The biological relevance of the widespread prokaryote–eukaryote symbioses as a source of evolutionary innovation has been unveiled by the advent of the Genomic era, allowing deep knowledge on single or consortia uncultivable species. The... more
The biological relevance of the widespread prokaryote–eukaryote symbioses as a source of evolutionary innovation has been unveiled by the advent of the Genomic era, allowing deep knowledge on single or consortia uncultivable species. The establishment and maintenance of symbiosis are complex issues where partners’ fitness determines the evolutionary outcome. Comparative genomics allows to dissect the evolutionary process that begins with host invasion, takes the path from facultative to obligate symbiosis, and ends up in replacement or coexistence with new bacterial symbionts. Whole genomes of several intracellular bacterial symbionts have been sequenced, allowing the comparison among the different evolutionary innovations carried out by these bacteria on their way from free-living to varied stages of integration with their respective hosts. The association and functional interaction of genomes from different species observed during symbiosis, like mutation, recombination, and other genome rearrangements, can be viewed as a source of genetic variation, the fuel for evolution. The action of forces such as natural selection and/or random drift will be responsible for transforming this variation in evolutionary novelties. Host can develop organs to allocate the symbionts and must modify its immune response and its growth rate appropriately to benefit from having one or more symbionts. The bacterial symbiont experiences dramatic changes on its genome, which can be detected by its comparison with free-living relatives. The mechanisms involved in the establishment, maintenance, and evolution of the association can be scrutinized thanks to comparative genomics, whereas systems biology approaches allow us to explore metabolic interdependences among the members of the symbiotic consortium.
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Endemic species and island populations are particularly prone to extinction (Reid and Mil-ler, 1989; Frankham, 1997). For this reason, their identification and protection is particular-ly important. Podarcis hispanica atrata is an... more
Endemic species and island populations are particularly prone to extinction (Reid and Mil-ler, 1989; Frankham, 1997). For this reason, their identification and protection is particular-ly important. Podarcis hispanica atrata is an en-dangered and endemic lacertid confined to ...
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From inbreeding avoidance to kin‐selected cooperation, social behaviours are frequently reliant on kin recognition. However, kin recognition mechanisms are costly to evolve and currently not very well understood. Recent evidence suggests... more
From inbreeding avoidance to kin‐selected cooperation, social behaviours are frequently reliant on kin recognition. However, kin recognition mechanisms are costly to evolve and currently not very well understood. Recent evidence suggests that, by altering their host's odour, gut and other host‐associated microorganisms may provide a promising avenue for understanding kin recognition. In Drosophila melanogaster, kin recognition can mediate mate choice, sexual conflict and larval competition/cooperation, underscoring its important functional role. As is commonly the case, kin recognition in this species depends on both familiarity (i.e. shared rearing environment) and relatedness, and seems to rely mainly on body odours determined by cuticular hydrocarbons. Here, we investigated the degree to which larval rearing environment and relatedness (full‐sibs versus unrelated) determine co‐variation between gut microbiota and cuticular hydrocarbons in D. melanogaster. We found that rearing environment strongly determined microbiota composition and cuticular hydrocarbon profiles, but that these effects were independent from each other. In contrast, relatedness did not influence microbiota composition, but had a strong influence on microbiota diversity, which in turn covaried significantly with cuticular hydrocarbon profiles. Our results show that, in D. melanogaster, odours may convey information about both familiarity and relatedness via an interaction between: 1) direct effects of the rearing environment on cuticular hydrocarbons and 2) indirect effects of relatedness on cuticular hydrocarbons via gut microbiota diversity.
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Resumen del trabajo presentado a la VII Biennial Congress of Sociedad Española de Biología Evolutiva (SEBE), celebrada en Sevilla (España) del 5 al 7 de febrero de 2020.Two symbiotic systems have been described, endosymbiosis and... more
Resumen del trabajo presentado a la VII Biennial Congress of Sociedad Española de Biología Evolutiva (SEBE), celebrada en Sevilla (España) del 5 al 7 de febrero de 2020.Two symbiotic systems have been described, endosymbiosis and ectosymbiosis, and generally insects harbour one of the two. However, Blattella germanica is an omnivorous insect in which both systems coexist: Blattabacterium cuenotii, an endosymbiont located in specialised cells (bacteriocytes) in the fat body, and a rich microbiota located in the hindgut. Blattabacterium is an obligate endosymbiont with an essential role in the nitrogen recycling and essential amino acids biosynthesis, as it has been proposed after its genome sequencing. The gut microbiome is a complex population similar to the human gut microbiome, with many potential functions that still have to be elucidated. To assess if there is a crosstalk between both symbiotic systems in B. germanica, despite being located in separate compartments, we planned to reduce the Blattabacterium population by antibiotic treatment, but affecting as little as possible to its microbiota. To do that, we treated adults with rifampicin (antibiotic that attacks Blattabacterium as well as Gram-negative and some Gram-positive bacteria) in short periods of time (12 days, when Blattabacterium is extracellular to infect the nextgeneration oocytes), during three generations. We have measured in adult females the amount of Blattabacterium by qPCR and the changes of the bacterial community of the gut microbiota by sequencing the 16S rRNA gene. We have also determined several fitness parameters (developmental time, sexual maturation time, reproductive rate and mortality) to assess the effect on the host of the reduction of the endosymbiont. Results indicate that the gut microbiota is not able to carry out Blattabacterium’s role.Peer reviewe
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In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins... more
In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins having close homologs of unexpected taxonomic affiliation. Once a set of putative xenologs are identified, Phylomizer is used to reconstruct phylogenetic trees. Phylomizer reproduces all the necessary steps to perform a basic phylogenetic analysis. The combined use of DarkHorse and Phylomizer allows the identification of genes incorporated into a given genome by HGT.
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Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they... more
Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species’ biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven—the minimum, ancestor–descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobac...
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Research Interests: Microbiology, Microbial Ecology, Biology, Ecology, Medicine, and 4 moreMetamorphosis, Microbiome, Insect, and Gut Flora
We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of... more
We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals and high ultraviolet B radiation. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina .
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The term “bacterial dysbiosis” is being used quite extensively in metagenomic studies, however, the identification of harmful bacteria often fails due to large overlap between the bacterial species found in healthy volunteers and... more
The term “bacterial dysbiosis” is being used quite extensively in metagenomic studies, however, the identification of harmful bacteria often fails due to large overlap between the bacterial species found in healthy volunteers and patients. We hypothesized that the pathogenic oral bacteria are individual-specific and they correlate with oxidative stress markers in saliva which reflect the inflammatory processes in the oral cavity. Temporally direct and lagged correlations between the markers and bacterial taxa were computed individually for 26 volunteers who provided saliva samples during one month (21.2 ± 2.7 samples/volunteer, 551 samples in total). The volunteers’ microbiomes differed significantly by their composition and also by their degree of microbiome temporal variability and oxidative stress markers fluctuation. The results showed that each of the marker-taxa pairs can have negative correlations in some volunteers while positive in others. Streptococcus mutans, which used t...
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Research Interests: Immunology, Medicine, Biological Sciences, HUMAN PAPILLOMAVIRUS, Humans, and 15 moreMale, AIDS, Middle Aged, Immune system, Adult, Anal Cancer, Microbiota, Sexual and Gender Minorities, Cross Sectional Studies, Dysbiosis, Psychology and Cognitive Sciences, Papillomavirus Infections, Medical and Health Sciences, HIV infections, and Gastrointestinal microbiome
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ABSTRACT
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Variability in the heat shock response has been studied in D. subobscura, both in individuals from different strains at the same moment of development and in individuals belonging to the same strain at different moments of prepupal... more
Variability in the heat shock response has been studied in D. subobscura, both in individuals from different strains at the same moment of development and in individuals belonging to the same strain at different moments of prepupal development. The heat shock response was independent of the genic background of the individuals, whereas a variability depending on the moment of development has been obtained. In relation to this variability two kinds of heat shock puffs have been found: those induced independently of the moment of development and those induced with a response dependent on it. In both cases a differential genic response that is dependent on the temperature of treatment has been detected.
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HAL - hal.archives-ouvertes.fr, CCSd - Centre pour la Communication Scientifique Direct. Accueil; Dépôt: S'authentifier; S'inscrire. Consultation: Par domaine; Les 30 derniers dépôts; Par année de publication, rédaction, dépôt;... more
HAL - hal.archives-ouvertes.fr, CCSd - Centre pour la Communication Scientifique Direct. Accueil; Dépôt: S'authentifier; S'inscrire. Consultation: Par domaine; Les 30 derniers dépôts; Par année de publication, rédaction, dépôt; Par type de publication; Par collection; Les portails de l'archive ouverte HAL; Par établissement (extraction automatique); ArXiv; Les Thèses (TEL). Recherche: Recherche simple; Recherche avancée; Accès par identifiant; Les Thèses ...
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Research Interests: Evolutionary Biology, Biology, Breeding, Argentina, Agricultural Biotechnology, and 15 moreFitness, Biological Sciences, DNA, Drosophila, Genetica, Female, Animals, Environmental Variables, Body Size, Evolutionary History, Biological evolution, Base Sequence, Body Height, Chromosomes, and Biochemistry and cell biology
Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their... more
Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism –which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphidCinara cedrithat harbors two co-primary endosymbionts,Buchnera aphidicolaBCc andCa.Serratia symbiotica SCc, and in which some metabolic pathways are partitioned between different partners. Here we present a genome scale metabolic network (GEM) for the bacterial consortium from the cedar aphidiBSCc. The analysis of this GEM allows us the confirmation of cases of metabolic complementation previous...
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Blattella germanica presents a very complex symbiotic system, involving the following two kinds of symbionts: the endosymbiont Blattabacterium and the gut microbiota. Although the role of the endosymbiont has been fully elucidated, the... more
Blattella germanica presents a very complex symbiotic system, involving the following two kinds of symbionts: the endosymbiont Blattabacterium and the gut microbiota. Although the role of the endosymbiont has been fully elucidated, the function of the gut microbiota remains unclear. The study of the gut microbiota will benefit from the availability of insects deprived of Blattabacterium. Our goal is to determine the effect of the removal (or, at least, the reduction) of the endosymbiont population on the cockroach’s fitness, in a normal gut microbiota community. For this purpose, we treated our cockroach population, over several generations, with rifampicin, an antibiotic that only affects the endosymbiont during its extracellular phase, and decreases its amount in the following generation. As rifampicin also affects gut bacteria that are sensitive to this antibiotic, the treatment was performed during the first 12 days of the adult stage, which is the period when the endosymbiont i...
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Defence systems against microbial pathogens are present in most living beings. The German cockroach Blattella germanica requires these systems to adapt to unhealthy environments with abundance of pathogenic microbes, in addition to... more
Defence systems against microbial pathogens are present in most living beings. The German cockroach Blattella germanica requires these systems to adapt to unhealthy environments with abundance of pathogenic microbes, in addition to potentially control its symbiotic systems. To handle this situation, four antimicrobial gene families (defensins, termicins, drosomycins and attacins) were expanded in its genome. Remarkably, a new gene family (blattellicins) emerged recently after duplication and fast evolution of an attacin gene, which is now encoding larger proteins with the presence of a long stretch of glutamines and glutamic acids. Phylogenetic reconstruction, within Blattellinae, suggests that this duplication took place before the divergence of Blattella and Episymploce genera. The latter harbours a long attacin gene (pre-blattellicin), but the absence of the encoded Glx-region suggests that this element evolved recently in the Blattella lineage. A screening of AMP gene expression...
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Research Interests: Humanities and Biology
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Compressed archive of nexus files used for phylogenetic reconstruction in phylobayes<br>
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Mutualistic stable symbioses are widespread in all groups of eukaryotes, especially in insects, where symbionts have played an essential role in their evolution. Many insects live in obligate relationship with different ecto- and... more
Mutualistic stable symbioses are widespread in all groups of eukaryotes, especially in insects, where symbionts have played an essential role in their evolution. Many insects live in obligate relationship with different ecto- and endosymbiotic bacteria, which are needed to maintain their hosts’ fitness in their natural environment, to the point of even relying on them for survival. The case of cockroaches (Blattodea) is paradigmatic, as both symbiotic systems coexist in the same organism in two separated compartments: an intracellular endosymbiont (Blattabacterium) inside bacteriocytes located in the fat body, and a rich and complex microbiota in the hindgut. The German cockroach Blattella germanica is a good model for the study of symbiotic interactions, as it can be maintained in the laboratory in controlled populations, allowing the perturbations of the two symbiotic systems in order to study the communication and integration of the tripartite organization of the host–endosymbion...
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Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans that continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage... more
Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans that continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified ...
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An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that... more
An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance wit...
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For the first time, we analyze the interkingdom hindgut microbiome of this species, including bacteria, fungi, archaea, and viruses. Network analysis reveals putative cooperation between core bacteria that could be key for ecosystem... more
For the first time, we analyze the interkingdom hindgut microbiome of this species, including bacteria, fungi, archaea, and viruses. Network analysis reveals putative cooperation between core bacteria that could be key for ecosystem equilibrium.
Research Interests: Microbiology, Biology, Medicine, Bacteria, Microbiome, and 3 moreCockroach, Gut Bacteria, and Resistome
Background: The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with... more
Background: The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. Results: We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal...
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Research Interests: Microbiology, Biology, Metagenomics, Medicine, Population, and 5 moreAntibiotics, Feces, Gut Flora, Ampicillin, and Cockroach
The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished... more
The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished bacterial genomes exclusively. It originally consisted of three modules where users could search for the bacteria involved in a specific symbiotic relationship, their genomes and their genes (including their orthologs). In this update, we present an additional module that includes a representation of the metabolic network of each organism included in the database, as Directed Acyclic Graphs (MetaDAGs). This module provides unique opportunities to explore the metabolism of each individual organism and/or to evaluate the shared and joint metabolic capabilities of the organisms of the same genera included in our listing, allowing users to construct predictive analyses of metabolic associations and complementation between systems. We also report a ~25% i...
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Background The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared... more
Background The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared towards human microbiomes. Microbiota are better understood when analyzed in their biological context, which is together with their host or environment, but this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Results Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomics, and metaproteomics in an integrative manner. The pipeline has been developed using the Snakemake framework in order to obtain an automated and reproducible workflow. One of the key features is the on-the-fly creation of a tailored proteogenomic database based on metagenomics and meta...
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Settled on the foundations laid by zoologists and embryologists more than a century ago, the study of symbiosis between prokaryotes and eukaryotes is an expanding field. In this review, we present several models of insect–bacteria... more
Settled on the foundations laid by zoologists and embryologists more than a century ago, the study of symbiosis between prokaryotes and eukaryotes is an expanding field. In this review, we present several models of insect–bacteria symbioses that allow for the detangling of most known features of this distinctive way of living, using a combination of very diverse screening approaches, including molecular, microscopic, and genomic techniques. With the increasing the amount of endosymbiotic bacteria genomes available, it has been possible to develop evolutionary models explaining the changes undergone by these bacteria in their adaptation to the intracellular host environment. The establishment of a given symbiotic system can be a root cause of substantial changes in the partners’ way of life. Furthermore, symbiont replacement and/or the establishment of bacterial consortia are two ways in which the host can exploit its interaction with environmental bacteria for endosymbiotic reinvigo...