Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes

DNA Research - Tập 14 Số 4 - Trang 169-181 - 2007
Ken Kurokawa1, Takehiko Itoh2, Tomomi Kuwahara3, Kenshiro Oshima4, Hidehiro Toh5,4, Atsushi Toyoda6, Hideto Takami7, Hidetoshi Morita8, Vijay K. Sharma6, Tulika P. Srivastava6, Todd D. Taylor6, Hideki Noguchi9, Hiroshi Mori1, Yoshitoshi Ogura10, Dusko S. Ehrlich11, Kikuji Itoh12, Toshihisa Takagi9, Yoshiyuki Sakaki6, Tetsuya Hayashi10, Masahira Hattori9,4,6
1Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
2Life Science Research Group, Research Center for Advanced Science and Technology, Mitsubishi Research Institute, 3-6 Otemachi 2-chome Chiyoda-ku, Tokyo 100-8141, Japan
3Department of Molecular Bacteriology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-5 Kuramoto-cho, Tokushima 770-8503, Japan
4Kitasato Institute for Life Science, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
5Center for Basic Research, Kitasato Institute, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
6RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
7Extremophiles Research Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
8School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
9Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561 Japan
10Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
11Institut National de la Recherche Agronomique, Domaine de Vilvet, 8352 Jouy en Josas, France
12Department of Veterinary Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan

Tóm tắt

Từ khóa


Tài liệu tham khảo

Backhed, 2005, Host-bacterial mutualism in the human intestine, Science, 307, 1915, 10.1126/science.1104816

Ley, 2006, Ecological and evolutionary forces shaping microbial diversity in the human intestine, Cell, 124, 837, 10.1016/j.cell.2006.02.017

Savage, 2001, Microbial biota of the human intestine: a tribute to some pioneering scientists, Curr. Issues. Intest. Microbiol, 2, 1

Tancrede, 1992, Role of human microflora in health and disease, Eur J Clin Microbiol. Infect. Dis., 11, 1012, 10.1007/BF01967791

Eckburg, 2005, Diversity of the human intestinal microbial flora, Science, 308, 1635, 10.1126/science.1110591

Fanaro, 2003, Intestinal microflora in early infancy: composition and development, Acta Paediatr., 91, 48, 10.1111/j.1651-2227.2003.tb00646.x

Gibson, 1995, Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics, J. Nutr., 125, 1401, 10.1093/jn/125.6.1401

Guarner, 2003, Gut flora in health and disease, Lancet, 361, 512, 10.1016/S0140-6736(03)12489-0

Hooper, 2001, Commensal host-bacterial relationships in the gut, Science, 292, 1115, 10.1126/science.1058709

Backhed, 2004, The gut microbiota as an environmental factor that regulates fat storage, Proc. Natl. Acad. Sci. USA, 101, 15718, 10.1073/pnas.0407076101

Rakoff-Nahoum, 2004, Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis, Cell, 118, 229, 10.1016/j.cell.2004.07.002

Samuel, 2006, A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism, Proc. Natl. Acad. Sci. USA, 103, 10011, 10.1073/pnas.0602187103

Ley, 2006, Microbial ecology: human gut microbes associated with obesity, Nature, 444, 1022, 10.1038/4441022a

Macdonald, 2005, Immunity, inflammation, and allergy in the gut, Science, 307, 1920, 10.1126/science.1106442

Manichanh, 2006, Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach, Gut, 55, 205, 10.1136/gut.2005.073817

McGarr, 2005, Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature, J. Clin. Gastroenterol, 39, 98

Seksik, 2006, Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease, Aliment. Pharmacol. Ther., 24, 11, 10.1111/j.1365-2036.2006.03053.x

Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414

Finegold, 1983, Normal indigenous flora, In, Human Intestinal Microflora in Health and Disease, 3, 10.1016/B978-0-12-341280-5.50007-0

Tringe, 2005, Nat. Rev. Genet., 6, 805, 10.1038/nrg1709

Gill, 2006, Metagenomic analysis of the human distal gut microbiome, Science, 312, 1355, 10.1126/science.1124234

Benno, 1989, Comparison of fecal microflora of elderly persons in rural and urban areas of Japan, Appl. Environ. Microbiol., 55, 1100, 10.1128/AEM.55.5.1100-1105.1989

Favier, 2002, Molecular monitoring of succession of bacterial communities in human neonates, Appl. Environ. Microbiol., 68, 219, 10.1128/AEM.68.1.219-226.2002

Hopkins, 2001, Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S RNA abundance, and community cellular fatty acid profiles, Gut, 48, 198, 10.1136/gut.48.2.198

Stewart, 2005, Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children, J. Med. Microbiol., 54, 1239, 10.1099/jmm.0.46189-0

Venter, 2004, Environmental genome shotgun sequencing of the Sargasso Sea, Science, 304, 66, 10.1126/science.1093857

Hattori, 1997, A novel method for making nested deletions and its application for sequencing of a 300 kb region of human APP locus, Nuc. Acids Res., 25, 1802, 10.1093/nar/25.9.1802

Huang, 2003, PCAP: a whole-genome assembly program, Genome Res., 13, 2164, 10.1101/gr.1390403

Noguchi, 2006, MetaGene: prokaryotic gene finding from environmental genome shotgun sequences, Nucl. Acids Res., 34, 5623, 10.1093/nar/gkl723

Garnier, 2000, Characterization of transposon Tn1549, conferring VanB-type resistance in Enterococcus spp, Microbiology, 146, 1481, 10.1099/00221287-146-6-1481

Sebaihia, 2006, The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome, Nat. Genet., 38, 779, 10.1038/ng1830

Paulsen, 2003, Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis, Science, 299, 2071, 10.1126/science.1080613

Beres, 2006, Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus, Proc. Natl. Acad. Sci. USA, 103, 7059, 10.1073/pnas.0510279103

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucl. Acids Res., 25, 3389, 10.1093/nar/25.17.3389

DeLong, 2006, Community genomics among stratified microbial assemblages in the ocean's interior, Science, 311, 496, 10.1126/science.1120250

Kunin, 2005, Measuring genome conservation across taxa: divided strains and united kingdoms, Nucl. Acids Res., 33, 616, 10.1093/nar/gki181

Korbel, 2002, SHOT: a web server for the construction of genome phylogenies, Trends Genet., 18, 158, 10.1016/S0168-9525(01)02597-5

de Hoon, 2004, Open source clustering software, Bioinformatics, 20, 1453, 10.1093/bioinformatics/bth078

Tringe, 2005, Comparative metagenomics of microbial communities, Science, 308, 554, 10.1126/science.1107851

Enright, 2002, An efficient algorithm for large-scale detection of protein families, Nucl. Acids Res, 30, 1575, 10.1093/nar/30.7.1575

Finn, 2006, Pfam: clans, web tools and services, Nucl. Acids Res., 34, D247, 10.1093/nar/gkj149

Bailey, 1994, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28

Peschel, 2006, The co-evolution of host cationic antimicrobial peptides and microbial resistance, Nat. Rev. Microbiol., 4, 529, 10.1038/nrmicro1441

Wakabayashi, 1992, Food-derived mutagens and carcinogens, Cancer Res., 52, 2092s

Bry, 1996, A model of host-microbial interactions in an open mammalian ecosystem, Science, 273, 1380, 10.1126/science.273.5280.1380

Domingo, 2005, Characterization of a Tn5382-like transposon containing the vanB2 gene cluster in a Clostridium strain isolated from human faeces, J. Antimicrob. Chemother., 55, 466, 10.1093/jac/dki029

Melville, 2004, The Butyrivibrio fibrisolvens tet(W) gene is carried on the novel conjugative transposon TnB1230, which contains duplicated nitroreductase coding sequences, J. Bacteriol., 186, 3656, 10.1128/JB.186.11.3656-3659.2004

Launay, 2006, Transfer of vancomycin resistance transposon Tn1549 from Clostridium symbiosum to Enterococcus spp. in the gut of gnotobiotic mice, Antimicrob. Agents. Chemother., 50, 1054, 10.1128/AAC.50.3.1054-1062.2006

Franke, 1981, Evidence for a chromosome-borne resistance transposon (Tn916) in Streptococcus faecalis that is capable of “conjugal” transfer in the absence of a conjugative plasmid, J. Bacteriol, 145, 494, 10.1128/JB.145.1.494-502.1981

Yachi, 1999, Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis, Proc. Natl. Acad. Sci. USA, 96, 1463, 10.1073/pnas.96.4.1463