Assembly of the human intestinal microbiota

Trends in Ecology & Evolution - Tập 21 - Trang 517-523 - 2006
Les Dethlefsen1, Paul B. Eckburg1, Elisabeth M. Bik1, David A. Relman1
1Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA

Tài liệu tham khảo

Hooper, 2001, Commensal host–bacterial relationships in the gut, Science, 292, 1115, 10.1126/science.1058709 Savage, 1977, Microbial ecology of the gastrointestinal tract, Annu. Rev. Microbiol., 31, 107, 10.1146/annurev.mi.31.100177.000543 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 Bäckhed, 2004, The gut microbiota as an environmental factor that regulates fat storage, Proc. Natl. Acad. Sci. U. S. A., 101, 15718, 10.1073/pnas.0407076101 Noverr, 2004, Does the microbiota regulate immune responses outside the gut?, Trends Microbiol., 12, 562, 10.1016/j.tim.2004.10.008 Macdonald, 2005, Immunity, inflammation, and allergy in the gut, Science, 307, 1920, 10.1126/science.1106442 Finegold, 2002, Gastrointestinal microflora studies in late-onset autism, Clin. Infect. Dis., 35, S6, 10.1086/341914 Hume, 2002, The pathogenesis of Crohn's disease in the 21st century, Pathology, 34, 561 McGarr, 2005, Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature, J. Clin. Gastroenterol., 39, 98 Freter, 1983, Mechanisms that control the microflora in the large intestine, 33 Moore, 1974, Human fecal flora: the normal flora of 20 Japanese-Hawaiians, Appl. Microbiol., 27, 961, 10.1128/AEM.27.5.961-979.1974 Finegold, 1983, Normal Indigenous Intestinal Flora, 3 Zoetendal, 2004, Molecular ecological analysis of the gastrointestinal microbiota: a review, J. Nutr., 134, 465, 10.1093/jn/134.2.465 Mai, 2004, Colonic bacterial flora: changing understandings in the molecular age, J. Nutr., 134, 459, 10.1093/jn/134.2.459 Eckburg, 2005, Diversity of the human intestinal microbial flora, Science, 308, 1635, 10.1126/science.1110591 Hayashi, 2005, Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism, J. Med. Microbiol., 54, 1093, 10.1099/jmm.0.45935-0 Franks, 1998, Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes, Appl. Environ. Microbiol., 64, 3336, 10.1128/AEM.64.9.3336-3345.1998 Zoetendal, 1998, Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria, Appl. Environ. Microbiol., 64, 3854, 10.1128/AEM.64.10.3854-3859.1998 Zoetendal, 2001, The host genotype affects the bacterial community in the human gastrointestinal tract, Microb. Ecol. Health Dis., 13, 129, 10.1080/089106001750462669 Vanhoutte, 2004, Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers, FEMS Microbiol. Ecol., 48, 437, 10.1016/j.femsec.2004.03.001 Matsuki, 2004, Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces, Appl. Environ. Microbiol., 70, 7220, 10.1128/AEM.70.12.7220-7228.2004 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 Mueller, 2006, Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study, Appl. Environ. Microbiol., 72, 1027, 10.1128/AEM.72.2.1027-1033.2006 Bäckhed, 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 Tannock, 2000, Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20, Appl. Environ. Microbiol., 66, 2578, 10.1128/AEM.66.6.2578-2588.2000 McCartney, 1996, Molecular analysis of the composition of the bifidobacterial and lactobacillus microflora of humans, Appl. Environ. Microbiol., 62, 4608, 10.1128/AEM.62.12.4608-4613.1996 Tilman, 2004, Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly, Proc. Natl. Acad. Sci. U. S. A., 101, 10854, 10.1073/pnas.0403458101 Curtis, 2004, Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology, Curr. Opin. Microbiol., 7, 221, 10.1016/j.mib.2004.04.010 Day, 2003, Rethinking adaptation: the niche-construction perspective, Perspect. Biol. Med., 46, 80, 10.1353/pbm.2003.0003 Sarr, 2005, A hierarchical perspective of plant diversity, Q. Rev. Biol., 80, 187, 10.1086/433058 Fons, 2000, Mechanisms of colonisation and colonisation resistance of the digestive tract Part 2: Bacteria/bacteria interactions, Microb. Ecol. Health Dis., 12, 240, 10.1080/089106000750060495 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 Harmsen, 2000, Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods, J. Pediatr. Gastroenterol. Nutr., 30, 61, 10.1097/00005176-200001000-00019 Finegold, 1978, Fecal flora in different populations, with special reference to diet, Am. J. Clin. Nutr., 31, S116, 10.1093/ajcn/31.10.S116 Gibson, 1993, Sulphate reducing bacteria and hydrogen metabolism in the human large intestine, Gut, 34, 437, 10.1136/gut.34.4.437 Roberfroid, 1998, The bifidogenic nature of chicory inulin and its hydrolysis products, J. Nutr., 128, 11, 10.1093/jn/128.1.11 Kolida, 2002, Prebiotic effects of inulin and oligofructose, Br. J. Nutr., 87, S193, 10.1079/BJN/2002537 Flint, 2004, Polysaccharide breakdown by anaerobic microorganisms inhabiting the mammalian gut, Adv. Appl. Microbiol., 56, 89, 10.1016/S0065-2164(04)56003-3 Hoskins, 1992, Mucin degradation in the human gastrointestinal tract and its significance to enteric microbial ecology, Eur. J. Gastroenterol. Hepatol., 5, 203 Cummings, 1991, The control and consequences of bacterial fermentation in the human colon, J. Appl. Bacteriol., 70, 443, 10.1111/j.1365-2672.1991.tb02739.x Macpherson, 2005, Immune responses that adapt the intestinal mucosa to commensal intestinal bacteria, Immunology, 115, 153, 10.1111/j.1365-2567.2005.02159.x Cebra, 1999, Influences of microbiota on intestinal immune system development, Am. J. Clin. Nutr., 69, 1046S, 10.1093/ajcn/69.5.1046s Toivanen, 2001, Influence of major histocompatibility complex on bacterial composition of fecal flora, Infect. Immun., 69, 2372, 10.1128/IAI.69.4.2372-2377.2001 Hooper, 1999, A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem, Proc. Natl. Acad. Sci. U. S. A., 96, 9833, 10.1073/pnas.96.17.9833 Becker, 2003, Fucose: biosynthesis and biological function in mammals., Glycobiology, 13, 41R, 10.1093/glycob/cwg054 Van de Merwe, 1983, The resident faecal flora is determined by genetic characteristics of the host. Implications for Crohn's disease?, Antonie Van Leeuwenhoek, 49, 119, 10.1007/BF00393669 Hooper, 2001, Glycans as legislators of host-microbial interactions: spanning the spectrum from symbiosis to pathogenicity, Glycobiology, 11, 1R, 10.1093/glycob/11.2.1R Riley, 2002, Bacteriocins: evolution, ecology, and application, Annu. Rev. Microbiol., 56, 117, 10.1146/annurev.micro.56.012302.161024 Coburn, 2003, The Enterococcus faecalis cytolysin: a novel toxin active against eukaryotic and prokaryotic cells, Cell. Microbiol., 5, 661, 10.1046/j.1462-5822.2003.00310.x Breitbart, 2003, Metagenomic analyses of an uncultured viral community from human feces, J. Bacteriol., 185, 6220, 10.1128/JB.185.20.6220-6223.2003 Brüssow, 2005, Phage ecology, 129 Kerr, 2002, Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors, Nature, 418, 171, 10.1038/nature00823 Czárán, 2002, Chemical warfare between microbes promotes biodiversity, Proc. Natl. Acad. Sci. U. S. A., 99, 786, 10.1073/pnas.012399899 Gordon, 1998, Temporal changes in the frequency of colicinogeny in Escherichia coli from house mice, Microbiology, 144, 2233, 10.1099/00221287-144-8-2233 Sloan, 2006, Quantifying the roles of immigration and chance in shaping prokaryote community structure, Environ. Microbiol., 8, 732, 10.1111/j.1462-2920.2005.00956.x Sonnenburg, 2004, Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?, Nat. Immunol., 5, 569, 10.1038/ni1079 Hopkins, 2001, Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles, Gut, 48, 198, 10.1136/gut.48.2.198 Fernández, 2000, Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose, Appl. Environ. Microbiol., 66, 4058, 10.1128/AEM.66.9.4058-4067.2000 Holdeman, 1976, Human fecal flora: variation in bacterial composition within individuals and a possible effect of emotional stress, Appl. Environ. Microbiol., 31, 359, 10.1128/AEM.31.3.359-375.1976 Ley, 2005, Obesity alters gut microbial ecology, Proc. Natl. Acad. Sci. U. S. A., 102, 11070, 10.1073/pnas.0504978102 Pavoine, 2004, From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis, J. Theor. Biol., 228, 523, 10.1016/j.jtbi.2004.02.014 Bik, 2006, Molecular analysis of the bacterial microbiota in the human stomach, Proc. Natl. Acad. Sci. U. S. A., 103, 732, 10.1073/pnas.0506655103 Horner-Devine, 2004, A taxa–area relationship for bacteria, Nature, 432, 750, 10.1038/nature03073 Green, 2006, Spatial scaling of microbial biodiversity, Trends Ecol. Ecol., 21 Palmer, 2006, Rapid quantitative profiling of complex microbial populations, Nucleic Acids Res., 34, e5, 10.1093/nar/gnj007 Whitaker, R.J. and Banfield, J.F. Population genomics in natural microbial communities. Trends Ecol. Evol. (in press) Aas, 2005, Defining the normal bacterial flora of the oral cavity, J. Clin. Microbiol., 43, 5721, 10.1128/JCM.43.11.5721-5732.2005 Pei, 2004, Bacterial biota in the human distal esophagus, Proc. Natl. Acad. Sci. U. S. A., 101, 4250, 10.1073/pnas.0306398101 Marteau, 2001, Comparative study of bacterial groups within the human cecal and fecal microbiota, Appl. Environ. Microbiol., 67, 4939, 10.1128/AEM.67.10.4939-4942.2001 Fredricks, 2005, Molecular identification of bacteria associated with bacterial vaginosis, N. Engl. J. Med., 353, 1899, 10.1056/NEJMoa043802 Ozaki, 2004, Clostridium difficile colonization in healthy adults: transient colonization and correlation with enterococcal colonization, J. Med. Microbiol., 53, 167, 10.1099/jmm.0.05376-0