450657 183 128 1660195 042

STM4477 -02 -103 -077 0473 -076 -0330044 [jjϊϊ] 0219 -0881548[TeI] -061 ]_-1_88J 0442 -064 144038 028 -042 073

STM4478 134 0737 0032 -1 -078 041 0007 -126 -081 -1 -069 -03 -01709920179 039 109086 2180731 115

STM4479 042 0073 -044 -119 -036 -003 -042 -112 -102 ##### -028 -0350358008205451419 177 122 1920998 ^'092

STM4480 032 •€47 -024 -064 -006 0429 -018 -125 -14 mtm -05102408620721 06340536 161 129 1840704 009

STM4481 019 -075 0301 -002 -013 -045 -059 -01 0178 -114 -071 -066 05 -01705290781 -05 -02 031 0061 082

STM4482 092 0207 0266 -044 1251 05340316 -089 -011070215540675037703590721 0885 106 105 1290504 04

STM4483 014 -092 -059 1052 -02 -0250089 -067 -054 -059 -012 -089 -102 -0440373 -045 034 -06 -12 -12 -0

STM4484 001 0282 0859 0456 0846 05340617024508270022 -14 -012 -010908 -006 -071 ^-16j -01 -32 -036 011

STM4485 001 -003 0083 0966 0092 0435 -0620865 -028 -053 -01 -01807280305 -045 -073 -09026 -1 -13 -08

STM4486 14 0744 -002 0431 -026 -0360122 -00602880167 -0260854 -042 -134 -00795 001 074 -040035 -02

STM4488 092 -009 0161 -094 0272 023 -0560073 -076 -046 -027 -07099300690489 1253 221 103 1841654 077

STM4489 072 0433 0941 -065 -004 0564 -005 -104 -0060348 -069056203850121 0650689 192 121 1690976 052

STM4490 066 0526 0739 0211 -012 0975 0220345 -067 -05903331187 -1330622 1131357 038 056 -03 -069 069

STM4491 109 08 -03 -052 0314 0797 091 02720224 -1130404066604431279 086 049 1340551 06

STM4492 -02 031 -107 0595 0242 -091 0853 -0041104

-114 -1 [764J 0691 -039 -06 -05 -13 -082 -03

STM4493 029 0394 0492 0297 0625 02020631 0558 -021 00160695 -027 1781 -021 0371 075 086 -0 056 -001 063

STM4494 003 -062 -039 0286 003 00360211 -007 -05 #####[^2 røj 0281 0736 -033 -0291004 -07 -01 -05 -016 002

STM4495 05 -001 -018 -003 -001 -05 -057 -13 -064 -0420195 -114 -0671622 -105 -063 -09 -04 -03H-Ie] -11

STM4496 015 -058 0017 0323 -021 02970105 -006 -103 -004 -011 -0420424 00410790781 201 075 17 1444 06

STM4497 06 -019 -036 -094 -112 -008 -08 -142 -06 -008 -089 -0530.231 012707690173 185 107 2150309 1

STM4498 147 -001 -084 1065 -046 -1 0317 -041 0885 -056 -215 -0520481 -0730692 -082 -07 086 -152433 -02

STM4499 014 -07 -039 029 -036 -092 -032 -0230276 028 -079 -10605190122 -033 -103 -08 -08 003 -125 -02

STM4SX) 106 0761 -045 -085 -041 01340847 -007 -018 -019 -031 -023050209620595 1311 193 136 211 0766 123

STM4501 2 0523 1501 0513 1022 0918050310891535 1581002 -07501540966 1021253 081 121 H571344 085

STM4502 02 -018 -039 078 0167 0356 -014 -0080439 -0030333 -073 -0161111 04840602 -12 01i[_-25J -064 01

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4515 040584 0923 -04 -003 -007 -0260544 -073 -028 -0210188 -127|_-1_56J 050801 -03 -05 -090844 -09

STM4516 0480403056806390626 0651020103810628116714810.2430263 06708010639 007036 -1 β| -116 038

STM4517 149 -007086804720307 -01800990059 -025mm -074 -105 011 -0380235 -011 -0 -01 0220019 032

STM4518 0680202 -037 -0570162 1168 -039f-152| -078 -09 -05500090782020308310232 216117 2481262 124

STM4519 06 021831 -035 -0210605 -0031586 -014 012157107171073023800440076 024014 26 -031 077

STM4520 0130198 -017 -071 -077 -0 -042 -05 -082 -052 -05701040J259 -033 -0441107 187118 1561161 06

STM4521 -08 -042 -045 -123 -039 002 -039 -063 -063 -1140148 -080056 -08 -038 -036 057 -02 088 -044 -03

STM4522 -09 -08800520416 -0250381 -08 -031 -074 -041 -128 -14 -101 -135 -094 -107 '| -1 β 'j -1 -12J~-189| -12

STM4523 0880412 -041 14840396 -013 -071 -0340752 041 -044 -026 -011 -098 -0960376 274017 I -21| -039 018

STM4524 005 -024 -01804890096 035 -019 -0450515 -047 -002 -004 -063 -04101340286 -07 -06 -12 -018 003

STM4525 1150793 -068[2L69] -057 -093 -04 -07 -113 -097 -007 -0970397 047 -0280538 103 111 182 126 061

STM4526 -061187 -051 -0040718 01250671 -025 -069 -03105720039 -00803331194 -034 049 151 -071621 107

STM4527 071 -016 -00192 013 -010246 -0270337

-088 -0210795 -0380043 04 -02 -1 -035 -09

STM4528 0790428 0556 -090099 -0207370323 -086 -044001307890582 0190966 043 094091 2120702 091

STM4529 0570084 -028 139 -111 -012 -033 -116 -051 ##### -034 -02406040218 050928 179 113 158 096 113

STM4530 0290321 0163 -003 -059 -13 -054 -08 -0810415^ -205J0156 -023(^219⁽0447 -132 -08 -08 -11 -124 006

STM4531 081 0204 -029 -084 -094 0171 -046 -053 -101 -073 -008 -05604660368 -020602 156 -01 181 -002 027

STM4532 055 -009 0028 -042 -02 -016016809641241 -069 -039 -07 -044042613010176 -02065 -08 -006 155

STM4533 0380418 102712430545 010303980813000900960263 -012 -098 -0270081 -019 -1 -02 T5] -098026

STM4534 014 -01600230289 -051 0918 -0090655 084 -02i[T_73] -067 -044 -0010022 -059 009052 029 -118091

STM4535 -06 -134 -047 -075 -043 -102 -101 -019 061 -0860352 -0090284 -082 -092 -04 -01 -02 -06 -105 -01

STM4536 -1 -061 016701840481 -069 -022 -052 -02816421112 -053 -018 -0380146 -055 -04 -01 -07 -016003

STM4537 -02 -041 -O 680235 -008 -023 -071 -012 015 -068 -018 -122 -131 -07704451355 -03 -07 -1 -077 031

STM4538 0230265 -0680634 -056 0084005702570222 -083 -086 -056 021 -06506521135 -07 -01J _-2/i] -082 107

STM4539 01 -013 065407990373 0148 -02901730332 -007[~Tτj 0687 -0.27 -101 -0540205 1 -07 12 -131 -05

STM4540 S -03 -04 -00507180296 012802230342 089 -012 -086 -0530519 -016 -0080404 -13 -i| -26|1132 -02

STM4541 0790325 1236 -039 -O 25 0755 -010382008103021226 -0590283 -051 0440344 037074 1170629 101

STM4542 -04 -0090014 -084[T(Ks] -021 -058 -09 -035 -15[-209J 0062 -095 -07 -13 -04 -131 064

STM4543 0710192 -04 -095 -03 -017 -031 -071 1368 -023 -087 -0110661033104320801 181 088 2081036 083

STM4544 0660723 009 -111 -011 -032 -006 -040939 -1360064 -0640423 00701651112 206 122 230222 057

STM4545 0560285 -026 -035 -035 0967 -0720266 -087 -023 -00904810944 -00405820584 184 104 2150334 019

STM4546 0340757079708190047 0289027502541031 -067 -044 -020246 -0440535 102

STM4547 -050137 -02905490597 -025 -002 -044 -101 ##### 0266 -0720764 -03 -028 -03

STM4548 -04 -068 -0300720372 0173 -057 -078 -07 -013 -062 -031 -05 -011 -044

STM4549 0270896 -O 2506730498 03220659 -0170945 -033 -13 -0350919 -096 -044

STM4550 16609130415 0570813 056909591711 1615015207480419066610130578 -03 109057 -08 -016 019

STM4551 066 -011 05590194 -132 0052 -007 -035 -0530092[-152J -147 -135 -09 -023 -OO1) -1 βj -1 i[ -1 βj -018 -04

STM4552 071 0147 -012 -139 -119 0245 -013 -053 -032 -029 -107 -073106805410684 041 118072 1480301 066

STM4556 0360263 -017 -102 -042 -01305070447 -033##### -006 -0190299019202520367 123037 21 1223 039

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM4570 160181 0288 -072 -045 0158 -03106240712 -001 -011 0670748 718 -02 -06 016 -01 021

STM4571 -03 -039 -002 -038 -004 0029 -042 -043 -00425640699 -0150144

^⁰⁸ -1 042 -111 GJT]

STM4572 04 -014 0907230225 055301561059 -092###S# -054 -0510029174600420067 -02 -02 -17 -001 -02

STM4573 -04 -029 -0204870301 00640123 -0140323 -042 -084 -0550539 -086049811791 -2.1 [ -09 243 -087 008

STM4574 031 -012 01940303 -036 -077 -062 -015 -035 -051 -064 -03 -023 -054 -04 -122 -08023 -19 -083 -04

STM4575 004013β 022406150424 02440392 0340325 -029 -068 -059 -069 -05 -0390597 06 -03 -25 -09 -08

STM4576 0210564 051500320889 -007113703530116 -0890345 -034 -089 -0451364 089 079023 0270709 094

STM4577 0960393 0019 -107 -023 0582 -023 -067 -073 ##### -03102820151027608210959 137096 1660652 102

STM4578 0420447 0534 038 -015 03930382 -0350778074700940446 -054 -1050941 -033 -02 -02 -07 -095 118

STM4579 1331137 045811340654 -007 -009 -021 [Jjjaj 086725480119007400072711 -04 -09024 036 -07 267

STM4580S -02 -038033205260155 -066 -07 -032 -032 -038 -1240551 -043 -033 -011 -052 -05 -08 0650958 -01

STM4581 0580571 -023 -075 -062 -027 -030496 -034 -04410460069 -003 -0304930606 14067 1270412 036

STM4582 063 -0050181 -1 0273 017104670476 -026|T75l -069 -05202810251 -011 -005 131 011 192 -018 086

STM4583 091 07940223 -111 -031 0015 -067 -11 -062 -005 -003 -0021298009308421136 21 11 2650034 083

STM4584 0840406 -026 -1360045 0008 -038 -095 -061 -111 -039 -0050364 04107771066 201 131 1910606 085

STM4585 06403860854 -13 -048 -081 -03401720417 -099 -04400520642 -121 0460419 115 144 157 -013 054

STM4586 035 -061 123311930257 0744 -11409791165 -004 -026 -0520515 -037 146 -027 156051 1292008 136

STM4587 1350421025i[^"-1β] -011 02150113 -093 -006 -024 -03 -041 -007087102380646 2 1 2250904 097

STM4588 092 1378 10404350242 0418 -0280864098619010498 002007412790427 051 129 161 1140986 085

STM4589 040553 0516003900120047007403130579 ##### -1112004 -0810491 -082 -

102[^?7] -03

STM4590 0650456 -027 -107 -035 -030116 -1461656 -035 -064 -0340557 -008 031 1663 188 148 17 001 078

STM4591 0870839 -07704760226 -0210118 -0631079044104040754 -026 -00803470119 -04033 Ji 60351 -02

STM4592 -0 -072 0368 -003 -05 -087 -026 -0340098 -012 -094 -019 -114 -085 -0371957 [Tjβ] 062 -1~7~} -121 002

STM4593 025 -024 -O 22 -0930023 -033 -043 -006 -049 -04 -033 -023 -043023101140282 063005 0860778 049

STM4594 0260014 002307960522 038500160068 -029 -033 -099 -011 0365 -029 -02 -02 -14 -014 022

STM4595 0820334 0050274 -025 0143 -032 -01 -0141024 -007 -06

0353 -091 -07 -04 -050011 013

STM4598 -05 -087 -0370252 -0240451 -024000302320028 -066 -095 -042 -041 -048[Ts] -02 ^"ill -¹ °⁵ °

STM4597 025 -042 08490656 -068 0622009504570474 -032 -0 -072 -08 -08218670545 -13 -1 320093 154

STM4598 085 -015 -044 -12 -04 003 -027 -074 -02 -061 -06602390113000806021061 192 143 224 09 109

STM4599 054 -011 -O 64 -121 -103 -042 006 -122 -088 -015 -111 -0690632 -0240068 084 184094 171 022 058

STM4600 0850367 -O 01 -145 -028 -0230524 -107 -102 -024 -02142650229041912790654 203 129 2580834 068

CHIP7_STfc 1050186 034609010721 0010779010704823583[j2.0il -133 -028 -09 -13 -03δ[T9J -12

CHIP7_STO 03 -038 -0340582 -012 0498012301690207 -007 -093 -0J52 04400320018 -075 -14

-°¹

CHIP7_STfc -11 -036 -119 -053 047 13430911 -1440586 -115 11i[~-1β] °28 -1283085 -019 054009 278 -134 235

CHIP7_STN 07 -011 "⁰⁰⁵Gi?] ^~°⁷² -017 187 -04 -095 -069 01 -0910517 -071 -044 -017 106038 131 -024 032

CHIP7_STN 0560316 -055 -134 -0390244 -05 -081 -052 -079 -065 -1090224038801620685 255 109 1490169 133

CHIP7_STfc 0080155 ■O12pTa] -081 -045 019 -036 -023 -0780273 -115 -026066106240537 149 102 1870603 047

CHIP7_STIv 051064302510327 -05300110611 -012 -02 -0140582 -066 -02006601360025 086021 1140319 018

CHIP7 STfc 0570324 -011 Hi 57) -092 -052 -002 -082 -027 -1 -09 -0560019 -024 -0020564 152 117 1450969 005

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

CHIP7_STN -0.3 0.409 0.462 -0.25 0.468 0.321 0.476 0.109 -1.1 -0.75 -0.36 -0.18 1.825 0.146 1.853 -0.44 -0.4 0.07 -1.4 1.356 1.88

CHIP7_STN 0.04 -0.32 0.62 0.377 0.781 0.974 0.058 -0.39 0.236 0.371 -0.72 0.699 1.581 2.368 1.116 0.098^-rs] -0.1 -1.1 -1.31 0.47

CHIP7_STN -0.7 -0.2 -0.79 -0.52 -0.44 -0.46 0.286 0.531 -0.16 -1.24pΛTJ -1.11 -0.35 -0.39 0.274 -0.42 0.3 -0.3 0.69 -1.03 -0.4

CHIP7_STN 0.97 0.402 0.172 0.998 0.517 -1.34 -0.28 -1.43 -0.56 0.35 0.175 -0.49 -0.4 -0.02 -0.68 -0.64 -0.6 -0.3 -1.4 -0.96 -0.5

CHIP7_STV 0.44 0.319 -0.31 -1.37 -0.71 0.69 -0.79 -0.36 -0.93 -0.93 -0.81 -0.38 0.154 0.604 0.387 0.294 2.15 1.26 2.1 0.538 0.53

CHIP7_ST1V 1.28 0.782 1.053 0.795 1.003 0.677 0.589 0.108 1.04 0.062 -0.02 0.185 0.931 0.818 0.5 -0.32 -0.2 0.37 -1 -0.62 0.67

CH!P7_STfc 0.54 0.216 -1.14 -1.37 -0.57 -0.12 -0.88 -0.59 -0.51 -1.01 -0.19 -0.44 0.008 0.711 0.153 1.383 2.25 1.3 1.88 0.434 0.44

CHIP7_S™ 0.4 0.353 0.007 0.211 -0.29 0.543 0.313 0.141 1.45 -0.39 -0.61 0.105 1.158 -0.01 1.076 0.001 0.4 0.72 0.38 2.895 1.28

STM_0326 0.68 0.684 0.272 0.796 0.475 0.004 0.626 -0.01 0.609 0.406 0.228 2.623 0.484 -0.01 -0.01 0.14 -0.9 0.23 -1.3 -0.11 0.7

STM_0924 0.88 0.579 -0.41 -1.25 -0.41 0.013 0.294 -0.64 -0.44 -0.78 -0.47 -0.4 0.812 0.195 0.674 0.596 2.51 1.62 1.64 0.502 0.65

STM_1629 -0.1 -0.35 0.271 0.611 -0.11 0.238 -0.25 -0.43 -1.17 0.22 0.52 0.733 -0.89 -0.32 0.112 1.733 -1.3 -θ[ ^AAl 0.032 -0.3

STM_4431 0.03 0.09 -0.78 -0.61 -0.56 0.044 -0.17 -0.62 -0.01 -0.77 -0.74 -0.14 0.188 -0.62 0.512 0.856 1.96 0.66 1.7 0.514 0.42

STMJiCJ -0.4 0.371 1.088 0.841 0.16 1.739 0.409 1.114 0.42 0.144 -0.07 -0.88 -1.45 -0.39 -0.84 -0.53 1.1 0.49 3.7β[^2L?9] -0.4

STM_fljB_i -0.8 -0.74 -1.12 0.026 -0.93 -1.42 -0.4 -1.14 -0.51 -0.9Sf-1.76] 0.013 -1.25 -1.45 -1.15 0.437 -1 -1.16 -0.7

STMjiuoH 0.02 -0.48 -0.85 -0.93 -0.83 0.06

-1.18^2.03 -1.83ij -0.09 -0.99 -0.63 1.242 1.056 0.23 0.503 1.63 0.8 1.28 0.66 0.55

STM_oxyS 0.69 0.028 0.317 -1.13 -0A6 -0.11 -0.04 -0.68 -0.27 -1.18 0.008 0.266 0.016 1.096 1.07 0.88 1.98 0.798 0.74

STM PSLTI 0.73 0.227 -0.24 -1.45[^f-i^'.β7l --00..4455 --00..4444 00..446688 --00..0044

-1.13MK52J -0.45| -1.87J -1.03 -0.4 -0.2 -1.3P-ZiTj -1.2 STM_PSLT⁽ 0.49 -0.15 -0.51 0.115 -0.64 -0.25 0.531 0.529 -1.14 ##### -0.71 -0.48 0.189 0.593 -0.31 1.101 0.85 0.43 099 0.403 0.15 STM PSLTI -0.2 0.002 -0.24 -1.37 0.38 0.075 -0.89 -0.6 -0.99 «## -0.49 -0.24 0.789 -0.51 0.112 0.794 1.31 1.15 1.62 0.825 0.6

STM_PSLT( -0 0.103 -0.55 -1.48 -0.22 0.063 -0.16 -1.43 -Z03j -0.45 -0.26 -0.37 0.452 0.059 0.578 0.677 1.33 0.63 1JM 3.424 0.9

STM_PSLT( -1.1 -0.34 -1.01 -0.83 -0.31 0.304 -0.42 0.252 -3.Ϊ2J -0.04 2.816 -0.62 0.233 -1.36 -0.41 -0.54 0.13 -0.4[ -2.i]θ.459 -0.2

STM-PSLTI -1.1 -0.81 -0.45 -1.07 0.159 -0.05 -0.16 -0.02 -0.9 -0.8 -0.17 -1.19 0.954 -1.2 0.213 -1.16 -1.4 -1.2[_-2^2j -1.39 -0.1

STM_PSLT( -0.3 -0.32 -0.55 -0.06 0.165 0.42 -0.12 -0.21 -1.11 0.182 0.555 -0.37 -0.45 -0.61 -0.14 -0.91 -0.4 -0.4 -0.4 0.408 0.23

STM_PSLT( -1.3 -0.16 -0.72 -1.08 0.213 0.234 0.282 0.547 -0.53 -0.65 0.718 -0.93 -0.19 -0.14 -0.1 -0.77 -1.3 -0.7 __Jlf-tβ7j 0.16

STM_PSLT( -0.8 0.131 -0.76 -0.4 -0.23 -0.19 -0.47 -0.15 -0.77 -0.61 -0.97 -0.23 0.712 -0.94 -1.01 -O.θθp-jj -O.δf -2.4| -1.47 -0.4

STM_PSLT⁽ -0.5 0.284 -0.41 -0.61 0.187 -0.38 0.16 -0.37 -0.99 -0.34 -0.43 2.485 -0.46 -0.38 -0.75 -0.25 j -1.9| -0.9 -0.3 -0.14 -0.6

STM_PSLT1 -0.1 0.537 -0.06 0.349 0.473 0.417 0.211 -0.25 -0.4 0.438 -0.23 0.171 -0.5 -0.33 -0.13 -0.55 -0.5 -0.2 3.4 -0.02 0.16

STM_PSLT( -1.2 -0.1 -0.68 -0.57 -0.21 -0.09 0.078 -0 -0.21 -0.36 -0.01 -1.19 -0.5 0.412 0.598 0.56

STM_PSLT( -0.9 -0.15 -0.51 -0.67 0.101 0.531 0.721 0.616 -0.59 -0.55 0.071 -1.25 -0.35 -0.71 -0.2

-0.2

STM_PSLT1 0.05 0.151 -0.3 -1.4 -0.68 -0.32 0.308

-0.29 -0.72 1.697 -0.91 -0.39 -0.12 0.55 -0.1 0.12 -0.85 0.33

STM_PSLT( -1.2 -0.55 -0.52 -0.76 -0.25 -0.22 -0.08 0.112 -1 -0.13 0.835 -004 -0.78 -1.41 0.056 -0.57 [ -1.7) -0.4 -0.3 -1.14 0.29

STM_PSLT( -0.4 0.387 -0.36 0.061 -0.07 -0.15 -0.15 -0.52 -0.82 0.054 -1.27 -0.06 -1.22 -1.32 0.09 -0.46 -1.1 0.03 -1.4 2.622 0.33

STM_PSLT⁽ -1.1 -0.07 -1.29 0.486 0.677 0.394 -0.04 -0.44 -0.42 -0.62 -1.31 -0.72 0.014 2.991 -0.13 -0.69 -1.2

"° ³

STM_PSLT⁽ -0.8 0.508 -0.36 -0.28 0.276 -0.13 0.568 -0.16 -0.64 0.589 1.499 0.28 0.571 0.338 0.321 0.022 -0.6 -0.3 -1.2 1.162 -0.3

STM_PSLT( -0.8 0.495 0.025 -1.21 0.011 -0.12 0.121 -0.43 -0.76 0.105 0.674 -0.31 1.54 0.219 -0.09 -0.66 -1.1 -1.1 4.21 0.702 -0.4 -0.06 -0.62 -0.13 0.094 0.087 -0.06 -0.74 -1.22 -0.16 -0.76 -0.63 -1.37 -0.3 H^] -1.05 -0.27 -0.27 -0.66 1.24 -1.11

-1.24 -0.22 }

-ZM] Λ.22 -0.2 -0.04 -O.4δ[si!sβ| -0.88 STM PSLTI 0.95 0.782 -0.98 -0.68 -0.06 0.132 0.355 0.536 -1.06 ##### 0.279 2.062 0.338 -0.99 0.457 -0.55 -0.4 0.36 1.22 -0.54 0.1

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

STM_PSIT< -1 0.164 -0.38 -0.44 -0.27 -0.25 0.15 -1.12 -1.05 -O.iθf_jUf] -0.91 -0.21 -0 -0.33 -0.66 -0.6 -0.8 -1.4 STM_PSLTt 0.06 -0.41 -0.33 -0.05 -0.4 0.562 -0.74 -0.14 -0.59 0.11 -0.4 -0.06 -0.84 HJfH -0.88 -1.5 -1.5 1.36 -1.4 STM_PSLT( -0.6 0.662 0.313 -0.4 0.143 0.486 0.539 0.429 -0.75 0.399 1.484 -0.73 -0.27 -0.99 0.324 -0.36 -1.2 -0 -1 STM_PSLT( -0.9 0.249 0.026 -0.5 0.441 -0.18 0.202 -0.21 -0.5 0.562 -0.44 -0.09 -0.82 -0.18 0.049 -1.28 -1.4 ^■O.β|"^'-2.4^'

STM_PSLTΪ -0.6 -0.29 -0.58 -1.27 -0.14 -0.25 0.983 0.55 -0.91 -0.44 -1.24 -0.07 -055 0.174 -069 -0.46 -1.4 -0.6 -0.9 0.573 -1.37 0.42 0.312 0.486 0.221 -0.37 -0.57 -1.5 -1.23 -0.77 -0.35p __Ee_§] -1.41 -0.8 - _|0.61 -2.1

-1.15 -1.631 -°-⁴⁶| -2.511 -0.42 -1.32 -1.27 ##ff##|;-f,72] -1.05 ############### 1.827J , -2 ÷ij -1.9

STM_PSLT( 0.28 -0.06 -0.94 -1.33 1.231 -0.06 0.659 -0.56 .-1.61 mm 0.556 -0.22 0.627 -0.09 0.406 0.673 1.37 0.8 1.6 STM_PSLT( -0.4 0.555 -0.27 -0.8 0.253 -0.49 0.68 0.054 '-1.53 mm 1.146 -1.22 0.31 -0.3 -1.06 -0.16 -1.1 -1.1 0.6 STM_PSLTI -0.7 -0.27 -0.13 -1.36 -0.35 -1.25 0.041 -0.5 -0.61 ##### -0.81 -1.36 -09 -0.67 -1.32 -1 32 -0.9 -0.8 -0.6| STM_PSLT( -1 4 -0.02 -0.11 -1.26 -0.37 -0 0.386 0.185 -0.13 -1.08 -1.93 0.33 -0.52 -0.8 -0.08 -093( .-2,1j -1,3 -1.4 STM-PSLTI -0.9 0.17 -0.36 -0.48 -0.12 -0.1 0.52 0.308 -1.33 -0.47 -0.33 -0.88 0.145 -0.43 -0.16 -08 -071 -2.2J STM_PSLT( -0.5 -0.37 -1.37 -0.83 -0.28 -0.19 -0.08 -0.02 -1.35 -0.95 -0.6 -1.08 -0.09 Z651 2.615 -0.24 0.42 -0.1 0.64 1 STM_PSLTt -06 -1.12

-008 -1 09

-1.22 -1.1 -0.87 -1.32 -0.91 -1.23 -0.5 -0.1 -0.4 STM_PSLT( -1.1 0.726 -0.43 -1.12 -0.38 0.547 -0.05 0.082 -089 ###S# 1.07 -0.29 -0.3p"t66l -0.76 -1.05 -1.3 0.22 [ -I.θi 1 STM_PSLT( 0.67 0.699 0.086 ^^•TeTj -0.26 0.296 -0.45 -0.74 -1.32 -0.43 -0.62 -0.51 0.209 0.338 0.785 0.702 1.6 0.95 2.06 C STM-PSLTl -0.3 -0.22 0.642 -0.79 0.239 0.664 0.427 STM_PSLT⁽ -1.1 1.44 0.17 -1.18 0.579 0.596 1.039 STM_PSLT( -0.2 0.767 -066 -0.77 -0.05 -1.01 0.504 STM_PSLT( -0.1 0.037 -028 -0.55 0.038 -0.27 0.117 STM_PSLT( -0.3 -1.46 -0.3 0.222 -0.08 0.211 -0.02 STM_PSLTI -0 0.915 -1.26 -1.44 0.225 -1.24 0.337 STM_PSLT( -09 -0.14 -0.12 -1.17 -0.57 -0.08 -0.01 STM_PSLTl -0.2 0.138 0.003 -1.03 -098 0.381 -0.06 STM_PSLT( -1 3 0.123 -044 -0.57 0.106 -0.09 -0.21 -0.66 -0.58 -094 -0.46 0.019 -0.25 -0.33 -0.53 -0.55 0.189 0.246 -0.22

-0.53 -1.2 -0.34 0.564 0.308 0.451 STM_PSLTl -1.3 -0.14 -0.64 -0.52 0389 0.148 -0.03 STM-PSLTt -1.1 0.096 -0.34 -0.4 0.202 -0.34 0.014

STM_PSLT( -0.5 0.281 -0.33 •0.19 0.118 0.073 -0.18 0.058 -0.58 0.55 0.331 -055 0.014 -0.27 -0.53 -0.62 -0.9 -0.2 0.54 STM_PSLTI -0.8 0.111 -0.17 -0.29 0.286 0.375 0.578 0.908 0.179 0.911 -0.44 -056 -OJH) 0.445 -0.45 STM_PSLT( 0.39 0.213 -0.18 -1.18 -0.27 -0.33 -0.01 0.211 -1.09 1.821 0.936 -0.65 Iξjjpj 0.382 0.279 STM_PSLTl -1 0.111 -0.49 -0.49 -0.11 -0.7 -0.12 -0.6 -1.08 ##### -0.77 -1.27 -0.68 -0.88 -1.33 STM_PSLT( -0.8 -0.11 -0.44 0.004 0.403 0.056 -0.27 -0.45 -083 -0.48 -0.59 -0.55 -1.24 -031 -0.29

STM-PSLTl -0 1 0608 -0.54 -0.58 0065 -035 0.318 0.011 -063 0.719 -0.52 0.514 -0.79 -0.83 -1.02 0.365 -1.3 -0.2 -0.2 1 STM-PSLTI -0.7 -0.02 -1 02 -0.07 0482 0.188 0.06 -0.55 -0.42 ##### -0.24 -0.2 0.184 0.182 -0.11 -0.36 1.33 -0.1 -0.3 STM PSLTl -0.5 0.092 -0.55 -0 0.375 0.193 0.088 -0.22 -0.01 -0.1 -0.27 -0.39 -0.42 0.041 -0.49 0.079 0.2 -0.5[~ii]

- Raw Microarray Fitness Data for Engineered Salmonella -032 -038 -039 -0040179 -05 -081 -0702030277 -05 -037 -049 276 006 -22 -115 -0

-079 -127 -038 -052 -08 -07 -041 0052 -003 -016 -024 -115 -066 -18; -1 -16 -097 -11 STM_PSLT -070107 -009 -054 005 -022 -05 -03 -0040574 -0440131 -035 -19! -04 -24 089 012 STM_PSLT -13 -009 -06 -026 -03 -006 -117 -027 -0691467 -017 -0220311 -028 111 -14 -07 -02 007 STM_PSLT -120708| -19S| -0760203 -027 -122 -029 -08 -098[-162J -051 -029 -086 -03 -03 -13 -142 -01 STMJ³SlT -01 -047 -044 -05601680717 -002 -053 -093 -016 -066 011 0336 -045 051 019 042 -036 041 STM_PSLT -1 0385 -08 -049 0240017 -08 ##### -058 -125 -049 -049 -081 -071 -12 -0

-065 -07 STMJ³SLT -0906970079 -020516 -021 -114 ##### -104 -061 -008[ -20β|θO22 -038 -14 -07 -15 -141 -01 STM_PSLT 0780492 -031 -037 -073 -061 -074 -074 -056 -039 -03 019 -108 -032 102 047 106 -091 069 STM_sRNA 03403220125 -034 -026 -111 -096 -091 -055 -070151 0156 -00654 179 064 1580513 096 STM_sRNA 0670755 -005 05170165 -03 -052 -0360669 -06 -013 -027 -0030724 101 -01 179 -017 064 STM_sRNA -0208670198 0442025215360584 -030307 -0260105 -0250752 -013 -01 179 -130787 049 STM_sRNA 06503740318 02920514 014 -006 -053 -071 -059 -044 -03900680936 14 093 1650435 003 STM_sRNA 094 -008 -068 -0720543 -0820576 -06089907820878 -06703120444 07 103 132 -08 005 STM_sRNA 1040455 -015 0368 -015 -114 -04 -059 -055 -061 0571 -03605240705 269 127 183 1296 116 STM_sRNA 0530009 -008 0265 -054 -116 -128 -084 -001 -01 -018 -03407350584 159 07 150696 047 STM_sRNA 06300470091 0399 -021 -09 -122 -047 -031 -0460441 011501860746 2.12 101 2581014 162 STM_sRNA 05207430084 0487 -063 -072[^"TsUl] -078 -076 -0391036 -0061081 1 206 177 1830488 078 STM_sRNA -01 -021 -036 -041 -02703030182 #####^ -17βj -132 -014 -115 -001 0262 012 01 071 -054 006 STM_sRNA 11 0456 -036 -151 -0840446 -013 -085 -022 ##### D 368 -0530059 0250277 07 227 091 2.48 -013 066 STM_sRNA 13 003 -093 -165 -1090656 -067 -11 -083 -053 -116 -059 -0290528 -0050803 202 14 256 049 -01 STM_sRNA 1240264 -01 -003 -028 -093 -031 -124 -051 -0490451 1154 -0430401 201 188 2420253 062 STM_sRNA 0360314 -045 0506 -038 -005 -061 -076 -13 -021 0327034306990691 231 051 211 049 085 STM_sRNA 0340913 -034 -047 -051 -057 -083 -117 -068 -03709270481 0360988 2.25 127 2080148 088 STM_sRNA 1040658 -O 28 -01 -017 -097 -015 -046 -02 -0150515 -01301321177 194 143 2250608 048 STM_sRNA.0450175 -063J 0386 -005 -04 -096 -099 -006 -011 02690586 -0261318 163 148 2010111 094 STM_sRNA 05404770244 051 -041 -087 -031 ##### -094 -0390761 042901180593 269 113 1780674 062 STM_sRNA 037 044 -024J -001 -01 -046 -048 ##### -016 -021 -0370359 -020702 215 088 2170539 004 STM_sRNA 05910281594 0674 -034024304753042 -046 -078 ############### 0201 137 134 323 -051 103 STM_sRNA 062 -065 -049 0994 -029 -134 -074 ##### -101 -0150823 041 0220606 134 178 195 002 089 STM_sRNA 0850776 109 0131 -03201881008 -0380495 -011 -042 -04 1051 -022 027 063 1122544 106 STM_sRNA 06404840031 0633 -035 -106 -081 -079 -061 -0130785 ########## 0799 205 146 2081075 079 STM_sRNA 0660591 4) 05 -007 -124L23 -108 -0320763 -0050455 -09606840912 139087 1340959 042 STM_sRNA 1030581 -031 0656 -021 -009 039 -062 -072 -00403430711 0080744 238 092 2090259 134 STM_sRNA 0570573 -O 51 -042 -063 -078 -049 -041 -132 -07500071166 -0070354 129 094 187 1074 026 STM_sRNA 0130203 -002 0139 -04 -084 -097 -037 -067 -065 -0340023 -001 0113 157061 201 1187 078 STM_sRNA 064 -005 051 05231171 138619530348 J -157J -08613370781 -01 -07 -0 047[ -26]θ094 -04 STM_sRNA 063 045 -099 -02 -0 I9QT59] -062 -072 -01 -0250078 -00401960763 196 067 2160954 -0

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

CTRLjλlA 0370021 -042 -085 -046 -016 -037 -058 -03 -106 -022 -0220659 -02701940658 209 053 1650648 026

CTRL_pTim 061 04Θ8 -007 -099 -071 08230081 01920075 -045 -004 -029 -016 -077 0060606 16 064 1920674 069

CTRL_pUC 0430314 -011 -142 -041 00890278 -005 -038 -06 -046 0120052 -03505190752 106083 1781054 091

152 065 0123 -159 -048 -013 -028 -09 -056##### -043 -05503720132 -0340965 211 165 251 0157 056

0920435 -007 -176 -054 -035 -042 -139 -099 -131 -092 -04601670244 -021 1182 179 053 1651213 102

047 056 -007| -184| -030624 -099 -108 -116 -094 -03 -033 -013055601761108 241 11 1990551 044

0640769 -014 -1270191 1107 -124 -041 -089 ##### 0153 -047 -003 01701690388 209 089 1730445 08

0531038 -036 -133 -0390124 -08 -084 -07 -081 -016 -04 -0020272 -0040739 226096 1830883 079

0770788 0092 -121 -081 -006 -027 -067 -074 -023 -01700050428 -02 0091257 291 078 226 -001 036

0660315 -048[-156[ -04806340296 -104 -119[-1jiiJ -013 -0360974074503351297 258 083 2670305 052

060357 -001 -13 -06503150313 -06 -02 -04 -044 -03905490217 008 098 251 166 209 035 083

087 126 -055 -093 -0380295 -052 -052 -105 -095 -077 -0630177 -021 0848 083 219 109 1920425 093

0750752 -075 _LA 88 -079 0011 -029 -128 -019 -082 -052 -018013300120141 0747 228 133 1580677 093

0860427 0017 -1 69 -096 -019 -007 -089 -067 -017 -056 -07703761027 -0381191 181 119 1790684 065

1390086 -054 -1 71 -087 0206 -034 -059 -086 -06 -033 -0190583 -04902430666 175 158 2.850237 05

0520694 -03 -1 66 -161 0008 -047 -069 -023 -041 -033 -02903190461 0171 -007 196 144 2030527 113 1420486 -045 -145 -064 -0670174 -073 -089 -127 -044 -0220172028500021158 189 128 293 1544 071

10111 -031 -193] -071 0401 -03 -098 -032 -089 -092 -0460641 048205640193 247 114 151 0797 044

1131017 -076 -115 -068 -0 -05 -065 -058 -103 -042 -0470084002401340506 247 123 1790974 068

1 0376 0191 ^~T«*j -051 0184 -028 -051 -09 -047 -0560625 073 -019 0570159 214 107 2350913 025 0250327 -043 -141 -1 0761 -061 -064 -001 -107 -017 -00903570286 -050289 274 133 1660807 142 1030613 -002 -143 -102 -0070345 -108 -039 -092 -095 -0150775028501531076 17 091 2420067 057

11 -011 0035 -22J| -08 0735 -062 -105 -052 -133 -050315 -0190821 03660548 182 129 221 0823 152 0480818 -017 -057 -068 07 -022 -068 -081 -132 -034 -054 076 -009 -03 071 223 113 221 1195 049 0560879 0441 -077 -08 -0220048 -079 -083 -096 -021 -042 -014 -00603990817 201 082 2331405 034

060122 0272 -07 -075 -024 -018 -099 -108 -07 -0350364 1193 -003 0261097 24 16 2690752 013 0850492 --0044 --116633 -104 0263 -05 -051 -08 -124 -095 -02700030391 00570747 199 115 3020662 099 0470194 -045 -157 -126 -0080053 -06 -057 -019 -047 -068 -018046803360668 238084 2460251 06 096 -0 -018 -14 -07 -003 -03 -123 -033f -153| 0076 -02 -001 01670509 054 234 155 1870395 085

060025 0115 -137 -0480099 -005 -079 -062 -069 -095 -041 0139 -01706470722 132 104 1840816 099

090377 -037 [Tw] -08701160101 [TfriJ -071 -109 -064 -05 -021 -01305760741 233 12 1660108 042 0230173 0135 121 -001 014 -022 -104 -068 -088 -051 -0330081 0821 01180146 12 127 1930338 035 0540673 -041 -152 -0470373 -022 -116 -109 -096 -072 -044 -006 -000381087 175 039 2570139 041 -010449 -026 -182 -0480804 -0.2 -096 -084 -095 -042 -0420834 008 0251025 312 134 220192 096 0430312 -066 -125 -055 -037 -022 -083 -041 -103 -078 -08309280215 -0070984 158 127 1890368 058 048 073 -007 -146 -068 -106 -014 -094 -132 -074 -107 -0640478 -03605990058 189 094 250692 102 0530104 -003 -141 -1.24 -023 -067 -02 001 -061 -038 -09308370638 -007 056 17 129 240979 098 0730648 -081 -149 -08201450194 -0 -103 -07 -014 -04902740393 -0180157 193 188 1730899 082

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella

0520771 -O25[2LZΪ3 -080416 -029 -117 -03 -118 -073 -04 -013018803090296204104 2080428 081 115 005 -145 -11 -057 -031 -017 -06 -041 -051 -063 -0505070141 00780907 237 15 1960497 147 060564 -007 -13 -0590339 -022 -095 -089 -117 -034 -034 -013 -029 -031 1159 181 074 2021254 144 0340187 -021 -074 -080128 -033 -035 -087 -056 -068 -0040292027707350271 175 074 1760808 -02 1010476 -011 -139 -060311 -01 -031 -055 -091 -037 -0270086022600420604 22 176 2.530857 081 0950549 -058[-176J -039 -027 -019 -0840032 -036 -116 -022 -025056204040157 205 222 1570657 05 056 -017 -057 -108 -08904050141 -077 -029 -083 -104 -043 -04902460364 019 186 109 2.60287 021 0730416 -021 -114 -0174E-04 -026 -116 -078 -079 -029 -004062903560377 081 194 084 1990.236 019

0390717 -035J -1 S3] -067 -020251 -072 -021 -143 -057 -0160141 012 -0161089 208 111 159 066 101

1130514 -034 -127 -036 -02302950144 -045 -099 -059 -02500540196 0930369 204 086 1930553 037 1420415 0066 -07 -086 -0040066 -033 -057 -075 -099 -0530071 -0690261 0952 148 175 2380737 036 097 102 -057 -113 -113 -022 -005 -078 -027 -066 -055 -0270259 -011 -0040714 148 094 0810317 045 1160434 0751 -134 -12 -037 -069 -095 -059 -126 -065 -0260606 -02600781109 209 18 2360626 061

14 026 0145 -¹ ∞, -001 0226 -033 -135 -095 ##### -029 -0620231 057305271111 181 13 230962 108 07208780429 -152 -080104 -027 -061 -023 -147 -073 -0260655 03800061095 283 143 147 132 039 106 -029 -044 -12500460463 -007 -053 -067 -029 -021 0147 -006050500271307 192 115 171 0393 066

0770753 -031 -098 -016 044 -097 -1 mmttU -055 -06506710246 -0080925 167 162 2350588 06

1510085 -005 -1 V7/2 -115 -080171 -124 -022 -096 -012 -05202030213 -014 145 233 131 3120589 063 0790436 -033 -164 -0050689 -008 -08 -046 -19 -082 -021 -019 009 -0060632 171 183 2240127 14

0820879 -063 -138 -0370224 -01 -088 -041L_-1jSj -003 -0490519026200340999 201 177 2 1377 054

1250493 0085 -117 -0450117 -023 -0.27 -031 mm -021 -08136300690683 102 16 144 3060827 106 0760239 042 -128 -0350293 -096 -022 -035 -027 -0990428049605460141 0831 216 102 2230292 058

0950597 0118 -104 -03200250269 -055 -059 -071 -03600770037050602690846 209095 281 1107 093 0390202 0257 -17 -0720186 -024 -071 -049 -031 -041 -070234 04800570726 188 2 1490807 099

1080929 -015|-159] -073 087 -031 -0760024 -062 -055 -0790601 0417 -0570905 253 118 1551022 029 1190086 -093 -134 -045 -003 -02 -059 -06##### -098 -05513680071 0227 115 245 148 2650489 087

040024 -003^2 iτ} -0850452 -036 -051 -046 -054 -051 -0270191 -0070368 033 179 071 2540724 -01 0080832 0173 -144 -086 -0020278 -052 -055 -118 -019 -0380835012606241136 2093 2.040368 066 0850425 -023 -0220264 -09 -055 -115 -063 -0.220131 076700080791 236092 1850319 095 061 0538 -02701420007 -086 -044 ##### -048 -0630468 -00600821273 219 13 183 065 066

086 1196 -076 -053 -002 -0520093[-182| -0532E-04 0490924 -0060985 197 104 279 04 029 0820589 -0.20795 -087 -116 -078 ##» -012 -0120352009201950716 218 1 1930434 084

1140435

-0630413 -049 -079 -058 -05 -056 -0090856057203381327 187 104 2210632 049

053 -011 -075 -118 -1070053 -084 -085 -091 -080021 -133 -0370468 0461195 259087 2090733 106

1270547 -021 -1290117 0340087 -149 -097 -101 -075 -038085503530633 1052 208 195 2.031006 039 0960621 0119 -111 -101 -003 -042 -068 -09 ##### -014 -06209450151 -0150335 188 089 1861055 04 0140543 0199 -103 -08701040309 -054 -026 -118 -027 -0530331 007606561149 193 112 1860369 079 0630301 0144[-209J -0590111 -016 -084 -021 -043 -061 -05 08407920006 095 189 126 248 022 056

TABLE 1 - Raw Microarray Fitness Data for Engineered Salmonella -085 -084 045 -088 -1 12 -069 -049 0253 -003 0793 0662 0453 0433 1 75 1 11 1 99 0608 046

TABLE 2 - Class 1 Mutants, Gene Function and Microarray Fitness

TABLE 2 - Class 1 Mutants, Gene Function and Microarray Fitness

TABLE 2 - Class 1 Mutants, Gene Function and Microarray Fitness

4-

TABLE 2 - Class 1 Mutants, Gene Function and Microarray Fitness

O

PATENT VIV-1002-PC

The entirety of each patent, patent application, publication and document referenced herein hereby is incorporated by reference. Citation of the above patents, patent applications, publications and documents is not an admission that any of the foregoing is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents.

Modifications may be made to the foregoing without departing from the basic aspects of the technology. Although the technology has been described in substantial detail with reference to one or more specific embodiments, those of ordinary skill in the art will recognize that changes may be made to the embodiments specifically disclosed in this application, yet these modifications and improvements are within the scope and spirit of the technology.

The technology illustratively described herein suitably may be practiced in the absence of any element(s) not specifically disclosed herein. Thus, for example, in each instance herein any of the terms "comprising," "consisting essentially of," and "consisting of may be replaced with either of the other two terms. The terms and expressions which have been employed are used as terms of description and not of limitation, and use of such terms and expressions do not exclude any equivalents of the features shown and described or portions thereof, and various modifications are possible within the scope of the claimed technology. The term "a" or "an" can refer to one of or a plurality of the elements it modifies (e.g., "a reagent" can mean one or more reagents) unless it is contextually clear either one of the elements or more than one of the elements is described. The term "about" as used herein refers to a value within 10% of the underlying parameter (i.e., plus or minus 10%), and use of the term "about" at the beginning of a string of values modifies each of the values (i.e., "about 1 , 2 and 3" refers to about 1 , about 2 and about 3). For example, a weight of "about 100 grams" can include weights between 90 grams and 110 grams. Further, when a listing of values is described herein (e.g., about 50%, 60%, 70%, 80%, 85% or 86%) the listing includes all intermediate and fractional values thereof (e.g., 54%, 85.4%). Thus, it should be understood that although the present technology has been specifically disclosed by representative embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and such modifications and variations are considered within the scope of this technology.

Certain embodiments of the technology are set forth in the claim(s) that follow(s).

Claims

PATENT VIV-1002-PCWhat is claimed is:

1. An orally active pharmaceutical composition, comprising: a mutant bacterium that contains a genetic mutation, wherein: the wild type counterpart of the mutant bacterium is virulent against non-cancer cells and/or non-cancer tissues, the virulence of the mutant bacterium against non-cancer cells and/or non-cancer tissues is substantially reduced compared to the virulence of the wild type counterpart bacterium against non-cancer cells and/or non-cancer tissues, and the virulence of the mutant bacterium against cancer cells and/or cancer tissues is not substantially reduced compared to the virulence of the wild type counterpart bacterium against cancer cells and/or cancer tissues.

2. The orally active pharmaceutical composition of embodiment 1 , wherein the genetic mutation comprises two or more genetic mutations.

3. The orally active pharmaceutical composition of embodiments 1 or 2, wherein the genetic mutation modulates an activity selected from the group consisting of: a secretion system activity; bacterial type III secretion system activity; a bacterial transcriptional regulator activity; a magnesium transport activity; an amino acid ligase activity; a D-alanine-D-alanine ligase activity; a protease activity; a serine protease activity; an oxidase activity; a cytochrome activity; an ubiquinol oxidase activity; a structural protein activity; a polymerase activity; an O-antigen polymerase activity; a reductase activity; a CDP-6-deoxy-delta3,4-glucoseen reductase activity; a pyrophosphorylase activity; a dTDP-glucose pyrophosphorylase activity; a sugar synthetase activity; a TDP-rhamnose synthetase activity; a sugar transferase activity; a glucose or galactose sugar transferase activity, UDP-D- glucose:(galactosyl)lipopolysaccharide glucosyltransferase activity, UDP-D- galactose:(glucosyl)lipopolysaccharide-alpha-1 ,3-D-galactosyltransferase activity; an oxidase activity; a monoamine oxidase activity; an activity that suppresses mutants of outer membrane protein assembly; a suppressor of porin (ompF) assembly mutant activity; a hydrolase activity; acetyl-CoA hydrolase activity; a phosphatase activity; phosphohistidine phosphatase activity; a transcriptional repressor activity; a glucitol operon transcriptional repressor activity; a protein synthesis chain elongation activity; a PATENT VIV-1002-PC protein synthesis chain elongation factor EF-Tu activity; a potassium uptake activity; a potassium transport activity; a chemotaxis activity; methyl-accepting chemotaxis protein (MCP) activity; an exporter activity; an ABC-type bacteriocin/antibiotic exporter activity; a dehydrogenase activity; succinate dehydrogenase activity; a redox factor activity; a thioredoxin 1 activity; a polysaccharide chain length modulator activity; an enterobacterium common antigen (ECA) polysaccharide chain length modulation activity); and a Hes-B like domain activity.

4. The orally active pharmaceutical composition of embodiments 1 or 2, wherein the genetic mutation modulates a secretion system activity.

5. The orally active pharmaceutical composition of embodiment 4, wherein the genetic mutation modulates a bacterial type III secretion system activity.

5. The orally active pharmaceutical composition of embodiments 1 or 2, wherein the genetic mutation modulates a bacterial transcriptional regulator activity.

6. The orally active pharmaceutical composition of embodiments 1 or 2, wherein the genetic mutation modulates a protease activity.

7. The orally active pharmaceutical composition of embodiments 1 or 2, wherein the genetic mutation modulates a periplasmic serine protease activity.

8. The orally active pharmaceutical composition of any one of embodiments 1 to 7, wherein the genetic mutation comprises an alteration to a gene selected from the group consisting of: ddlB gene, htrA gene, cyoA gene, sdhA gene, sifA gene, phoP gene, rfc gene, sufA gene, ssrA gene, ssaB gene, ssaC gene, ssaD gene, sseB gene, sscA gene, sseC gene, sseD gene, sseE gene, ssaJ gene, ssaK gene, ssaL gene, ssaM gene, ssaV gene, ssaN gene, ssaP gene, ssaQ gene, yscR gene, ssaT gene, yebC gene, rfbl gene, rfbA gene, rfbD gene, asmA gene, sixA gene, srlR gene, yhdP gene, tufA gene, rfaK gene, rfaJ gene, rfal gene, rfaB gene, mgtC gene, trxA gene, wzzE gene, ubiB gene, trkH gene, purH gene, STM1410 gene, STM0278 gene, STM4262 gene, STM4258 gene, STM3118 gene, STM31 19 gene, STM3120 gene, STM3121 gene, a substantially PATENT VIV-1002-PC identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes.

9. The orally active pharmaceutical composition of any one of embodiments 1 to 3, 5 and 8, wherein the genetic mutation comprises an alteration to a STM3120 gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

10. The orally active pharmaceutical composition of any one of embodiments 1 to 3 and 6 to 8, wherein the genetic mutation comprises an alteration to a htrA gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

11. The orally active pharmaceutical composition of any one of embodiments 1 to 5 and 8, wherein the genetic mutation comprises an alteration to a SPI-2 gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

12. The orally active pharmaceutical composition of embodiment 1 1 , wherein the genetic mutation comprises an alteration to a gene selected from the group consisting of: ssrA gene, ssaB gene, ssaC gene, ssaD gene, sseB gene, sscA gene, sseC gene, sseD gene, sseE gene, ssaJ gene, ssaK gene, ssaL gene, ssaM gene, ssaV gene, ssaN gene, ssaP gene, ssaQ gene, yscR gene, ssaT gene, a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes.

13. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssrA gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

14. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaB gene, a substantially identical gene PATENT VIV-1002-PC to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

15. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaC gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

16. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaD gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

17. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a sseB gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

18. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a sscA gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

19. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a sseC gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

20. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a sseD gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene. PATENT VIV-1002-PC

21. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaJ gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

22. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaK gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

23. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaL gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

24. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaM gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

25. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaV gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

26. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaN gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

27. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaP gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene. PATENT VIV-1002-PC

28. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaQ gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

29. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a ssaT gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

30. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a yscR gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

31. The orally active pharmaceutical composition of embodiment 12, wherein the genetic mutation comprises an alteration to a STM1410 gene, a substantially identical gene to the forgoing gene, and an associated regulatory element of the foregoing gene or a substantially identical gene.

32. The orally active pharmaceutical composition of any one of embodiments 1 to 31 , wherein the mutant bacterium is a mutant pathogenic bacterium.

33. The orally active pharmaceutical composition of embodiment 32, wherein the mutant bacterium is a mutant enteric bacterium.

34. The orally active pharmaceutical composition of embodiment 32, wherein the mutant bacterium is a mutant Salmonella bacterium.

35. A method, comprising: administering a mutant bacterium that contains one or more genetic mutations to subject having a tumor in an amount effective to treat the tumor, wherein: PATENT VIV-1002-PC the wild type counterpart of the mutant bacterium is virulent against non-cancer cells and/or non-cancer tissues, the virulence of the mutant bacterium against non-cancer cells and/or non-cancer tissues is substantially reduced compared to the virulence of the wild type counterpart bacterium against non-cancer cells and/or non-cancer tissues, and the virulence of the mutant bacterium against cancer cells and/or cancer tissues is not substantially reduced compared to the virulence of the wild type counterpart bacterium against cancer cells and/or cancer tissues.

36. The method of embodiment 35, wherein the mutant bacterium is administered orally.

37. The method of embodiments, 35 and 36, wherein the genetic mutation comprises two or more genetic mutations.

38. The method of any one of embodiments 35 to 37, wherein the genetic mutation modulates an activity selected from the group consisting of: a secretion system activity; bacterial type III secretion system activity; a bacterial transcriptional regulator activity; a magnesium transport activity; an amino acid ligase activity; a D-alanine-D-alanine ligase activity; a protease activity; a serine protease activity; an oxidase activity; a cytochrome activity; an ubiquinol oxidase activity; a structural protein activity; a polymerase activity; an O-antigen polymerase activity; a reductase activity; a CDP-6-deoxy-delta3,4- glucoseen reductase activity; a pyrophosphorylase activity; a dTDP-glucose pyrophosphorylase activity; a sugar synthetase activity; a TDP-rhamnose synthetase activity; a sugar transferase activity; a glucose or galactose sugar transferase activity, UDP-D-glucose:(galactosyl)lipopolysaccharide glucosyltransferase activity, UDP-D- galactose:(glucosyl)lipopolysaccharide-alpha-1 ,3-D-galactosyltransferase activity; an oxidase activity; a monoamine oxidase activity; an activity that suppresses mutants of outer membrane protein assembly; a suppressor of porin (ompF) assembly mutant activity; a hydrolase activity; acetyl-CoA hydrolase activity; a phosphatase activity; phosphohistidine phosphatase activity; a transcriptional repressor activity; a glucitol operon transcriptional repressor activity; a protein synthesis chain elongation activity; a protein synthesis chain elongation factor EF-Tu activity; a potassium uptake activity; a potassium transport activity; a chemotaxis activity; methyl-accepting chemotaxis protein (MCP) activity; an exporter activity; an ABC-type bacteriocin/antibiotic exporter activity; a PATENT VIV-1002-PC dehydrogenase activity; succinate dehydrogenase activity; a redox factor activity; a thioredoxin 1 activity; a polysaccharide chain length modulator activity; an enterobacterium common antigen (ECA) polysaccharide chain length modulation activity); and a Hes-B like domain activity.

39. The method of any one of embodiments 35 to 38, wherein the genetic mutation comprises an alteration to a gene selected from the group consisting of: ddlB gene, htrA gene, cyoA gene, sdhA gene, sifA gene, phoP gene, rfc gene, sufA gene, ssrA gene, ssaB gene, ssaC gene, ssaD gene, sseB gene, sscA gene, sseC gene, sseD gene, sseE gene, ssaJ gene, ssaK gene, ssaL gene, ssaM gene, ssaV gene, ssaN gene, ssaP gene, ssaQ gene, yscR gene, ssaT gene, yebC gene, rfbl gene, rfbA gene, rfbD gene, asmA gene, sixA gene, srlR gene, yhdP gene, tufA gene, rfaK gene, rfaJ gene, rfal gene, rfaB gene, mgtC gene, trxA gene, wzzE gene, ubiB gene, trkH gene, purH gene, STM1410 gene, STM0278 gene, STM4262 gene, STM4258 gene, STM3118 gene, STM31 19 gene, STM3120 gene, STM3121 gene, a substantially identical gene of one of the foregoing genes, and an associated regulatory element of one of the foregoing genes or one of the substantially identical genes.

40. The method of any one of embodiments 35 to 39, wherein the mutant bacterium is a mutant pathogenic bacterium.

41. The method of embodiment 40, wherein the mutant bacterium is a mutant enteric bacterium.

42. The method of embodiment 40, wherein the mutant bacterium is a mutant Salmonella bacterium.

43. A high throughput method to identify a bacterial strain that will selectively infect tumor tissue in comparison to normal tissue, which method comprises:

(a) providing an input library of bacteria that are mutants of a wild type strain:

(b) administering the library to tumor-bearing subjects and to normal subjects;

(c) recovering DNA from bacteria that have survived in tumor tissue of the tumor- bearing subject and that have survived in the tissues of the normal subject; PATENT VIV-1002-PC

(d) analyzing the DNA obtained in (c) to determine the relative representation of mutants in tumor and normal tissues.

44. The method of claim 43, wherein the DNA obtained in (c) is analyzed against a panel containing open reading frames of wild type bacterial genes.

45. The method of claim 43 or 44, wherein the DNA obtained in (c) is analyzed by microarray analysis.

46. The method of any one of claims 43 to 45, wherein the DNA obtained in (c) is analyzed by sequencing analysis.

47. The method of any one of claims 43 to 46, wherein the analysis in (d) determines mutations in genes and/or associated regulatory elements of bacteria that preferentially survive in tumor tissue as compared to non-tumor tissue.

48. A bacterial mutant selective for tumor tissue identified by the method of any one of claims 43 to 47.

49. A method to obtain an attenuated strain of bacteria, which method comprises administering a library of mutant bacteria to a multiplicity of subjects and identifying a mutant strain that is present in the tissues of a subject having a predetermined survival time.

50. The method of claim 48, wherein the mutant bacteria are prepared by a method of any one of claims 43 to 49.

51. An attenuated strain identified by the method of embodiment 49.

50. A library of mutant bacteria obtained by transfecting a bacterial culture with transposons that result in disruption of genes and/or associated regulatory elements in transfected bacteria, wherein the library is selective for tumor tissue identified by the method of claim 43. PATENT VIV-1002-PC

51. The library of claim 50, wherein the transposons are fused to an expression system for a selectable marker that includes a promoter and wherein the fused expression system results in disruption of genes and/or associated regulatory elements.

52. The library of claim 51 , wherein the promoter is a T7 promoter.

53. A library of mutant bacteria obtained by homologous recombination that result in disruption of genes and/or associated regulatory elements in transfected bacteria, wherein the library is selective for tumor tissue identified by the method of claim 43.

54. A library of mutant bacteria obtained by random mutagenesis, including the use of mutagenic chemicals that result in disruption of genes and/or associated regulatory elements in transfected bacteria, wherein the library is selective for tumor tissue identified by the method of claim 43.