title: Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.
abstract: Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes.
authors.affiliation: Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Kurokawa
authors.forename: Takehiko
authors.initials: T
authors.lastname: Itoh
authors.forename: Tomomi
authors.initials: T
authors.lastname: Kuwahara
authors.forename: Kenshiro
authors.initials: K
authors.lastname: Oshima
authors.forename: Hidehiro
authors.initials: H
authors.lastname: Toh
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Hideto
authors.initials: H
authors.lastname: Takami
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Morita
authors.forename: Vineet K
authors.initials: VK
authors.lastname: Sharma
authors.forename: Tulika P
authors.initials: TP
authors.lastname: Srivastava
authors.forename: Todd D
authors.initials: TD
authors.lastname: Taylor
authors.forename: Hideki
authors.initials: H
authors.lastname: Noguchi
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Mori
authors.forename: Yoshitoshi
authors.initials: Y
authors.lastname: Ogura
authors.forename: Dusko S
authors.initials: DS
authors.lastname: Ehrlich
authors.forename: Kikuji
authors.initials: K
authors.lastname: Itoh
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Takagi
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Sakaki
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Hayashi
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
mesh_terms: D000328:Adult; D002675:Child, Preschool; D016000:Cluster Analysis; D005260:Female; D041981:Gastrointestinal Tract / Q000378:metabolism* / Q000382:microbiology*; D005798:Genes, Bacterial; D023281:Genomics; D006801:Humans; D007223:Infant; D007422:Intestines; D008297:Male; D054892:Metagenome / Q000235:genetics*; D008875:Middle Aged; D010802:Phylogeny; D017422:Sequence Analysis, DNA