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  • Ahmed, S., Macfarlane, G.T., Fite, A., McBain, A.J., Gilbert, P., and Macfarlane, S. (2007) Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples. Appl Environ Microbiol 73: 74357442.
  • Aries, V., Crowther, J.S., Drasar, B.S., Hill, M.J., and Williams, R.E. (1969) Bacteria and aetiology of cancer of large bowel. Gut 10: 334335.
  • Atuma, C., Strugala, V., Allen, A., and Holm, L. (2001) The adherent gastrointestinal mucus gel layer: thickness and physical state in vivo. Am J Physiol Gastrointest Liver Physiol 280: G922G929.
  • Avivi-Green, C., Polak-Charcon, S., Madar, Z., and Schwartz, B. (2002) Different molecular events account for butyrate-induced apoptosis in two human colon cancer cell lines. J Nutr 132: 18121818.
  • Azcarate-Peril, M.A., Altermann, E., Goh, Y.J., Tallon, R., Sanozky-Dawes, R.B., Pfeiler, E.A., et al. (2008) Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. Appl Environ Microbiol 74: 46104625.
  • Bäckhed, F., Ding, H., Wang, T., Hooper, L.V., Koh, G.Y., Nagy, A., et al. (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 101: 1571815723.
  • Bäckhed, F., Manchester, J.K., Semenkovich, C.F., and Gordon, J.I. (2007) Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA 104: 979984.
  • Barrow, P.A., Brooker, B.E., Fuller, R., and Newport, M.J. (1980) Attachment of bacteria to the gastric epithelium of the pig and its importance in the microecology of the intestine. J Appl Bacteriol 48: 147154.
  • Bates, J.M., Mittge, E., Kuhlman, J., Baden, K.N., Cheesman, S.E., and Guillemin, K. (2006) Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation. Dev Biol 297: 374386.
  • Brandtzaeg, P. (2007) Induction of secretory immunity and memory at mucosal surfaces. Vaccine 25: 54675484.
  • Bry, L., Falk, P.G., Midtvedt, T., and Gordon, J.I. (1996) A model of host–microbial interactions in an open mammalian ecosystem. Science 273: 13801383.
  • Caballero-Franco, C., Keller, K., De Simone, C., and Chadee, K. (2007) The VSL#3 probiotic formula induces mucin gene expression and secretion in colonic epithelial cells. Am J Physiol Gastrointest Liver Physiol 292: G315G322.
  • Cani, P.D., Amar, J., Iglesias, M.A., Poggi, M., Knauf, C., Bastelica, D., et al. (2007a) Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56: 17611772.
  • Cani, P.D., Neyrinck, A.M., Fava, F., Knauf, C., Burcelin, R.G., Tuohy, K.M., et al. (2007b) Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxemia. Diabetologia 50: 23742383.
  • Cattoli, G., Van Vugt, R., Zanoni, R.G., Sanguinetti, V., Chiocchetti, R., Gualtieri, M., et al. (1999a) Occurrence and characterization of gastric Helicobacter spp. in naturally infected dogs. Vet Microbiol 70: 239250.
  • Cattoli, G., Bart, A., Van Vugt, R., Kuijper, S.M., Gerrits, M.M., Vandenbroucke-Grauls, C.M.J.E., et al. (1999b) Characterization of Helicobacters from exotic carnivores. Gut 45: A64.
  • Chowdhury, S.R., King, D.E., Willing, B.P., Band, M.R., Beever, J.E., Lane, A.B., et al. (2007) Transcriptome profiling of the small intestinal epithelium in germfree versus conventional piglets. BMC Genomics 8: 215.
  • Claus, S.P., Tsang, T.M., Wang, Y., Cloarec, O., Skordi, E., and Martin, F.P. (2008) Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Mol Syst Biol 4: 219.
  • Clavel, T., and Haller, D. (2007) Bacteria- and host-derived mechanisms to control intestinal epithelial cell homeostasis: implications for chronic inflammation. Inflamm Bowel Dis 13: 11531164.
  • Conly, J.M., and Stein, K. (1992) The production of menaquinones (vitamin K2) by intestinal bacteria and their role in maintaining coagulation homeostasis. Prog Food Nutr Sci 16: 307343.
  • Cronin, M., Sleator, R.D., Hill, C., Fitzgerald, G.F., and Van Sinderen, D. (2008) Development of a luciferase-based reporter system to monitor Bifidobacterium breve UCC2003 persistence in mice. BMC Microbiol 8: 161.
  • Crowther, J.S. (1970) Distribution of anaerobic Sarcinae in human faeces. J Med Microbiol 3: RP9.
  • De Groote, D., Van Doorn, L.J., Ducatelle, R., Verschuuren, A., Haesebrouck, F., Quint, W.G.V., et al. (1999a) ‘Candidatus Helicobacter suis’, a gastric helicobacter from pigs, and its phylogenetic relatedness to other gastrospirilla. Int J Syst Bacteriol 49: 17691777.
  • De Groote, D., Van Doorn, L.J., Ducatelle, R., Verschuuren, A., Tilmant, K., Quint, W.G.V., et al. (1999b) Phylogenetic characterization of ‘Candidatus Helicobacter bovis’, a new gastric helicobacter in cattle. Int J Syst Bacteriol 49: 17071715.
  • Della Ragione, F., Criniti, V., Della Pietra, V., Borriello, A., Oliva, A., Indaco, S., et al. (2001) Genes modulated by histone acetylation as new effectors of butyrate activity. FEBS Lett 499: 199204.
  • Dore, M.P., Sepulveda, A.R., El-Zimaity, H., Yamaoka, Y., Osato, M.S., Mototsugu, K., et al. (2001) Isolation of Helicobacter pylori from sheep – implications for transmission to humans. Am J Gastroenterol 96: 13961401.
  • Dumas, M.E., Barton, R.H., Toye, A., Cloarec, O., Blancher, C., Rothwell, A., et al. (2006) Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci USA 103: 1251112516.
  • Duncan, S.H., Belenguer, A., Holtrop, G., Johnstone, A.M., Flint, H.J., and Lobley, G.E. (2007) Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 73: 10731078.
  • Duncan, S.H., Lobley, G.E., Holtrop, G., Ince, J., Johnstone, A.M., Louis, P., and Flint, H.J. (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 32: 17201724.
  • Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 16351638.
  • Favier, C.F., Vaughan, E.E., De Vos, W.M., and Akkermans, A.D.L. (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68: 219226.
  • Fitch, M.D., and Fleming, S.E. (1999) Metabolism of short-chain fatty acids by rat colonic mucosa in vivo. Am J Physiol 277: G31G40.
  • Gibson, G.R., and Roberfroid, M.B. (1995) Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 125: 14011412.
  • Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P.B., Turnbaugh, P.J., Samuel, B.S., et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 13551359.
  • Gordon, H.A. (1968) Is the germfree animal normal? In The Germfree Animal in Research. Coates, M.E. (ed.). New York, USA: Academic Press, pp. 127150.
  • Handelsman, J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669685.
  • Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J., and Goodman, R.M. (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5: R245R249.
  • Hattori, M., and Taylor, T.D. (2009) The human intestinal microbiome: a new frontier of human biology. DNA Res 16: 112.
  • Hoffmann, M., Rath, E., Holzlwimmer, G., Quintanilla-Martinez, L., Loach, D., Tannock, G., and Haller, D. (2008) Lactobacillus reuteri 100-23 transiently activates intestinal epithelial cells of mice that have a complex microbiota during early stages of colonization. J Nutr 138: 16841691.
  • Hooper, L.V., Wong, M.H., Thelin, A., Hansson, L., Falk, P.G., and Gordon, J.I. (2001) Molecular analysis of commensal host–microbial relationships in the intestine. Science 291: 881884.
  • Hume, I.D. (1997) Fermentation in the hindgut of mammals. In Gastrointestinal Microbiology, Vol. I; Gastrointestinal Ecosystems and Fermentations. Mackie, R.I., and White, B.A. (eds). New York, USA: Chapman & Hall, pp. 84108.
  • Huse, S.M., Dethlefsen, L., Huber, J.A., Welch, D.M., Relman, D.A., and Sogin, M.L. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255.
  • Jernberg, C., Lofmark, S., Edlund, C., and Jansson, J.K. (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1: 5666.
  • Johansson, M.E., Phillipson, M., Petersson, J., Velcich, A., Holm, L., and Hansson, G.C. (2008) The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci USA 105: 1506415069.
  • Jones, B.V., Begley, M., Hill, C., Gahan, C.G.M., and Marchesi, J.R. (2008) Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci USA 105: 1358013585.
  • Karow, J. (2008) MetaHIT, gut microbiome initiative harness sequencing to link gut microbes and disease. Genomeweb Daily News 24: 13.
  • Kaunitz, J.D., and Akiba, Y. (2006) Review article: duodenal bicarbonate – mucosal protection, luminal chemosensing and acid-base balance. Aliment Pharmacol Ther 24: 169176.
  • Kowalchuk, G.A., Speksnijder, A.G.C.L., Zhang, K., Goodman, R.M., and Van Veen, J.A. (2007) Finding the needles in the metagenome haystack. Microb Ecol 53: 475485.
  • Kozakova, H., Kolinska, J., Lojda, Z., Rehakova, Z., Sinkora, J., Zakostelecka, M., et al. (2006) Effect of bacterial monoassociation on brush-border enzyme activities in ex-germ-free piglets: comparison of commensal and pathogenic Escherichia coli strains. Microbes Infect 8: 26292639.
  • Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14: 169181.
  • Laux, D.C., Cohen, P.S., and Conway, T. (2005) Role of the mucus layer in bacterial colonization of the intestine. In Mucosal Surfaces. Nataro, J.P., Cohen, P.S., Mobley, H.L.T., and Weiser, J.N. (eds). Washington, DC, USA: American Society for Microbiology Press, pp. 199212.
  • Lee, A. (1999) Helicobacter pylori: opportunistic member of the normal microflora or agent of communicable disease. In Medical Importance of the Normal Microflora. Tannock, G.W. (ed.). London, UK: Kluwer Academic Publishers, pp. 128163.
  • Leser, T.D., Amenuvor, J.Z., Jensen, T.K., Lindecrona, R.H., Boye, M., and Moller, K. (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68: 673690.
  • Leser, T.D., Knarreborg, A., and Worm, J. (2008) Germination and outgrowth of Bacillus subtilis and Bacillus licheniformis spores in the gastrointestinal tract of pigs. J Appl Microbiol 104: 10251033.
  • Ley, R.E., Bäckhed, F., Turnbaugh, P., Lozupone, C.A., Knight, R.D., and Gordon, J.I. (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102: 1107011075.
  • Ley, R.E., Turnbaugh, P.J., Klein, S., and Gordon, J.I. (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 10221023.
  • Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., et al. (2008a) Evolution of mammals and their gut microbes. Science 320: 16471651.
  • Ley, R.E., Lozupone, C.A., Hamady, M., Knight, R., and Gordon, J.I. (2008b) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6: 776788.
  • Li, M., Wang, B., Zhang, M., Rantalainen, M., Wang, S., Zhou, H., et al. (2008) Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA 105: 21172122.
  • Lievin-Le Moal, V., and Servin, A.L. (2006) The front line of enteric host defence against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota. Clin Microbiol Rev 19: 315337.
  • Luckey, T.D. (1972) Introduction to intestinal microecology. Am J Clin Nutr 25: 12921294.
  • Maaroos, H.I. (1995) Helicobacter pylori infection in Estonian population – is it a health problem? Ann Med 27: 613616.
  • McCracken, V.J., and Lorenz, R.G. (2001) The gastrointestinal ecosystem: a precarious alliance among epithelium, immunity and microbiota. Cell Microbiol 3: 111.
  • Macfarlane, S., and Macfarlane, G.T. (2006) Composition and metabolic activities of bacterial biofilms colonizing food residues in the human gut. Appl Environ Microbiol 72: 62046211.
  • Macfarlane, S., Furrie, E., Cummings, J.H., and Macfarlane, G.T. (2004) Chemotaxonomic analysis of bacterial populations colonizing the rectal mucosa in patients with ulcerative colitis. Clin Infect Dis 38: 16901699.
  • Macfarlane, S., Macfarlane, G.T., and Cummings, J.H. (2006) Review article: prebiotics in the gastrointestinal tract. Aliment Pharmacol Ther 24: 701714.
  • Mach, T. (2006) Clinical usefulness of probiotics in inflammatory bowel diseases. J Physiol Pharmacol 57 (Suppl. 9): 2333.
  • Mack, D.R., Michail, S., Wei, S., McDougall, L., and Hollingsworth, M.A. (1999) Probiotics inhibit enteropathogenic E. coli adherence in vitro by inducing intestinal mucin gene expression. Am J Physiol 276: G941G950.
  • McNeil, N.I. (1984) The contribution of the large intestine to energy supplies in man. Am J Clin Nutr 39: 338342.
  • Macpherson, A.J., and Uhr, T. (2004) Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303: 16621665.
  • Macpherson, A.J., Geuking, M.B., and McCoy, K.D. (2005) Immune responses that adapt the intestinal mucosa to commensal intestinal bacteria. Immunology 115: 153162.
  • Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., et al. (2006) Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55: 205211.
  • Martin, F.P.J., Dumas, M.E., Wang, Y.L., Legido-Quigley, C., Yap, I.K.S., Tang, H.R., et al. (2007) A top-down systems biology view of microbiome–mammalian metabolic interactions in a mouse model. Mol Syst Biol 3: 112.
  • Martin, F.P.J., Wang, Y.L., Sprenger, N., Yap, I.K.S., Rezzi, S., Ramadan, Z., et al. (2008) Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model. Mol Syst Biol 4: 205.
  • Medini, D., Serruto, D., Parkhill, J., Relman, D.A., Donati, C., Moxon, R., et al. (2008) Microbiology in the post-genomic era. Nat Rev Microbiol 6: 419430.
  • Ménard, O., Butel, M.J., Gaboriau-Routhiau, V., and Waligora-Dupriet, A.J. (2008) Gnotobiotic mouse immune response induced by Bifidobacterium sp. strains isolated from infants. Appl Environ Microbiol 74: 660666.
  • Meslin, J.C., Fontaine, N., and Andrieux, C. (1999) Variation of mucin distribution in the rat intestine, caecum and colon: effect of the bacterial flora. Comp Biochem Physiol A Mol Integr Physiol 123: 235239.
  • Meyer-Hoffert, U., Hornef, M.W., Henriques-Normark, B., Axelsson, L.G., Midtvedt, T., Putsep, K., and Andersson, M. (2008) Secreted enteric antimicrobial activity localises to the mucus surface layer. Gut 57: 764771.
  • Müller, C.A., Autenrieth, I.B., and Peschel, A. (2005) Innate defences of the intestinal epithelial barrier. Cell Mol Life Sci 62: 12971307.
  • Mutch, D.M., Simmering, R., Donnicola, D., Fotopoulos, G., Holzwarth, J.A., Williamson, G., and Corthesy-Theulaz, I. (2004) Impact of commensal microbiota on murine gastrointestinal tract gene ontologies. Physiol Genomics 19: 2231.
  • Nanthakumar, N.N., Dai, D., Meng, D., Chaudry, N., Newburg, D.S., and Walker, W.A. (2005) Regulation of intestinal ontogeny: effect of glucocorticoids and luminal microbes on galactosyltransferase and trehalase induction in mice. Glycobiology 15: 221232.
  • Nerstedt, A., Nilsson, E.C., Ohlson, K., Hakansson, J., Thomas, S.L., Lowenadler, B., et al. (2007) Administration of Lactobacillus evokes coordinated changes in the intestinal expression profile of genes regulating energy homeostasis and immune phenotype in mice. Br J Nutr 97: 11171127.
  • Nicholson, J.K., and Lindon, J.C. (2008) Systems biology: metabonomics. Nature 455: 10541056.
  • Palmer, C., Bik, E.M., DiGiulio, D.B., Relman, D.A., and Brown, P.O. (2007) Development of the human infant intestinal microbiota. PLoS Biol 5: 15561573.
  • Rajilic-Stojanovic, M., Smidt, H., and De Vos, W.M. (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9: 21252136.
  • Rescigno, M., Lopatin, U., and Chieppa, M. (2008) Interactions among dendritic cells, macrophages, and epithelial cells in the gut: implications for immune tolerance. Curr Opin Immunol 20: 669675.
  • Sansonetti, P. (2001) Phagocytosis of bacterial pathogens: implications in the host response. Semin Immunol 13: 381390.
  • Savage, D.C., Dubos, R., and Schaedler, R.W. (1968) Gastrointestinal epithelium and its autochthonous bacterial flora. J Exp Med 127: 6776.
  • Savage, D.C., Siegel, J.E., Snellen, J.E., and Whitt, D.D. (1981) Transit time of epithelial cells in the small intestines of germfree mice and ex-germfree mice associated with indigenous microorganisms. Appl Environ Microbiol 42: 9961001.
  • Sharma, R., Schumacher, U., Ronaasen, V., and Coates, M. (1995) Rat intestinal mucosal responses to a microbial flora and different diets. Gut 36: 209214.
  • Sheehan, V.M., Sleator, R.D., Hill, C., and Fitzgerald, G.F. (2007) Improving gastric transit, gastrointestinal persistence and therapeutic efficacy of the probiotic strain Bifidobacterium breve UCC2003. Microbiology 153: 35633571.
  • Shibolet, O., and Podolsky, D.K. (2007) TLRs in the Gut. IV. Negative regulation of Toll-like receptors and intestinal homeostasis: addition by subtraction. Am J Physiol Gastrointest Liver Physiol 292: G1469G1473.
  • Siggers, R.H., Siggers, J., Boye, M., Thymann, T., Molbak, L., Leser, T., et al. (2008) Early administration of probiotics alters bacterial colonization and limits diet-induced gut dysfunction and severity of necrotizing enterocolitis in preterm pigs. J Nutr 138: 14371444.
  • Smith, K., McCoy, K.D., and Macpherson, A.J. (2007) Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol 19: 5969.
  • Sonnenburg, J.L., Chen, C.T., and Gordon, J.I. (2006) Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol 4: e413.
  • Stein, J.L., Marsh, T.L., Wu, K.Y., Shizuya, H., and Delong, E.F. (1996) Characterization of uncultivated prokaryotes: Isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178: 591599.
  • Stewart, J.A., Chadwick, V.S., and Murray, A. (2005) Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children. J Med Microbiol 54: 12391242.
  • Swidsinski, A., Loening-Baucke, V., Lochs, H., and Hale, L.P. (2005) Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice. World J Gastroenterol 11: 11311140.
  • Swidsinski, A., Loening-Baucke, V., Theissig, F., Engelhardt, H., Bengmark, S., Koch, S., et al. (2007) Comparative study of the intestinal mucus barrier in normal and inflamed colon. Gut 56: 343350.
  • Szentkuti, L., Riedesel, H., Enss, M.L., Gaertner, K., and Von Engelhardt, W. (1990) Pre-epithelial mucus layer in the colon of conventional and germ-free rats. Histochem J 22: 491497.
  • Tannock, G.W. (2005) Microbiota of mucosal surfaces in the gut of monogastric animals. In Mucosal Surfaces. Nataro, J.P., Cohen, P.S., Mobley, H.L.T., and Weiser, J.N. (eds). Washington, DC, USA: American Society for Microbiology Press, 163178.
  • Tannock, G.W., and McConnell, M.A. (1994) Lactobacilli inhabiting the digestive-tract of mice do not influence serum-cholesterol concentration. Microb Ecol Health Dis 7: 331334.
  • Tannock, G.W., Dashkevicz, M.P., and Feighner, S.D. (1989) Lactobacilli and bile-salt hydrolase in the murine intestinal-tract. Appl Environ Microbiol 55: 18481851.
  • Tannock, G.W., Tangerman, A., Vanschaik, A., and McConnell, M.A. (1994) Deconjugation of bile-acids by lactobacilli in the mouse small-bowel. Appl Environ Microbiol 60: 34193420.
  • Tannock, G.W., Munro, K., Harmsen, H.J., Welling, G.W., Smart, J., and Gopal, P.K. (2000) Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 66: 25782588.
  • Tannock, G.W., Munro, K., Bibiloni, R., Simon, M.A., Hargreaves, P., Gopal, P., et al. (2004) Impact of consumption of oligosaccharide-containing biscuits on the fecal microbiota of humans. Appl Environ Microbiol 70: 21292136.
  • Torrallardona, D., Harris, C.I., and Fuller, M.F. (2003a) Lysine synthesized by the gastrointestinal microflora of pigs is absorbed, mostly in the small intestine. Am J Physiol Endocrinol Metab 284: E1177E1180.
  • Torrallardona, D., Harris, C.I., and Fuller, M.F. (2003b) Pigs' gastrointestinal microflora provide them with essential amino acids. J Nutr 133: 11271131.
  • Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., Magrini, V., Mardis, E.R., and Gordon, J.I. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 10271031.
  • Turnbaugh, P.J., Ley, R.E., Hamady, M., Fraser-Liggett, C.M., Knight, R., and Gordon, J.I. (2007) The Human Microbiome Project. Nature 449: 804810.
  • Turnbaugh, P.J., Bäckhed, F., Fulton, L., and Gordon, J.I. (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3: 213223.
  • Umesaki, Y., Okada, Y., Matsumoto, S., Imaoka, A., and Setoyama, H. (1995) Segmented filamentous bacteria are indigenous intestinal bacteria that activate intraepithelial lymphocytes and induce MHC class II molecules and fucosyl asialo GM1 glycolipids on the small intestinal epithelial cells in the ex-germ-free mouse. Microbiol Immunol 39: 555562.
  • Vanderhoof, J.A. (2008) Probiotics in allergy management. J Pediatr Gastroenterol Nutr 47 (Suppl. 2): S38S40.
  • Van Der Waaij, L.A., Harmsen, H.J., Madjipour, M., Kroese, F.G., Zwiers, M., Van Dullemen, H.M., et al. (2005) Bacterial population analysis of human colon and terminal ileum biopsies with 16S rRNA-based fluorescent probes: commensal bacteria live in suspension and have no direct contact with epithelial cells. Inflamm Bowel Dis 11: 865871.
  • Wellen, K.E., and Hotamisligil, G.S. (2005) Inflammation, stress, and diabetes. J Clin Invest 115: 11111119.
  • Wheeler, D.A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872875.
  • Whitt, D.D., and Savage, D.C. (1988) Influence of indigenous microbiota on activities of alkaline phosphatase, phosphodiesterase I, and thymidine kinase in mouse enterocytes. Appl Environ Microbiol 54: 24052410.
  • Wikoff, W.R., Anfora, A.T., Liu, J., Schultz, P.G., Lesley, S.A., Peters, E.C., and Siuzdak, G. (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci USA 106: 36983703.
  • Xu, J., Mahowald, M.A., Ley, R.E., Lozupone, C.A., Hamady, M., Martens, E.C., et al. (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5: 15741586.
  • Yan, F., and Polk, D.B. (2006) Probiotics as functional food in the treatment of diarrhea. Curr Opin Clin Nutr Metab Care 9: 717721.
  • Yuki, N., Shimazaki, T., Kushiro, A., Watanabe, K., Uchida, K., Yuyama, T., and Morotomi, M. (2000) Colonization of the stratified squamous epithelium of the nonsecreting area of horse stomach by lactobacilli. Appl Environ Microbiol 66: 50305034.
  • Zaph, C., Troy, A.E., Taylor, B.C., Berman-Booty, L.D., Guild, K.J., Du, Y., et al. (2007) Epithelial-cell-intrinsic IKK-beta expression regulates intestinal immune homeostasis. Nature 446: 552556.
  • Zoetendal, E.G., Akkermans, A.D.L., and De Vos, W.M. (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: 38543859.
  • Zoetendal, E.G., Akkermans, A.D.L., Akkermans van Vliet, W.M., De Viosser, J.A.G.M., and De Vos, W.M. (2001) The host genotype affects the bacterial community in the human gastrointestinal tract. Microb Ecol Health Dis 13: 129134.
  • Zoetendal, E.G., Von Wright, A., Vilpponen-Salmela, T., Ben-Amor, K., Akkermans, A.D.L., and De Vos, W.M. (2002) Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68: 34013407.
  • Zoetendal, E.G., Rajilic-Stojanovic, M., and De Vos, W.M. (2008) High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57: 16051615.