title: Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human.
abstract: BACKGROUND
  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.
authors.affiliation: Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. vinodgupta299@gmail.com.
authors.forename: Vinod Kumar
authors.initials: VK
authors.lastname: Gupta
authors.affiliation: Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. naren.niper@gmail.com.
authors.forename: Narendrakumar M
authors.initials: NM
authors.lastname: Chaudhari
authors.affiliation: Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. suchismithaiskepalli@gmail.com.|Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. suchismithaiskepalli@gmail.com.
authors.forename: Suchismitha
authors.initials: S
authors.lastname: Iskepalli
authors.affiliation: Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. cdutta@iicb.res.in.
authors.forename: Chitra
authors.initials: C
authors.lastname: Dutta
mesh_terms: D041981:Gastrointestinal Tract / Q000382:microbiology; D016680:Genome, Bacterial; D006801:Humans; D054892:Metagenome; D064307:Microbiota / Q000235:genetics*; D009055:Mouth / Q000382:microbiology; D010802:Phylogeny; D018720:Prevotella / Q000235:genetics*; D012867:Skin / Q000382:microbiology; D014018:Tissue Distribution; D014566:Urogenital System / Q000382:microbiology