Genes Nutr (2011) 6:209–240 Biagi E, Nylund L, Candela M, Ostan R, Bucci L, Pini E, Nikk¨ıla J, Monti D, Satokari R, Franceschi C, Brigidi P, De Vos W (2010) Through ageing, and beyond: gut microbiota and inﬂammatory status in seniors and centenarians. PLoS One 5(5):e10667 Bibiloni R, Mangold M, Madsen KL, Fedorak RN, Tannock GW (2006) The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn’s disease and ulcerative colitis patients. J Med Microbiol 55(Pt 8):1141–1149 Bjo¨rkste´n B, Naaber P, Sepp E, Mikelsaar M (1999) The intestinal microﬂora in allergic Estonian and Swedish 2-year-old children. Clin Exp Allergy 29(3):342–346 Bjo¨rkste´n B, Sepp E, Julge K, Voor T, Mikelsaar M (2001) Allergy development and the intestinal microﬂora during the ﬁrst year of life. J Allergy Clin Immunol 108(4):516–520 Boesten RJ, De Vos WM (2008) Interactomics in the human intestine: Lactobacilli and Biﬁdobacteria make a difference. J Clin Gas- troenterol 42(Suppl 3, Pt 2):S163–S167 Booijink CC, Zoetendal EG, Kleerebezem M, De Vos WM (2007) Microbial communities in the human small intestine: coupling diversity to metagenomics. Future Microbiol 2(3):285–295 Booijink CC, El-Aidy S, Rajilic´-Stojanovic´ M, Heilig HG, Troost FJ, Smidt H, Kleerebezem M, De Vos WM, Zoetendal EG (2010) High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 12(12):3213–3227 Buddington RK, Sangild PT (2011) Development of the mammalian gastrointestinal tract, the resident microbiota, and the role of diet in early life. J Anim Sci 89:1506–1519 Cabana MD, McKean M, Wong AR, Chao C, Caughey AB (2007) Examining the hygiene hypothesis: the Trial of Infant Probiotic Supplementation. Paediatr Perinat Epidemiol 21(Suppl 3):23–28 Cani PD, Delzenne NM (2009) The role of the gut microbiota in energy metabolism and metabolic disease. Curr Pharm Des 15(13):1546–1558 Carroll IM, Chang YH, Park J, Sartor RB, Ringel Y (2010) Luminal and mucosal-associated intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Gut Pathog 2(1):19 Cerf-Bensussan N, Gaboriau-Routhiau V (2010) The immune system and the gut microbiota: friends or foes? Nat Rev Immunol 10(10):735–744 Chang JY, Talley NJ (2011) An update on irritable bowel syndrome: from diagnosis to emerging therapies. Curr Opin Gastroenterol 27(1):72–78 Chapman CM, Gibson GR, Rowland I (2011) Health beneﬁts of probiotics: are mixtures more effective than single strains? Eur J Nutr 50(1):1–17 Claesson MJ, Cusack S, O’Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O’Connor M, Harnedy N, O’Connor K, Henry C, O’Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O’Toole PW (2010) Microbes and Health Sackler Colloquium: Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci USA. Epub Codling C, O’Mahony L, Shanahan F, Quigley EM, Marchesi JR (2010) A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome. Dig Dis Sci 55(2):392–397 Collado MC, Calabuig M, Sanz Y (2007) Differences between the fecal microbiota of coeliac infants and healthy controls. Curr Issues Intest Microbiol 8(1):9–14 Collado MC, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y (2008a) Imbalances in faecal and duodenal Biﬁdobacterium species composition in active and non-active coeliac disease. BMC Microbiol 8:232 233 Collado MC, Isolauri E, Laitinen K, Salminen S (2008b) Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr 88(4):894–899 Collado MC, Isolauri E, Laitinen K, Salminen S (2010) Effect of mother’s weight on infant’s microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy. Am J Clin Nutr 92(5):1023–1030 Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez- Garayzabal J, Garcia P, Cai J, Hippe H, Farrow JA (1994) The phylogeny of the genus Clostridium: proposal of ﬁve new genera and eleven new species combinations. Int J Syst Bacteriol 44(4):812–826 Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2009) Bacterial community variation in human body habitats across space and time. Science 326(5960):1694–1697 Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P (2005) Metagenomic gene discovery: past, present and future. Trends Biotechnol 23(6):321–329 Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SV (2010) Lacto- bacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One 5(1):e8745 Darfeuille-Michaud A (2002) Adherent-invasive Escherichia coli: a putative new E. coli pathotype associated with Crohn’s disease. Int J Med Microbiol 292(3–4):185–193 Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser AL, Barnich N, Bringer MA, Swidsinski A, Beaugerie L, Colombel JF (2004) High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterol- ogy 127(2):412–421 De Palma G, Nadal I, Medina M, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y (2010) Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol 10:63 De Preter V, Hamer HM, Windey K, Verbeke K (2010) The impact of pre- and/or probiotics on human colonic metabolism: does it affect human health? Mol Nutr Food Res 55(1):46–57 Dethlefsen L, Eckburg PB, Bik EM, Relman DA (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21(9):517–523 Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6(11):e280 Dicksved J, Halfvarson J, Rosenquist M, Ja¨rnerot G, Tysk C, Apajalahti J, Engstrand L, Jansson JK (2008) Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. ISME J 2(7):716–727 Dridi B, Henry M, El Khe´chine A, Raoult D, Drancourt M (2009) High prevalence of Methanobrevibacter smithii and Metha- nosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4(9):e7063 Dumas ME, Wilder SP, Bihoreau MT, Barton RH, Fearnside JF, Argoud K, D’Amato L, Wallis RH, Blancher C, Keun HC, Baunsgaard D, Scott J, Sidelmann UG, Nicholson JK, Gauguier D (2007) Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models. Nat Genet 39(5):666–672 Duncan SH, Belenguer A, Holtrop G, Johnstone AM, Flint HJ, Lobley GE (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(4):1073–1078 Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P, Flint HJ (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 32(11):1720–1724 123