Biology subjects

Shouche, Y. S.

Publications and source records attributed to Shouche, Y. S..

3 recordsLinked to original sources

bioRxiv2018

Functional and Comparative Genomics of Niche-Specific Adapted Actinomycetes Kocuria rhizophila Strain D2 Isolated from Healthy Human Gut

Incidences 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 has given insights into the phylogeny while the accessory and unique genes has led to the identification of niche specific genes. Bacteriophage, virulence factors and biofilm formation genes were absent with this species. Housing CRISPR and antibiotic resistance gene was strain specific. The integrated approach of functional, genomic and comparative analysis denotes the niche specific adaption to gut dynamics of strain D2. Moreover the study has comprehensively characterized genome sequence of each strain to know the genetic difference and intern recognize the effects of on phenotype and functionality complexity. The evolutionary relationship among strains along and adaptation strategies has been included in this study.\n\nSignificanceReports of Kocuria rhizophila isolation from various sources have been reported but the few disease outbreaks in humans and fishes have been prominent, but no supportive evidence about the survival ability of Kocuria spp. within human GIT. Here, we report the gut adaption potential of K. rhizophila strain D2 by functional and genomic analysis. Further; comparative genomics reveals this adaption to be strain specific (Gluten degradation). Genetic difference, evolutionary relationship and adaptation strategies have been including in this study.

genomics↗

bioRxiv2018

Comparative Genome Analysis Reveals Important Genetic Factors Associated with Probiotic Property in Enterococcus faecium strains

Enterococcus 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. Beyond shared genetic features; this study particularly identified genes that are responsible to impart probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. The study also provides insights into the acquired and intrinsic drug resistance genes, which will be helpful for better understanding of the physiology of antibiotic resistance in E. faecium strains. In addition, we could identify genes contributing to the intrinsic ability of 17OM39 E. faecium isolate to be a potential probiotic.\n\nThe study has comprehensively characterized genome sequence of each strain to find the genetic variation and understand effects of these on functionality, phenotypic complexity. Further the evolutionary relationship of species along with adaptation strategies have been including in this study.

bioinformatics↗

bioRxiv2017

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls

Recent studies on celiac disease (CeD) have shown the role of gut microbiota alterations in CeD pathogenesis. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific taxa between pre-diseases and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to faecal samples indicating larger disruption of microbiota at disease site. Increased abundance of specific Helicobacter ASVs were observed in duodenum of CeD when compared to FDR (p < 0.01). In case of fecal samples CeD microbiome and Actinomyces. In addition, predicted functional metagenome showed reduced ability of gluten that ecosystem level diversity measures (except in the duodenum) were not significantly different is characterized by reduced abundance of beneficial taxa such as Akkermansia, Ruminococcus degradation by CeD faecal microbiota in comparison to FDRs and controls.

microbiology↗