The gut microbiome: scourge, sentinel or spectator?

References

• Andrews M. Life that lives on man. London: Faber & Faber. 1976.
   Google Scholar
• Savage DC. Microbial ecology of the gastrointestinal tract. Ann Rev Microb. 1977; 31: 107–133.
   PubMed Web of Science ®Google Scholar
• Peterson J, Garges S, Giovanni M, et al.. The NIH uuman microbiome project. Genome Res. 2009; 19: 2317–323.
   PubMed Web of Science ®Google Scholar
• Palmer C, Bik EM, DiGiulio DB, et al.. Development of the human infant intestinal microbiota. PLoS Biol. 2007; 5: e177.
   PubMed Web of Science ®Google Scholar
• De Filippo C, Cavalieri D, Di Paola M, et al.. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Nat Acad Sci USA. 2010; 107: 14691–6.
   PubMed Web of Science ®Google Scholar
• Wu GD, Chen J, Hoffmann C, et al.. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011; 334: 105–8.
   PubMed Web of Science ®Google Scholar
• Ley RE, Hamady M, Lozupone C, et al.. Evolution of mammals and their gut microbes. Science. 2008; 320: 1647–1.
   PubMed Web of Science ®Google Scholar
• Eckburg PB, Bik EM, Bernstein CN, et al.. Diversity of the human intestinal microbial flora. Science. 2005; 308: 1635–8.
   PubMed Web of Science ®Google Scholar
• Gill SR, Pop M, Deboy RT, et al.. Metagenomic analysis of the human distal gut microbiome. Science. 2006; 312: 1355–9.
   PubMed Web of Science ®Google Scholar
• Horz HP, Conrads G. The discussion goes on: what is the role of Euryarchaeota in humans?. Archea. 2010; 2010: 967271.
   Google Scholar
• Turnbaugh PJ, Hamady M, Yatsunenko T, et al.. A core gut microbiome in obese and lean twins. Nature. 2009; 457: 480–4.
   PubMed Web of Science ®Google Scholar
• Qin J, Li R, Raes J, et al.. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464: 59–65.
   PubMed Web of Science ®Google Scholar
• Arumugam M, Raes J, Pelletier E, et al.. Enterotypes of the human gut microbiome. Nature. 473: 174–80.
   Google Scholar
• Gosalbes MJ, Durban A, Pignatelli M, et al.. Metatranscriptomic approach to analyze the functional human gut microbiota. PloS One 6. : e17447.
   Google Scholar
• Surwit RS, Kuhn CM, Cochrane C, et al.. Diet-induced type II diabetes in C57BL/6J mice. Diabetes. 1988; 37: 1163–67.
   PubMed Web of Science ®Google Scholar
• West DB, Boozer CN, Moody DL, et al.. Dietary obesity in nine inbred mouse strains. Amer J Phys. 1992; 262: R1025–32.
   PubMedGoogle Scholar
• Klaus S. Increasing the protein: carbohydrate ratio in a high-fat diet delays the development of adiposity and improves glucose homeostasis in mice. J Nutr. 2005; 135: 1854–8.
   PubMed Web of Science ®Google Scholar
• Backhed F, Manchester JK, Semenkovich CF, et al.. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Nat Acad Sci USA. 2007; 104: 979–84.
   PubMed Web of Science ®Google Scholar
• Fleissner CK, Huebel N, Abd El-Bary MM, et al.. Absence of intestinal microbiota does not protect mice from diet-induced obesity. Brit J Nutr. 104: 919–29.
   Google Scholar
• Wolever TM, Spadafora P, Eshuis H. Interaction between colonic acetate and propionate in humans. Amer J Clin Nutr. 1991; 53: 681–7.
   PubMed Web of Science ®Google Scholar
• Scheppach W. Effects of short chain fatty acids on gut morphology and function. Gut. 1994; 35: S35–38.
   PubMed Web of Science ®Google Scholar
• Backhed F, Ding H, Wang T, et al.. The gut microbiota as an environmental factor that regulates fat storage. Proc Nat Acad Sci USA. 2004; 101: 15718–3.
   PubMed Web of Science ®Google Scholar
• Samuel BS, Shaito A, Motoike T, et al.. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc Nat Acad Sci USA. 2008; 105: 16767–2.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Ley RE, Mahowald MA, et al.. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006; 444: 1027–31.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Backhed F, Fulton L, et al.. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008; 3: 213–23.
   PubMed Web of Science ®Google Scholar
• Murphy EF, Cotter PD, Healy S, et al.. Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut. 2010; 59: 1635–42.
   PubMed Web of Science ®Google Scholar
• Tartaglia LA, Dembski M, Weng X, et al.. Identification and expression cloning of a leptin receptor. OB-R. Cell. 1995; 83: 1263–71.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Proenca R, Maffei M, et al.. Positional cloning of the mouse obese gene and its human homologue. Nature. 1994; 372: 425–32.
   PubMed Web of Science ®Google Scholar
• Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Nat Acad Sci USA. 2005; 102: 11070–5.
   PubMed Web of Science ®Google Scholar
• Are A, Aronsson L, Wang S, et al.. Enterococcus faecalis from newborn babies regulate endogenous PPARgamma activity and IL-10 levels in colonic epithelial cells. Proc Nat Acad Sci USA. 2008; 105: 1943–8.
   PubMed Web of Science ®Google Scholar
• Aronsson L, Huang Y, Parini P, et al.. Decreased fat storage by Lactobacillus paracasei is associated with increased levels of angiopoietin-like 4 protein (ANGPTL4). PloS One. 2010; 5: e13087.
   PubMed Web of Science ®Google Scholar
• Kadooka Y, Sato M, Imaizumi K, et al.. Regulation of abdominal adiposity by probiotics (Lactobacillus gasseri SBT2055) in adults with obese tendencies in a randomized controlled trial. Eur J Clin Nutr. 2010; 64: 636–43.
   PubMed Web of Science ®Google Scholar
• Hamad EM, Sato M, Uzu K, et al.. Milk fermented by Lactobacillus gasseri SBT2055 influences adipocyte size via inhibition of dietary fat absorption in Zucker rats. Brit J Nutr. 2009; 101: 716–24.
   PubMed Web of Science ®Google Scholar
• Ley RE, Turnbaugh PJ, Klein S, et al.. Microbial ecology: human gut microbes associated with obesity. Nature. 2006; 444: 1022–23.
   PubMed Web of Science ®Google Scholar
• Schwiertz A, Taras D, Schafer K, et al.. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010; 18: 190–95.
   PubMed Web of Science ®Google Scholar
• Duncan SH, Lobley GE, Holtrop G, et al.. Human colonic microbiota associated with diet, obesity and weight loss. International J Obesity ; 32. 2005; 2008: 1720–24.
   Google Scholar
• Velazquez OC, Lederer HM, Rombeau JL. Butyrate and the colonocyte. Production, absorption, metabolism, and therapeutic implications. Adv Exp Med Biol. 1997; 427: 123–34.
   PubMed Web of Science ®Google Scholar
• Flint HJ, Bayer EA, Rincon MT, et al.. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nature Reviews. 2008; 6: 121–31.
   Web of Science ®Google Scholar
• Faith JJ, McNulty NP, Rey FE, et al.. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science. 2011; 333: 101–4.
   PubMed Web of Science ®Google Scholar
• Podolsky DK. Inflammatory bowel disease. New Engl J Med. 2002; 347: 417–29.
   PubMed Web of Science ®Google Scholar
• Xavier RJ, Podolsky DK. Unravelling the pathogenesis of inflammatory bowel disease. Nature. 2007; 448: 427–34.
   PubMed Web of Science ®Google Scholar
• Ott SJ, Musfeldt M, Wenderoth DF, et al.. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut. 2004; 53: 685–93.
   PubMed Web of Science ®Google Scholar
• Manichanh C, Rigottier-Gois L, Bonnaud E, et al.. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut. 2006; 55: 205–11.
   PubMed Web of Science ®Google Scholar
• Seksik P, Sokol H, Lepage P, et al.. Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease. Aliment Pharm Therap. 2006; 24: 11–18.
   PubMed Web of Science ®Google Scholar
• Hoffmann JC, Pawlowski NN, Kuhl AA, et al.. Animal models of inflammatory bowel disease: an overview. Pathobiology. 2002; 70: 121–30.
   PubMed Web of Science ®Google Scholar
• Saleh M, Elson CO. Experimental inflammatory bowel disease: insights into the host-microbiota dialog. Immunity. 2011; 34: 293–302.
   PubMed Web of Science ®Google Scholar
• Garrett WS, Lord GM, Punit S, et al.. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell. 2007; 131: 33–45.
   PubMed Web of Science ®Google Scholar
• Elinav E, Strowig T, Kau AL, et al.. 2 NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell. 2011; 145: 745–57.
   PubMed Web of Science ®Google Scholar
• Takeda K, Kaisho T, Akira S. Toll-like receptors. Ann Rev Immunol. 2003; 21: 335–76.
   PubMed Web of Science ®Google Scholar
• Inohara N. Nunez G. NODs: intracellular proteins involved in inflammation and apoptosis. Nature Revs. 2003; 3: 371–82.
   Web of Science ®Google Scholar
• Franchi L, McDonald C, Kanneganti TD, et al.. Nucleotide-binding oligomerization domain-like receptors: intracellular pattern recognition molecules for pathogen detection and host defense. J Immunol. 2006; 177: 3507–513.
   Web of Science ®Google Scholar
• Kaparakis M, Philpott DJ, Ferrero RL. Mammalian NLR proteins; discriminating foe from friend. Immunol. Cell Biol. 2007; 85: 495–502.
   Google Scholar
• Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, et al.. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell. 2004; 118: 229–41.
   PubMed Web of Science ®Google Scholar
• Rakoff-Nahoum S, Hao L, Medzhitov R. Role of toll-like receptors in spontaneous commensal-dependent colitis. Immunity. 2006; 25: 319–29.
   PubMed Web of Science ®Google Scholar
• Hugot JP, Chamaillard M, Zouali H, et al.. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature. 2001; 411: 599–603.
   PubMed Web of Science ®Google Scholar
• Ogura Y, Lala S, Xin W, et al.. Expression of NOD2 in Paneth cells: a possible link to Crohn's ileitis. Gut. 2003; 52: 1591–7.
   PubMed Web of Science ®Google Scholar
• Wehkamp J, Harder J, Weichenthal M, et al.. NOD2 (CARD15) mutations in Crohn's disease are associated with diminished mucosal alpha-defensin expression. Gut. 2004; 53: 1658–64.
   PubMed Web of Science ®Google Scholar
• Frank DN, Robertson CE, Hamm CM, et al.. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2011; 17: 179–84.
   PubMed Web of Science ®Google Scholar
• Rehman A, Sina C, Gavrilova O, et al.. Nod2 is essential for temporal development of intestinal microbial communities. Gut. 2011; 60: 1354–62.
   PubMed Web of Science ®Google Scholar
• Schroder K, Tschopp J. The inflammasomes. Cell. 2010; 140: 821–32.
   PubMed Web of Science ®Google Scholar
• Martinon F, Burns K, Tschopp J. The inflammasome: a molecular platform triggering activation of inflammatory caspases and processing of proIL-beta. Mol. Cell. 2002; 10: 417–26.
   Web of Science ®Google Scholar
• Agostini L, Martinon F, Burns K, et al.. NALP3 forms an IL-1beta-processing inflammasome with increased activity in Muckle-Wells autoinflammatory disorder. Immunity. 2004; 20: 319–25.
   PubMed Web of Science ®Google Scholar
• Kleessen B, Kroesen AJ, Buhr HJ, et al.. Mucosal and invading bacteria in patients with inflammatory bowel disease compared with controls. Scan J Gastroentero. 2002; 37: 1034–41.
   PubMed Web of Science ®Google Scholar
• Lucke K, Miehlke S, Jacobs E, et al.. Prevalence of Bacteroides and Prevotella spp. in ulcerative colitis. J Med Microb. 2006; 55: 617–24.
   PubMed Web of Science ®Google Scholar
• Kumar PS, Griffen AL, Barton JA, et al.. New bacterial species associated with chronic periodontitis. J Dent Res. 2003; 82: 338–44.
   PubMed Web of Science ®Google Scholar
• Van Winkelhoff AJ, Winkel EG, Barendregt D, et al.. Beta-lactamase producing bacteria in adult periodontitis. J Clin Periodontol. 1997; 24: 538–43.
   PubMed Web of Science ®Google Scholar
• Kuehbacher T, Rehman A, Lepage P, et al.. Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease. J Med Microb. 2008; 57: 1569–76.
   PubMed Web of Science ®Google Scholar
• Brinig MM, Lepp PW, Ouverney CC, et al.. Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease. Appl Environ Microb. 2003; 69: 1687–94.
   Web of Science ®Google Scholar
• Ouverney CC, Armitage GC, Relman DA. Single-cell enumeration of an uncultivated TM7 subgroup in the human subgingival crevice. Appl Environ Microb. 2003; 69: 6294–98.
   PubMed Web of Science ®Google Scholar
• Marcy Y, Ouverney C, Bik EM, et al.. Dissecting biological dark matter with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Nat Acad Sci USA. 2007; 104: 11889–94.
   PubMed Web of Science ®Google Scholar
• Garrett WS, Gallini CA, Yatsunenko T, et al.. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe. 2010; 8: 292–300.
   PubMed Web of Science ®Google Scholar
• Goncalves MO, Coutinho-Filho WP, Pimenta FP, et al.. Periodontal disease as reservoir for multi-resistant and hydrolytic enterobacterial species. Lett Appl Microbiol. 2007; 44: 488–94.
   PubMed Web of Science ®Google Scholar
• Frank DN, St Amand AL, Feldman RA, et al.. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Nat Acad Sci USA. 2007; 104: 13780–5.
   PubMed Web of Science ®Google Scholar
• The Wellcome Trust Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007; 447: 661–78.
   PubMed Web of Science ®Google Scholar
• Rioux JD, Xavier RJ, Taylor KD, et al.. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nature Genetics. 2007; 39: 596–604.
   PubMed Web of Science ®Google Scholar
• Hampe J, Franke A, Rosenstiel P, et al.. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nature Genetics. 2007; 39: 207–11.
   PubMed Web of Science ®Google Scholar
• Cadwell K, Liu JY, Brown SL, et al.. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature. 2008; 456: 259–63.
   PubMed Web of Science ®Google Scholar
• Ju JS, Miller SE, Jackson E, et al.. Quantitation of selective autophagic protein aggregate degradation in vitro and in vivo using luciferase reporters. Autophagy. 2009; 5: 511–9.
   PubMed Web of Science ®Google Scholar
• Cadwell K, Patel KK, Maloney NS, et al.. Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine. Cell. 2010; 141: 1135–45.
   PubMed Web of Science ®Google Scholar
• Khan KJ, Ullman TA, Ford AC, et al.. Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis. Amer J Gastroenterol. 2011; 106: 661–73.
   PubMed Web of Science ®Google Scholar
• Eaden JA, Abrams KR, Mayberry JF. The risk of colorectal cancer in ulcerative colitis: a meta-analysis. Gut. 2001; 48: 526–35.
   PubMed Web of Science ®Google Scholar
• Xie J, Itzkowitz SH. Cancer in inflammatory bowel disease. World J Gastroentero. 2008; 14: 378–89.
   PubMed Web of Science ®Google Scholar
• Garrett WS, Punit S, Gallini CA, et al.. Colitis-associated colorectal cancer driven by T-bet deficiency in dendritic cells. Cancer Cell. 2009; 16: 208–19.
   Web of Science ®Google Scholar
• Wu S, Rhee KJ, Albesiano E, et al.. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nature medicine. 2009; 15: 1016–22.
   PubMed Web of Science ®Google Scholar
• Ivanov II, Frutos Rde L, Manel N, et al.. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe. 2008; 4: 337–49.
   PubMed Web of Science ®Google Scholar
• Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature. 2008; 453: 620–5.
   PubMed Web of Science ®Google Scholar
• Round JL\, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Nat Acad Sci USA. 2010; 107: 12204–9.
   PubMed Web of Science ®Google Scholar
• Kitajima S, Morimoto M, Sagara E, et al.. Dextran sodium sulfate-induced colitis in germ-free IQI/Jic mice. Exp Anim. 2001; 50: 387–95.
   Web of Science ®Google Scholar
• Maslowski KM, Vieira AT, Ng A, et al.. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature. 2009; 461: 1282–6.
   PubMed Web of Science ®Google Scholar
• Fukuda S, Toh H, Hase K, et al.. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature. 469: 543–7.
   Web of Science ®Google Scholar
• Dumas ME, Barton RH, Toye A, et al.. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Nat Acad Sci USA. 2006; 103: 12511–6.
   PubMed Web of Science ®Google Scholar
• Wang Z, Klipfell E, Bennett BJ, et al.. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature. 2011; 472: 57–63.
   PubMed Web of Science ®Google Scholar
• Al-Waiz M, Mikov M, Mitchell SC, et al.. The exogenous origin of trimethylamine in the mouse. Metabolism. 1992; 41: 135–6.
   PubMed Web of Science ®Google Scholar
• Vijay-Kumar M, Sanders CJ, Taylor RT, et al.. Deletion of TLR5 results in spontaneous colitis in mice. The J.Clin. Invest. 2007; 117: 3909–21.
   Google Scholar
• Vijay-Kumar M, Aitken JD, Carvalho FA, et al.. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science. 2010; 328: 228–31.
   PubMed Web of Science ®Google Scholar
• Heijtz RD, Wang S, Anuar F, et al.. Normal gut microbiota modulates brain development and behavior. Proc Nat Acad Sci USA. 108: 3047–52.
   Web of Science ®Google Scholar
• Bravo JA, Forsythe P, Chew MV, et al.. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Nat Acad Sci USA. 2011; 108: 16050–5.
   PubMed Web of Science ®Google Scholar
• Cani PD, Delzenne NM. The gut microbiome as therapeutic target. Pharmacol Therapeut. 130: 202–12.
   Web of Science ®Google Scholar
• O'Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Reports. 2006; 7: 688–93.
   PubMed Web of Science ®Google Scholar