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Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human

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Title Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human
 
Creator Gupta, Vinod Kumar
Chaudhari, Narendrakumar M
Iskepalli, Suchismitha
Dutta, Chitra
 
Subject Structural Biology & Bioinformatics
 
Description The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations, if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium.
Results: The pan-genome for Prevotella remains “open”. On an average, 17% of predicted protein-coding genes of
any particular Prevotella genome represent the conserved core genes, while the remaining 83% contribute to the
flexible and singletons. The study reveals exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. Distribution of various functional COG categories differs significantly among the habitat-specific genes. No niche-specific variations could be observed in distribution of KEGG pathways.
Conclusions: Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting
that these microbiome components might have developed distinct genetic strategies for niche adaptation within the
host. Each individual microbe might also have a component of its own genetic machinery for host adaptation,
as appeared from the huge number of singletons
 
Publisher BioMed Central
 
Date 2015
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/2203/1/BMC_GENOMICS__Volume_16_____Article_Number_153;2015[46].pdf
Gupta, Vinod Kumar and Chaudhari, Narendrakumar M and Iskepalli, Suchismitha and Dutta, Chitra (2015) Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human. BMC Genomics, 16 (153).
 
Relation http://dx.doi.org/10.1186/s12864-015-1350-6
http://www.eprints.iicb.res.in/2203/