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Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic... more
Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC) testing. The results demonstrated that 7-strains had a similar pattern of drug resistance under both conditions, while the remaining ten strains had significant differences in resistance patterns between aerobic and anaerobic conditions for at least one antibiotic. We conclude that successful antibiotic therapy for host-associated pathogens requires proper assessment of the oxygen condition of the growth environment and MIC testing of each pathogen under anaerobic and aerobic conditions.
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Research Interests:
We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic... more
We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10–20 mg carbon L−1) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level alt...
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The genome of Ignatzschineria sp. strain RMDPL8A was sequenced and analyzed. This draft genome sequence was 2,175,527 bp long, with a GC content of 45.12% and 1,890 protein coding genes.
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Research Interests:
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ABSTRACTConcerning the biological interactions within the gut microbiome, the specialized small molecules encoded by commensal microbes mediate distinct functional aspects. However, the landscape of antagonistic interactions mediated by... more
ABSTRACTConcerning the biological interactions within the gut microbiome, the specialized small molecules encoded by commensal microbes mediate distinct functional aspects. However, the landscape of antagonistic interactions mediated by specialized strains and their small molecules broadly remains. Here, we sought to evaluate antimicrobial interactions as a defensive contributor to gain new insights into structure-related functions or to bring the therapeutic potential of derived molecules. We elucidated the antagonistic landscape within a collection of 330 human-gut-derived commensal microbial strains cultivated from healthy human subjects. We characterized potential antagonistic strains and found a strain-specific selective inhibition contrary to common antimicrobial drugs that wipe out a broad range of species usually found in environmental microbes. Using functional and genomic approaches for accessing biologically active natural product molecules, we identified significant bios...
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In the manuscript, we have developed a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. The method used gradient centrifugation combined with serial... more
In the manuscript, we have developed a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. The method used gradient centrifugation combined with serial dilution (two-dimensional cell separation) to improve taxum recovery from samples.
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Detailed information on genes present in genomic islands in all the strains. (XLSX 137Â kb)
Detailed information on the unique genes present in the strains under study. (XLSX 29Â kb)
Detailed information on the accessory genes present in the strains under study. (XLSX 115Â kb)
Detailed information on the core genes present in the genomes under study (XLSX 57Â kb)
Figure S1 Features assigned to subsystems from RAST present in all ten Enterococcus strains. Figure S2. (A) Proportion of known, hypothetical and unknown proteins in the group of core, accessory and unique genes (B) Venn Diagram for... more
Figure S1 Features assigned to subsystems from RAST present in all ten Enterococcus strains. Figure S2. (A) Proportion of known, hypothetical and unknown proteins in the group of core, accessory and unique genes (B) Venn Diagram for accessory genome between probiotic, non-pathogenic and pathogenic group. Figure S3. Functional analysis of the accessory genes in COG categories. Table S1. IS elements found in Enterococcus genomes by ISfinder tool. + Present, â Absent. Table S2. Number of Phage elements present in Enterococcus genomes as intact, questionable and incomplete. Table S3. Number of Genomic Islands in Enterococcus genomes. Table S4. Antibiotic Resistance genes found in Enterococcus plasmids as performed by CARD analysis, where + Present and - Absent. Table S5. IS elements found in Enterococcus plasmids by ISfinder tool. + Present, â Absent. Table S6. Table showing the various genes used in the study for generating PCA plot. (DOCX 351Â kb)
A yellow Gram-stain-positive, non-motile, non-endospore -forming, spherical endophytic actinobacterium, designated strain AE-6(T), was isolated from the inner fleshy leaf tissues of Aloe barbadensis (Aloe vera) collected from Pune,... more
A yellow Gram-stain-positive, non-motile, non-endospore -forming, spherical endophytic actinobacterium, designated strain AE-6(T), was isolated from the inner fleshy leaf tissues of Aloe barbadensis (Aloe vera) collected from Pune, Maharashtra, India. Strain AE-6(T) grew at high salt concentrations [10% (w/v) NaCl], temperatures of 15-41 °C and a pH range of 5-12. It showed highest (99.7%) 16S rRNA gene sequence similarity with Micrococcus yunnanensis YIM 65004(T) followed by Micrococcus luteus NCTC 2665(T) (99.6%) and Micrococcus endophyticus YIM 56238(T) (99.0%). Ribosomal protein profiling by MALDI-TOF/MS also showed it was most closely related to M. yunnanensis YIM 65004(T) and M. luteus NCTC 2665(T). Like other members of the genus Micrococcus, strain AE-6(T) had a high content of branched chain fatty acids (iso-C15:0 and anteiso-C15:0). MK-8(H2) and MK-8 were the predominant isoprenoid quinones. Cell wall analysis showed an 'A2 L-Lys-peptide subunit' type of peptidogly...
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Research Interests:
Probiotics are live microbial cells or cultures which promote host growth and vigour. The study of the role of microorganisms in soil and plant health and plant-microbe interactions has been the area of interest for plant pathologists and... more
Probiotics are live microbial cells or cultures which promote host growth and vigour. The study of the role of microorganisms in soil and plant health and plant-microbe interactions has been the area of interest for plant pathologists and soil microbiologists since beginning of microbiology. Plant probiotics have garnered a considerable amount of attention due to success of human probiotics in improved human health. Plant probiotics are microorganisms or group of microorganisms which by virtue of their potential role in improved nutrient acquisition and/or biocontrol activities can promote soil health, plant growth and enhance plant tolernace or immunity against various abiotic and biotic stresses. Plant growth-promoting bacteria (PGPBs) are good examples of plant probiotics which augment crop production by different activities like nitrogen fixation, growth hormones production, and phosphorus- and mineral- solubilization, enhancing water and nutrient use efficiency, and act as bioc...
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Microbes are the provider of ecosystem services and act as a key component for environmental sustainability and human health. It is believed that the cultivation and preservation of new taxa with innovative traits is essential for... more
Microbes are the provider of ecosystem services and act as a key component for environmental sustainability and human health. It is believed that the cultivation and preservation of new taxa with innovative traits is essential for biotechnological growth even in the era of omics-driven science. Cultivation and preservation of entire microbial diversity is impossible even with extra efforts and use of novel high-throughput cultivation approaches. Therefore, development of protocols for community and habitat preservation should be priorities. In current article, we discussed about importance of microbes for biotechnological growth and their preservation for future reference research and application. In addition we also incorporated the loopholes of current preservation research and tried to incorporate the suggestion to fill the existing gaps. We tried to give a brief overview of different preservation methods used for preservation of bacteria and fungi and also incorporated the conce...
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Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic... more
Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC...
Research Interests:
Research Interests:
ABSTRACTIncidences of infection and occurrence of Kocuria rhizophila in human gut are prominent but certainly no reports on the species ability to withstand human gastrointestinal dynamics. Kocuria rhizophila strain D2 isolated from... more
ABSTRACTIncidences of infection and occurrence of Kocuria rhizophila in human gut are prominent but certainly no reports on the species ability to withstand human gastrointestinal dynamics. Kocuria rhizophila strain D2 isolated from healthy human gut was comprehensively characterized. The functional analysis revealed the ability to produce various gastric enzymes and sensitive to major clinical antibiotics. It also exhibited tolerance to acidic pH and bile salts. Strain D2 displayed bile-salt hydrolytic (BSH) activity, strong cell surface traits such as hydrophobicity, auto-aggregation capacity and adherence to human HT-29 cell line. Prominently, it showed no hemolytic activity and was susceptible to the human serum. Exploration of the genome led to the discovery of the genes for the above said properties and has ability to produce various essential amino acids and vitamins. Further, comparative genomics have identified core, accessory and unique genetic features. The core genome ha...
ABSTRACTEnterococcus faecium though commensals in human gut, few strains provide beneficial effect to humans as probiotics, few are responsible for nosocomial infection and few as non-pathogens. Comparative genomics of E. faecium will... more
ABSTRACTEnterococcus faecium though commensals in human gut, few strains provide beneficial effect to humans as probiotics, few are responsible for nosocomial infection and few as non-pathogens. Comparative genomics of E. faecium will help to reveal the genomic differences responsible for the said properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. The core genome analysis revealed, 17OM39 was closely related with marketed probiotic strain T110. Strain 17OM39 was found to be devoid of known vancomycin, tetracycline resistance genes and functional virulence genes. Moreover, 17OM39 is „less open‟ due to absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Additional, genes associated with colonization within gastrointestinal tract were detected across all the strains....
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Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic... more
Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. E. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal t...
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The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces... more
The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity. The strain was able to tolerate bile salts and showed bile salt hydrolytic (BSH) activity, exopolysaccharide production and adherence to human HT-29 cell line. Importantly, partial haemolytic activity was detected and the strain was susceptible to the human serum. Genomics investigation of strain 17OM39 revealed the presence of diverse genes encoding for proteolytic enzymes, stress response systems and the ability to produce essent...
Research Interests: Genetics, Probiotics, Humans, SALT TOLERANCE, Adult, and 3 moreFeces, Enterococcus faecium, and Hemolysis
An endophytic species of Micrococcus was isolated from Aloe vera leaf (syn. Aloe barbadensis) and screened for protease production with five other species of Micrococcus. Data indicated that endophytic Micrococcus aloeverae AE-6 MCC... more
An endophytic species of Micrococcus was isolated from Aloe vera leaf (syn. Aloe barbadensis) and screened for protease production with five other species of Micrococcus. Data indicated that endophytic Micrococcus aloeverae AE-6 MCC 2184(T) and Micrococcus yunnanensis DSM 21948(T) showed efficient protease production potential and secreted active protease at high salt (10%), temperature (40 °C) and in wide range of pH 8-10. Unlike M. yunnanensis DSM 21948(T), protease production by M. aloeverae AE-6 MCC 2184(T) was stringently controlled by pH. Protease induction study using different group of peptides, peptide carbohydrates and peptide macronutrient combinations showed variable response with both the organisms. Result indicated that the amount of protease was not directly related to cell biomass but it depends on nature of inducible peptides. In this study we also developed a modified agar-well assay for semi-quantitative data from large number of replicates.
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In present study, a Gram-stain-positive, non-motile, non-spore-forming, small spherical bacterium, strain S31T was isolated from skin surface (external ear lobe) of a healthy human subject and characterized using polyphasic approach of... more
In present study, a Gram-stain-positive, non-motile, non-spore-forming, small spherical bacterium, strain S31T was isolated from skin surface (external ear lobe) of a healthy human subject and characterized using polyphasic approach of bacterial taxonomy. Based on 1507 bp 16S rRNA gene sequence comparison, strain S31T showed highest (92.8%, AY119686) sequence similarity with Macrococcus brunensis CCUG 47200T followed by Macrococcus caseolyticus DSM 20597T (92.7% AP009484) and formed a separate clade with 65% bootstrap support. The DNA G+C content was found to be 34 mol%. Anteiso C15:0, Anteiso C17:0 and iso C16:0 are the predominant fatty acids in fatty acid methyl ester (FAME) profile of strain S31T. It contained A3α type peptidoglycan with L-Lys- Gly3-L-Ala peptide. Comparative study of morphological and physiological traits indicated that strain S31T phenetically diverged from its closest relatives. Based on morphological, chemotaxonomic and genotypic data, strain S31T showed suf...
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Soda lake is hyper alkaline and saline habitat located in closed craters with high evaporation rate. In current study fungal diversity from water and sediment samples of a soda lake (Lonar lake) located in Buldhana district of... more
Soda lake is hyper alkaline and saline habitat located in closed craters with high evaporation rate. In current study fungal diversity from water and sediment samples of a soda lake (Lonar lake) located in Buldhana district of Maharashtra, India was investigated using extensive culturomics approach and mimicking the natural conditions of Lonar lake in culture media. A total of 104 diverse isolates of extremophilic fungi were recovered from this study and phylogenetically characterized by internal transcribed spacer (ITS) region sequencing. In addition, due to important role of phenol oxidase, and peroxidase in degradation of toxic phenol, lignin, etc., all isolated pure cultures were also screened for extracellular phenol oxidase and peroxidase production potential. Diversity analysis indicated that different groups of extremophilic fungi are present in the water and sediment samples of Lonar lake. A total of 38 species of fungi belonging to 18-different genera were recovered. Out o...
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A novel bacterial strain, 29Y89BT, was isolated from a faecal sample of a healthy human subject. Cells were Gram-stain-negative, motile, non-spore-forming and rod-shaped. Strain 29Y89BT formed cream-coloured colonies 2 mm in diameter on... more
A novel bacterial strain, 29Y89BT, was isolated from a faecal sample of a healthy human subject. Cells were Gram-stain-negative, motile, non-spore-forming and rod-shaped. Strain 29Y89BT formed cream-coloured colonies 2 mm in diameter on trypticase soy agar and showed optimum growth at 35 °C. Strain 29Y89BT showed highest 16S rRNA gene sequence similarity to Pantoea gaviniae A18/07T (98.4 %) followed by Pantoea calida 1400/07T (97.2 %). Multi-locus sequence analysis using atpD (ATP synthase β subunit), gyrB (DNA gyrase), infB (initiation translation factor 2) and rpoB (RNA polymerase β subunit) genes also supported the result of 16S rRNA gene sequence based phylogeny. Strain 29Y89BT showed 62 and 40.7 % DNA-DNA relatedness with P. calida DSM 22759T and P. gaviniae DSM 22758T. Strain 29Y89BT contained C17 : 0 cyclo, C19 : 0 cyclo ω8c, C16 : 0, C14 : 0 and C12 : 0 as predominant fatty acids. In addition, strain 29Y89BT showed physiological and phenotypic differences from its closest ...
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Research Interests:
Micrococcus lactis MCC 2278T and Zhihengliuella aestuarii JCM 16166T were published in International Journal of Systematic and Evolutionary Microbiology in 2011. They showed high levels of 16S rRNA gene sequence similarity (99.3%).... more
Micrococcus lactis MCC 2278T and Zhihengliuella aestuarii JCM 16166T were published in International Journal of Systematic and Evolutionary Microbiology in 2011. They showed high levels of 16S rRNA gene sequence similarity (99.3%). Phylogenetic analysis revealed that M. lactis MCC 2278T and Z. aestuarii JCM 16166T formed monophyletic clade and showed distant relationship with other members of the closely related genera like Micrococcus, Zhihengliuella, Arthrobacter and Citricoccus. Presence of high proportion of iso-C14:0 and iso-C16:0 with low iso-C15:0 distinguished M. lactis MCC 2278T and Z. aestuarii JCM 16166T from other members of the genera Micrococcus and Zhihengliuella. Unlike other members of the genera Zhihengliuella and Micrococcus; M. lactis MCC 2278T and Z. aestuarii JCM 16166T showed growth at low concentrations of NaCl. Thus, based on distinctive phylogenetic, chemotaxonomic and physiological features of these two organisms from other members of the genera Micrococcu...
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A Gram-stain-negative, motile, non-spore-forming, coccoid bacterium was isolated from a stool sample of a healthy human subject and formed cream colour colonies on tryptic soy agar. Almost full-length (1500 bp) small subunit rRNA (16S... more
A Gram-stain-negative, motile, non-spore-forming, coccoid bacterium was isolated from a stool sample of a healthy human subject and formed cream colour colonies on tryptic soy agar. Almost full-length (1500 bp) small subunit rRNA (16S rRNA) gene sequences were generated and a similarity search was conducted by blast. The results of the similarity search indicated that the bacterium belongs to the class Betaproteobacteria , family Alcaligenaceae . It showed maximum sequence similarity (96.5 %) with Pelistega europaea CCUG 39967T followed by Advenella mimigardefordensis DSM 17166T (96.1 %) and Taylorella asinigenitalis LMG 19572T (95.3 %). The DNA G+C content of strain HM-7T was 42 mol%. Strain HM-7T contained C14 : 0, C16 : 0, C16 : 0 3-OH and C18 : 0 as the dominant fatty acids. Morphological, physiological and biochemical data also indicated that strain HM-7T represents a member of the genus Pelistega , but at the same time distinguished it from Pelistega europaea CCUG 39967T, the ...