DNA Research Advance Access first published online on October 3, 2007
This version published online on October 16, 2007
DNA Research, doi:10.1093/dnares/dsm018
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes
1 Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
2 Life Science Research Group, Research Center for Advanced Science and Technology, Mitsubishi Research Institute, 3-6 Otemachi 2-chome Chiyoda-ku, Tokyo 100-8141, Japan
3 Department of Molecular Bacteriology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-5 Kuramoto-cho, Tokushima 770-8503, Japan
4 Kitasato Institute for Life Science, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
5 Center for Basic Research, Kitasato Institute, 5-9-1 Shirokane, Minato-ku, Tokyo 108- 8641, Japan
6 RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
7 Extremophiles Research Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
8 School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
9 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
10 Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
11 Institut National de la Recherche Agronomique, Domaine de Vilvet, 8352 Jouy en Josas, France
12 Department of Veterinary Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Received 22 June 2007 ; accepted 30 July 2007.
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.
Key words: metagenomics; human gut microbiota; gene family; conjugative transposon
* To whom correspondence should be addressed. Masahira Hattori. Tel. +81-7136-4070. Fax. +81-4-7136-4084. E-mail: hattori{at}k.u-tokyo.ac.jp; or Tetsuya Hayashi. Tel. +81-985-85-0871. Fax. +81-985-85-6475.
These authors contributed equally to this work.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. A. Vaishampayan, J. V. Kuehl, J. L. Froula, J. L. Morgan, H. Ochman, and M. P. Francino Comparative Metagenomics and Population Dynamics of the Gut Microbiota in Mother and Infant Gen Biol Evol, January 28, 2010; 2010(0): 53 - 66. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Nakayama-Imaohji, H. Hirakawa, M. Ichimura, S. Wakimoto, S. Kuhara, T. Hayashi, and T. Kuwahara Identification of the Site-Specific DNA Invertase Responsible for the Phase Variation of SusC/SusD Family Outer Membrane Proteins in Bacteroides fragilis J. Bacteriol., October 1, 2009; 191(19): 6003 - 6011. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Tumbale and K. Brew Characterization of a Metal-independent CAZy Family 6 Glycosyltransferase from Bacteroides ovatus J. Biol. Chem., September 11, 2009; 284(37): 25126 - 25134. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. C. Martens, R. Roth, J. E. Heuser, and J. I. Gordon Coordinate Regulation of Glycan Degradation and Polysaccharide Capsule Biosynthesis by a Prominent Human Gut Symbiont J. Biol. Chem., July 3, 2009; 284(27): 18445 - 18457. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Barrangou, E. P. Briczinski, L. L. Traeger, J. R. Loquasto, M. Richards, P. Horvath, A.-C. Coute-Monvoisin, G. Leyer, S. Rendulic, J. L. Steele, et al. Comparison of the Complete Genome Sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04 J. Bacteriol., July 1, 2009; 191(13): 4144 - 4151. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Kovatcheva-Datchary, E. G. Zoetendal, K. Venema, W. M. de Vos, and H. Smidt Review: Tools for the tract: understanding the functionality of the gastrointestinal tract Therapeutic Advances in Gastroenterology, July 1, 2009; 2(4_suppl): s9 - s22. [Abstract] [PDF]
|
|
|
|
 |
|
 M. Gueimonde, C. Garrigues, D. van Sinderen, C. G. de los Reyes-Gavilan, and A. Margolles Bile-Inducible Efflux Transporter from Bifidobacterium longum NCC2705, Conferring Bile Resistance Appl. Envir. Microbiol., May 15, 2009; 75(10): 3153 - 3160. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Matsuda, H. Tsuji, T. Asahara, K. Matsumoto, T. Takada, and K. Nomoto Establishment of an Analytical System for the Human Fecal Microbiota, Based on Reverse Transcription-Quantitative PCR Targeting of Multicopy rRNA Molecules Appl. Envir. Microbiol., April 1, 2009; 75(7): 1961 - 1969. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Hattori and T. D. Taylor The Human Intestinal Microbiome: A New Frontier of Human Biology DNA Res, February 1, 2009; 16(1): 1 - 12. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. A. Sela, J. Chapman, A. Adeuya, J. H. Kim, F. Chen, T. R. Whitehead, A. Lapidus, D. S. Rokhsar, C. B. Lebrilla, J. B. German, et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome PNAS, December 2, 2008; 105(48): 18964 - 18969. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Kunin, A. Copeland, A. Lapidus, K. Mavromatis, and P. Hugenholtz A Bioinformatician's Guide to Metagenomics Microbiol. Mol. Biol. Rev., December 1, 2008; 72(4): 557 - 578. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Suzuki, M. Sota, C. J. Brown, and E. M. Top Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes Nucleic Acids Res., December 1, 2008; 36(22): e147 - e147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Oshima, H. Toh, Y. Ogura, H. Sasamoto, H. Morita, S.-H. Park, T. Ooka, S. Iyoda, T. D. Taylor, T. Hayashi, et al. Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult DNA Res, December 1, 2008; 15(6): 375 - 386. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Noguchi, T. Taniguchi, and T. Itoh MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes DNA Res, December 1, 2008; 15(6): 387 - 396. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E G Zoetendal, M Rajilic-Stojanovic, and W M de Vos High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota Gut, November 1, 2008; 57(11): 1605 - 1615. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Brochet, C. Rusniok, E. Couve, S. Dramsi, C. Poyart, P. Trieu-Cuot, F. Kunst, and P. Glaser Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae PNAS, October 14, 2008; 105(41): 15961 - 15966. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. V. Jones, M. Begley, C. Hill, C. G. M. Gahan, and J. R. Marchesi Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome PNAS, September 9, 2008; 105(36): 13580 - 13585. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Wada, T. Ando, M. Kiyohara, H. Ashida, M. Kitaoka, M. Yamaguchi, H. Kumagai, T. Katayama, and K. Yamamoto Bifidobacterium bifidum Lacto-N-Biosidase, a Critical Enzyme for the Degradation of Human Milk Oligosaccharides with a Type 1 Structure Appl. Envir. Microbiol., July 1, 2008; 74(13): 3996 - 4004. [Abstract] [Full Text] [PDF]
|
|