1Tsuji, H, Oozeer, R, Matsuda, K, et al. (2012) Molecular monitoring of the development of intestinal microbiota in Japanese infants. Benef Microbes 3, 113–125.
2Penders, J, Thijs, C, Vink, C, et al. (2006) Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118, 511–521.
3Dominguez-Bello, MG, Costello, EK, Contreras, M, et al. (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 107, 11971–11975.
4Schloissnig, S, Arumugam, M, Sunagawa, S, et al. (2013) Genomic variation landscape of the human gut microbiome. Nature 493, 45–50.
5Makino, H, Kushiro, A, Ishikawa, E, et al. (2011) Transmission of intestinal Bifidobacterium longum subsp. longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism. Appl Environ Microbiol 77, 6788–6793.
6Mitsuoka, T (1982) Recent trends in research on intestinal flora. Bifido Microflora 1, 3–24.
7Woodmansey, E (2007) Intestinal bacteria and ageing. J Appl Microbiol 102, 1178–1186.
8Claesson, MJ, O'Sullivan, O, Wang, Q, et al. (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLOS ONE 4, e6669.
9Claesson, MJ, Wang, Q, O'Sullivan, O, et al. (2010) Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38, e200.
10O'Sullivan, Ó, Coakely, M, Lakshiminarayanan, B, et al. (2011) Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects. J Appl Microbiol 111, 467–473.
11Claesson, MJ, Cusak, S, O'Sullivan, O, et al. (2011) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A 108, Suppl. 1, 4586–4591.
12Claesson, MJ, Jeffery, IB, Conde, S, et al. (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178–184.
13O'Sullivan, O, Coakley, M, Lashminarayanan, B, et al. (2013) Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy. J Antimicrob Chemother 68, 214–221.
14Rea, MC, O'Sullivan, O, Shanahan, F, et al. (2011) Clostridium difficile carriage in elderly subjects and associated changes in the intestinal microbiota. J Clin Microbiol 50, 867–875.
15Walker, AW, Ince, J, Duncan, SH, et al. (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5, 220–230.
16Flint, HJ, Scott, KP, Duncan, SH, et al. (2012) Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3, 289–306.
17Louis, P, Duncan, SH, McCrae, SI, et al. (2004) Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J Bacteriol 186, 2099–2106.
18Duncan, SH, Louis, P & Flint, HJ (2004) Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol 70, 5810–5817.
19Louis, P, Young, P, Holtrop, G, et al. (2010) Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. Environ Microbiol 12, 304–314.
20Duncan, SH, Belengeuer, A, Holtrop, G, et al. (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, 1073–1078.
21Russell, WR, Gratz, SW, Duncan, SH, et al. (2011) High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am J Clin Nutr 93, 1062–1072.
22Walker, AW, Duncan, SH, McWilliam Leitch, EC, et al. (2005) pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl Environ Microbiol 71, 3692–3700.
23Duncan, SH, Louis, P, Thomson, JM, et al. (2009) The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol 11, 2112–2122.
24Flint, HJ, Duncan, SH, Scott, KP, et al. (2007) Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol 9, 1101–1111.
25Khan, MT, Duncan, SH, Stams, AJ, et al. (2012) The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic–anoxic interphases. ISME J 6, 1578–1585.
26Scott, KP, Martin, JC, Campbell, G, et al. (2006) Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium “Roseburia inulinivorans”. J Bacteriol 188, 4340–4349.
27Ze, X, Duncan, SH, Louis, P, et al. (2012) Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 6, 1535–1543.
28Ze, X, Le Mougen, F, Duncan, SH, et al. (2013) Some are more equal than others. The role of “keystone” species in the degradation of recalcitrant substrates. Gut Microbes 4, 236–240.
29Walker, AW, Duncan, SH, Harmsen, HJ, et al. (2008) The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities. Environ Microbiol 10, 3275–3283.
30Russell, WR, Duncan, SH, Scobbie, L, et al. (2013) Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein. Mol Nutr Food Res 57, 523–535.
31McIntosh, FM, Maison, N, Holtrop, G, et al. (2012) Phylogenetic distribution of genes encoding β-glucuronidase activity in human colonic bacteria and the impact of diet on faecal glycosidase activities. Environ Microbiol 14, 1876–1887.
32Eckburg, PB, Bik, EM, Bernstein, CN, et al. (2005) Diversity of the human intestinal microbial flora. Science 308, 1635–1638.
33Li, K, Bihan, M & Methé, BA (2013) Analyses of the stability and core taxonomic memberships of the human microbiome. PLOS ONE 8, e63139.
34Bach, J-F (2002) The effect of infections on susceptibility to autoimmune and allergic diseases. N Engl J Med 347, 911–920.
35Okada, H, Kuhn, C, Feillet, H, et al. (2010) The ‘hygiene hypothesis’ for autoimmune and allergic diseases: an update. Clin Exp Immunol 160, 1–9.
36Yatsunenko, T, Rey, FE, Manary, MJ, et al. (2012) Human gut microbiome viewed across age and geography. Nature 486, 222–227.
37Manichanh, C, Chapple, CE, Frangeul, L, et al. (2008) A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res 36, 5180–5188.
38Gill, SR, Pop, M, DeBoy, RT, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359.
39Kurokawa, K, Itoh, T, Kuwahara, T, et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14, 169–181.
40Mullard, A (2008) Microbiology: the inside story. Nature 453, 578–580.
41Qin, J, Li, R, Raes, J, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65.
42Arumugam, M, Raes, J, Pelletir, E, et al. (2011) Enterotypes of the human gut microbiome. Nature 473, 174–180.
43Sokol, H, Pigneur, B, Watterlot, L, et al. (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105, 16731–16736.
44Lepage, P, Leclerc, MC, Joossens, M, et al. (2013) A metagenomic insight into our gut's microbiome. Gut 62, 146–158.
45Le Chatelier, E, Nielsen, T, Qin, J, et al. (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546.
46Cotillard, A, Kennedy, SP, Kong, LC, et al. (2013) Dietary intervention impact on gut microbial gene richness. Nature 500, 585–588.
47Spor, A, Koren, O & Ley, R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9, 279–289.
48Lepage, P, Hasler, R, Spehlmann, ME, et al. (2011) Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 141, 227–236.
49Lakhdari, O, Cultrone, A, Tap, J, et al. (2010) Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut. PLOS ONE 5, e13092.
50Kaci, G, Lakhdari, O, Doré, J, et al. (2011) Inhibition of the NF-κB pathway in human intestinal epithelial cells by commensal Streptococcus salivarius. Appl Environ Microbiol 77, 4681–4684.
51Lakhdari, O, Tap, J, Béguet-Crespel, F, et al. (2011) Identification of NF-κB modulation capabilities within human intestinal commensal bacteria. J Biomed Biotechnol 2011, 282356.
52Madi, A, Lakhdari, O, Blottière, HM, et al. (2010) The clinical Pseudomonas fluorescens MFN1032 strain exerts a cytotoxic effect on epithelial intestinal cells and induces interleukin-8 via the AP-1 signaling pathway. BMC Microbiol 10, 215.
53Nepelska, M, Cultrone, A, Béguet-Crespel, F, et al. (2012) Butyrate produced by commensal bacteria potentiates phorbol esters induced AP-1 response in human intestinal epithelial cells. PLOS ONE 7, e52869.
54Cani, PD, Amar, J, Iglesias, MA, et al. (2007) Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56, 1761–1772.
55Cani, PD, Neyrinck, AM, Fava, F, et al. (2007) Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia 50, 2374–2383.
56Delzenne, NM, Neyrinck, AM, Bäckhed, F, et al. (2011) Targeting gut microbiota in obesity: effects of prebiotics and probiotics. Nat Rev Endocrinol 7, 639–646.
57Cani, PD, Bilbiloni, R, Knauf, C, et al. (2008) Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes 57, 1470–1481.
58Cani, PD, Possemiers, S, Van de Wiele, T, et al. (2009) Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut 58, 1091–1103.
59Gibson, GR & Roberfroid, MB (1995) Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 125, 1401–1412.
60Cani, PD, Lecourt, E, Dewulf, EM, et al. (2009) Gut microbiota fermentation of prebiotics increases satietogenic and incretin gut peptide production with consequences for appetite sensation and glucose response after a meal. Am J Clin Nutr 90, 1236–1243.
61Muccioli, GG, Naslain, D, Bäckhed, F, et al. (2010) The endocannabinoid system links gut microbiota to adipogenesis. Mol Syst Biol 6, 392.
62Everard, A, Lazarevic, V, Derrien, M, et al. (2011) Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes 60, 2775–2786.
63Everard, A, Belzer, C, Geurts, L, et al. (2013) Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A 110, 9066–9071.
64Owens, B (2013) Gut microbes may fight obesity and diabetes. Nature .
65Bäckhed, F, Ding, H, Wang, T, et al. (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101, 15718–15723.
66Ley, RE, Turnbaugh, PJ, Klein, S, et al. (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023.
67Turnbaugh, PJ, Ley, RE, Mahowald, MA, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031.
68Turnbaugh, PJ, Hamady, M, Yatsunenko, T, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457, 480–484.
69Qin, J, Li, Y, Cai, Z, et al. (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55–60.
70Karlsson, FH, Tremaroli, V, Nookaew, I, et al. (2013) Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498, 99–103.
71Karlsson, FH, Fåk, F, Nookaew, I, et al. (2012) Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun 3, 1245.
72Caesar, R, Reigstad, CS, Bäckhed, HK, et al. (2012) Gut-derived lipopolysaccharide augments adipose macrophage accumulation but is not essential for impaired glucose or insulin tolerance in mice. Gut 61, 1701–1707.
73Drucker, DJ (2007) The role of gut hormones in glucose homeostasis. J Clin Invest 117, 24–32.
74Inagaki, T, Choi, M, Moschetta, A, et al. (2005) Fibroblast growth factor 15 functions as an enterohepatic signal to regulate bile acid homeostasis. Cell Metab 2, 217–225.
75Sayin, SI, Wahlström, A, Felin, J, et al. (2013) Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 17, 225–235.
76Hylemon, PB, Zhou, H, Pandak, WM, et al. (2009) Bile acids as regulatory molecules. J Lipid Res 50, 1509–1520.
77Van Wijck, K, Lenaerts, K, van Loon, LJC, et al. (2011) Exercise-induced splanchnic hypoperfusion results in gut dysfunction in healthy men. PLOS ONE 6, e22366.
78Guerts, L, Neyrinck, AM, Delzenne, NM, et al. (2014) Gut microbiota controls adipose tissue expansion, gut barrier and glucose metabolism: novel insights into molecular targets and interventions using prebiotics. Benef Microbes 5, 3–17.
79Grootjans, J, Thuijls, G, Verdam, F, et al. (2010) Non-invasive assessment of barrier integrity and function of the human gut. World J Gastrointest Surg 2, 61–69.
80Arrieta, MC, Bistritz, L & Meddings, JB (2006) Alterations in intestinal permeability. Gut 55, 1512–1520.
81Derikx, JPM, Luyer, MDP, Heineman, E, et al. (2010) Non-invasive markers of gut wall integrity in health and disease. World J Gastroenterol 16, 5272–5279.
82Bischoff, S (2011) ‘Gut health’: a new objective in medicine? BMC Med 9, 24.
83Abu-Shanab, A & Quigley, EM (2010) The role of the gut microbiota in nonalcoholic fatty liver disease. Nat Rev Gastroenterol Hepatol 7, 691–701.
84Zhao, L (2013) The gut microbiota and obesity: from correlation to causality. Nat Rev Microbiol 11, 639–647.
85Lahtinen, SJ, Davis, E & Ouwehand, AC (2012) Lactobacillus species causing obesity in humans: where is the evidence? Benef Microbes 3, 171–174.
86Tremaroli, V & Bäckhed, F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489, 242–249.
87Verdam, FJ, Greve, JWM, Roosta, S, et al. (2011) Small intestinal alterations in severely obese hyperglycemic subjects. J Clin Endocrinol Metab 96, E379–E383.
88Wagnerberger, S, Spruss, A, Kanuri, G, et al. (2012) Lactobacillus casei Shirota protects from fructose-induced liver steatosis: a mouse model. J Nutr Biochem 24, 531–538.
89Dobrindt, U, Hocchut, B, Hentschel, U, et al. (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2, 414–424.
90Schmidt, H & Hensel, M (2004) Pathogenicity islands in bacterial pathogenesis. Clin Microbiol Rev 17, 14–56.
91Schroeder, GN & Hilbi, H (2008) Molecular pathogenesis of Shigella spp.: controlling host cell signalling, invasion, and death by type III secretion. Clin Microbiol Rev 21, 134–156.
92Mogensen, TH (2009) Pathogen recognition and inflammatory signaling in innate immune defenses. Clin Microbiol Rev 22, 240–273.
93Liew, FY, Xu, D, Brint, EK, et al. (2005) Negative regulation of Toll-like receptor-mediated immune responses. Nat Rev Immunol 5, 446–458.
94Medzhitov, R (2007) Recognition of microorganisms and activation of the immune response. Nature 449, 819–826.
95Broz, P, Ohlson, MB & Monack, DM (2012) Innate immune response to Salmonella typhimurium, a model enteric pathogen. Gut Microbes 3, 62–70.
96Ruby, T & Monack, DM (2011) At home with hostility: how do pathogenic bacteria evade mammalian immune surveillance to establish persistent infection? F1000 Biol Rep 3, 1.
97Lawley, TD & Walker, AW (2013) Intestinal colonization resistance. Immunology 138, 1–11.
98Muniz, LR, Knosp, C & Yeretssian, G (2012) Intestinal antimicrobial peptides during homeostasis, infection, and disease. Front Immunol 3, 310.
99Pirofski, L & Casadevall, A (2012) Q and A: What is a pathogen? A question that begs the point. BMC Biol 10, 6.
100Terahara, K, Yoshida, M, Igarashi, O, et al. (2008) Comprehensive gene expression profiling of Peyer's patch M Cells, villous M-like cells, and intestinal epithelial cells. J Immunol 180, 7840–7846.
101Hase, K, Kawano, K, Nochi, T, et al. (2009) Uptake through glycoprotein 2 of FimH(+) bacteria by M cells initiates mucosal immune response. Nature 462, 226–230.
102Sato, S, Kaneto, S, Shibata, N, et al. (2012) Transcription factor Spi-B-dependent and -independent pathways for the development of Peyer's patch M cells. Mucosal Immunol 6, 838–846.
103Terahara, K, Nochi, T, Yoshida, M, et al. (2011) Distinct fucosylation of M cells and epithelial cells by Fut1 and Fut2, respectively, in response to intestinal environmental stress. Biochem Biophys Res Commun 404, 822–828.
104De Lau, W, Kujala, P, Schneeberger, K, et al. (2012) Peyer's patch M cells derived from Lgr5(+) stem cells require SpiB and are induced by RankL in cultured ‘miniguts’. Mol Cell Biol 32, 3639–3647.
105Kanaya, T, Hase, K, Takahashi, D, et al. (2012) The Ets transcription factor Spi-B is essential for the differentiation of intestinal microfold cells. Nat Immunol 13, 729–736.
106Michalek, SM, Kiyono, H, Wannemuehler, MJ, et al. (1982) Lipopolysaccharide (LPS) regulation of the immune response: LPS influence on oral tolerance induction. J Immunol 128, 1992–1998.
107Umesaki, Y, Setoyama, H, Matsumoto, S, et al. (1999) Differential roles of segmented filamentous bacteria and clostridia in development of the intestinal immune system. Infect Immun 67, 3504–3511.
108Obata, T, Goto, Y, Kunisawa, J, et al. (2010) Indigenous opportunistic bacteria inhabit mammalian gut-associated lymphoid tissues and share a mucosal antibody-mediated symbiosis. Proc Natl Acad Sci U S A 107, 7419–7424.
109Sonnenberg, GF, Monticelli, LA, Alenghat, T, et al. (2012) Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science 336, 1321–1325.
110Franke, A, McGovern, DPB, Barrett, JC, et al. (2010) Meta-analysis increases to 71 the tally of confirmed Crohn's disease susceptibility loci. Nat Genet 42, 1118–1125.
111McGovern, DPB, Jones, MR, Taylor, KD, et al. (2010) Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. Hum Mol Genet 19, 3468–3476.
112Bry, L, Falk, PG, Midtvedt, T, et al. (1996) A model of host–microbial interactions in an open mammalian ecosystem. Science 273, 1380–1383.
113Hooper, LV, Xu, J, Falk, PG, et al. (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, 9833–9838.
114Chassaing, B & Darfeuille-Michaud, A (2011) The commensal microbiota and enteropathogens in the pathogenesis of inflammatory bowel diseases. Gastroenterology 140, 1720–1728.
115Frank, DN, St Amand, AL, Feldman, RA, et al. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104, 13780–13785.
116Papa, E, Docktor, M, Smillie, C, et al. (2012) Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLOS ONE 7, e39242.
117Duncan, SH, Hold, GL, Harmsen, HJM, et al. (2002) Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol 52, 2141–2146.
118Johansson, MEV, Gustafsson, JK, Sjöberg, KE, et al. (2010) Bacteria penetrate the inner mucus layer before inflammation in the dextran sulphate colitis model. PLOS ONE 5, e12238.
119Johansson, MEV, Gustafsson, JK, Holmen-Larsson, J, et al. (2013) Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis. Gut 63, 281–291.
120Miquel, S, Martin, R, Rossi, O, et al. (2013) Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol 16, 1–7.
121Rescigno, M & Di Sabatino, A (2009) Dendritic cells in intestinal homeostasis and disease. J Clin Invest 119, 2441–2450.
122Chieppa, M, Rescigno, M, Huang, AYC, et al. (2006) Dynamic imaging of dendritic cell extension into the small bowel lumen in response to epithelial cell TLR engagement. J Exp Med 203, 2841–2852.
123Mileti, E, Matteoli, G, Iliev, ID, et al. (2009) Comparison of the immunomodulatory properties of three probiotic strains of Lactobacilli using complex culture systems: prediction for in vivo efficacy. PLOS ONE 4, e7056.
124Tsilingiri, K & Rescigno, M (2013) Postbiotics: what else? Benef Microbes 4, 101–107.
125Tsilingiri, K, Barbosa, T, Penna, G, et al. (2012) Probiotic and postbiotic activity in health and disease: comparison on a novel polarised ex-vivo organ culture model. Gut 61, 1007–1015.
126Tsilingiri, K & Rescigno, M (2012) Should probiotics be tested on ex vivo organ culture models? Gut Microbes 3, 442–448.
127Ott, SJ, Plamondon, S, Hart, A, et al. (2008) Dynamics of the mucosa-associated flora in ulcerative colitis patients during remission and clinical relapse. J Clin Microbiol 46, 3510–3513.
128McLaughlin, SD, Walker, AW, Churcher, C, et al. (2010) The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing. Ann Surg 252, 90–98.
129Hansen, R, Russell, RK, Reiff, C, et al. (2012) Microbiota of de-novo pediatric IBD: increased Faecalibacterium prausnitzii and reduced bacterial diversity in Crohn's but not in ulcerative colitis. Am J Gastroenterol 107, 1913–1922.
130Morgan, XC, Tickle, TL, Sokol, H, et al. (2012) Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13, R79.
131Thia, KT, Mahadevan, U, Feagan, BG, et al. (2009) Ciprofloxacin or metronidazole for the treatment of perianal fistulas in patients with Crohn's disease: a randomized, double-blind, placebo-controlled pilot study. Inflamm Bowel Dis 15, 17–24.
132Rutgeerts, P, Hiele, M, Geboes, K, et al. (1995) Controlled trial of metronidazole treatment for prevention of Crohn's recurrence after ileal resection. Gastroenterology 108, 1617–1621.
133Kruis, W, Frič, J, Poktrotnieks, J, et al. (2004) Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine. Gut 53, 1617–1623.
134Sood, A, Midha, V, Makharia, GK, et al. (2009) The probiotic preparation, VSL#3 induces remission in patients with mild-to-moderately active ulcerative colitis. Clin Gastroenterol Hepatol 7, 1202–1209.
135Mimura, T, Rizzello, F, Helwig, U, et al. (2004) Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis. Gut 53, 108–114.
136Benjamin, JL, Hedin, CR, Koutsoumpas, A, et al. (2011) Randomised, double-blind, placebo-controlled trial of fructo-oligosaccharides in active Crohn's disease. Gut 60, 923–929.
137Hart, AL, Lammers, K, Brigidi, P, et al. (2004) Modulation of human dendritic cell phenotype and function by probiotic bacteria. Gut 53, 1602–1609.
138Ng, SC, Plamandon, S, Kamm, MA, et al. (2010) Immunosuppressive effects via human intestinal dendritic cells of probiotic bacteria and steroids in the treatment of acute ulcerative colitis. Inflamm Bowel Dis 16, 1286–1298.
139Rachmilewitz, D, Katakura, K, Karmeili, F, et al. (2004) Toll-like receptor 9 signaling mediates the anti-inflammatory effects of probiotics in murine experimental colitis. Gastroenterol 126, 520–528.
140Lammers, KM, Hart, AL, Brigidi, P, et al. (2012) Probiotic bacterial DNA induces interleukin-10 production by human dendritic cells via Toll-like receptor-9. Int J Probiotics Prebiotics 7, 39–48.
141Bernardo, D, Sanchez, B, Al-Hassi, HO, et al. (2012) Microbiota/host crosstalk biomarkers: regulatory response of human intestinal dendritic cells exposed to Lactobacillus extracellular encrypted peptide. PLOS ONE 7, e36262.
142Landy, J, Al-Hassi, HO, McLaughlin, SD, et al. (2011) Review article: faecal transplantation therapy for gastrointestinal disease. Aliment Pharmacol Ther 34, 409–415.
143Van Nood, E, Vrieze, A, Nieuwdorp, M, et al. (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 368, 407–415.
144Lawley, TD, Clare, S, Walker, AW, et al. (2012) Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog 8, e1002995.
145Damman, CJ, Miller, SI, Surawicz, CM, et al. (2012) The microbiome and inflammatory bowel disease: is there a therapeutic role for fecal microbiota transplantation? Am J Gastroenterol 107, 1452–1459.
146Anderson, JL, Edney, RJ & Whelan, K (2012) Systematic review: faecal microbiota transplantation in the management of inflammatory bowel disease. Aliment Pharmacol Ther 36, 503–516.
147Landy, J, Al-Hassi, HO, Ronde, E, et al. (2013) P591 A prospective controlled pilot study of faecal microbiota transplantation for chronic refractory pouchitis. J Crohn's Colitis 7, S247–S248.
148Solis, G, de Los Reyes-Gavilan, CG, Fernandez, N, et al. (2010) Establishment and development of lactic acid bacteria and bifidobacteria microbiota in breast-milk and the infant gut. Anaerobe 16, 307–310.
149Akobeng, AK, Ramanan, AV, Buchan, I, et al. (2006) Effect of breast feeding on risk of coeliac disease: a systematic review and meta-analysis of observational studies. Arch Dis Child 91, 39–43.
150Mårild, K, Stephansson, O, Montogmery, S, et al. (2012) Pregnancy outcome and risk of celiac disease in offspring: a nationwide case–control study. Gastroenterology 142, 39–45.
151Jabri, B & Sollid, LM (2009) Tissue-mediated control of immunopathology in coeliac disease. Nat Rev Immunol 9, 858–870.
152Stene, LC, Honeyman, MC, Hoffenberg, EJ, et al. (2006) Rotavirus infection frequency and risk of celiac disease autoimmunity in early childhood: a longitudinal study. Am J Gastroenterol 101, 2333–2340.
153Nadal, I, Donant, E, Ribes-Koninckx, C, et al. (2007) Imbalance in the composition of the duodenal microbiota of children with coeliac disease. J Med Microbiol 56, 1669–1674.
154Collado, MC, Donat, E, Ribes-Koninckx, C, et al. (2009) Specific duodenal and faecal bacterial groups associated with paediatric coeliac disease. J Clin Pathol 62, 264–269.
155Sánchez, E, Laparra, JM & Sanz, Y (2012) Discerning the role of Bacteroides fragilis in celiac disease pathogenesis. Appl Environ Microbiol 78, 6507–6515.
156Sears, CL (2009) Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes. Clin Microbiol Rev 22, 349–369.
157Wacklin, P, Kaukinen, K, Tuovinen, E, et al. (2013) The duodenal microbiota composition of adult celiac disease patients is associated with the clinical manifestation of the disease. Inflamm Bowel Dis 19, 934–941.
158Margaritte-Jeannin, P, Babron, MC, Bourgey, M, et al. (2004) HLA-DQ relative risks for coeliac disease in European populations: a study of the European Genetics Cluster on Coeliac Disease. Tissue Antigens 63, 562–567.
159Sánchez, E, Ribes-Koninckx, C, Calabuig, M, et al. (2012) Intestinal Staphylococcus spp. and virulent features associated with coeliac disease. J Clin Pathol 65, 830–834.
160Cinova, J, De Palma, G, Stepankova, R, et al. (2011) Role of intestinal bacteria in gliadin-induced changes in intestinal mucosa: study in germ-free rats. PLOS ONE 6, e16169.
161De Meij, TG, Budding, AE, Grasman, ME, et al. (2013) Composition and diversity of the duodenal mucosa-associated microbiome in children with untreated coeliac disease. Scand J Gastroenterol 48, 530–536.
162Ou, G, Hörstedt, P, Baranov, V, et al. (2009) Proximal small intestinal microbiota and identification of rod-shaped bacteria associated with childhood celiac disease. Am J Gastroenterol 104, 3058–3067.
163Schippa, S, Iebba, V, Barbato, M, et al. (2010) A distinctive ‘microbial signature’ in celiac pediatric patients. BMC Microbiol 10, 175.
164Di Cagno, R, De Angelis, M, De Pasquale, I, et al. (2011) Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol 11, 219.
165De Palma, G, Capilla, A, Nova, E, et al. (2012) Influence of milk-feeding type and genetic risk of developing coeliac disease on intestinal microbiota of infants: the PROFICEL study. PLOS ONE 7, e30791.
166Myléus, A, Hernell, O, Gothefors, L, et al. (2012) Early infections are associated with increased risk for celiac disease: an incident case-referent study. BMC Pediatr 12, 194.
167Mårild, K, Ye, W, Lebwohl, B, et al. (2013) Antibiotic exposure and the development of coeliac disease: a nationwide case–control study. BMC Gastroenterol 13, 109.
168Dolcino, M, Zanoni, G, Bason, C, et al. (2013) A subset of anti-rotavirus antibodies directed against the viral protein VP7 predicts the onset of celiac disease and induces typical features of the disease in the intestinal epithelial cell line T84. Immunol Res 56, 465–476.
169Nau, AL, Fayad, L, Lazzarotto, C, et al. (2013) Prevalence and clinical features of celiac disease in patients with hepatitis B virus infection in Southern Brazil. Rev Soc Bras Med Trop 46, 397–402.
170Pozo-Rubio, T, de Palma, G, Mujico, JR, et al. (2013) Influence of early environmental factors on lymphocyte subsets and gut microbiota in infants at risk of celiac disease; the PROFICEL study. Nutr Hosp 28, 464–473.
171Riddle, MS, Murray, JA, Cash, BD, et al. (2013) Pathogen-specific risk of celiac disease following bacterial causes of foodborne illness: a retrospective cohort study. Dig Dis Sci 58, 3242–3245.
172Tjernberg, AR & Ludvigsson, JF (2014) Children with celiac disease are more likely to have attended hospital for prior respiratory syncytial virus infection. Dig Dis Sci .