236 Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sørensen SJ, Hansen LH, Jakobsen M (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5(2):e9085 Lepage P, Seksik P, Sutren M, de la Cochetie`re MF, Jian R, Marteau P, Dore´ J (2005) Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inﬂamm Bowel Dis 11(5):473–480 Ley RE (2010) Obesity and the human microbiome. Curr Opin Gastroenterol 26(1):5–11 Ley RE, Ba¨ckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102(31):11070–11075 Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444(7122):1022–1023 Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut micro- biota. Nat Rev Microbiol 6(10):776–788 Lim M, Adams JD, Wilcox M, Finan P, Sagar P, Burke D (2009) An assessment of bacterial dysbiosis in pouchitis using terminal restriction fragment length polymorphisms of 16S ribosomal DNA from pouch efﬂuent microbiota. Dis Colon Rectum 52(8):1492–1500 Longstreth GF, Thompson WG, Chey WD, Houghton LA, Mearin F, Spiller RC (2006) Functional bowel disorders. Gastroenterology 130(5):1480–1491 Lo´pez P, Gueimonde M, Margolles A, Sua´rez A (2010) Distinct Biﬁdobacterium strains drive different immune responses in vitro. Int J Food Microbiol 138(1–2):157–165 Lyra A, Rinttila¨ T, Nikk¨ıla J, Krogius-Kurikka L, Kajander K, Malinen E, Ma¨tto¨ J, Ma¨kela¨ L, Palva A (2009) Diarrhoea- predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantiﬁcation. World J Gastroenterol 15(47):5936–5945 Mackie RI, Sghir A, Gaskins HR (1999) Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 69(5):1035S–1045S Mai V, Greenwald B, Morris JG Jr, Raufman JP, Stine OC (2006) Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition. Gut 55(12):1822–1823 Malinen E, Rinttila¨ T, Kajander K, Ma¨tto¨ J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A (2005) Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol 100(2):373– 382 Malinen E, Krogius-Kurikka L, Lyra A, Nikk¨ıla J, Ja¨a¨skela¨inen A, Rinttila¨ T, Vilpponen-Salmela T, von Wright AJ, Palva A (2010) Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World J Gastroenterol 16(36):4532–4540 Mangin I, Bonnet R, Seksik P, Rigottier-Gois L, Sutren M, Bouhnik Y, Neut C, Collins MD, Colombel JF, Marteau P, Dore´ J (2004) Molecular inventory of faecal microﬂora in patients with Crohn’s disease. FEMS Microbiol Ecol 50(1):25–36 Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore´ J (2006) Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55(2):205– 211 Mariat D, Firmesse O, Levenez F, Guimara˘es V, Sokol H, Dore´ J, Corthier G, Furet JP (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9:123 Martin FP, Sprenger N, Montoliu I, Rezzi S, Kochhar S, Nicholson JK (2010) Dietary modulation of gut functional ecology studied by fecal metabonomics. J Proteome Res 9(10):5284–5295 123 Genes Nutr (2011) 6:209–240 Martinez C, Antolin M, Santos J, Torrejon A, Casellas F, Borruel N, Guarner F, Malagelada JR (2008) Unstable composition of the fecal microbiota in ulcerative colitis during clinical remission. Am J Gastroenterol 103(3):643–648 Martinez-Medina M, Aldeguer X, Gonzalez-Huix F, Acero D, Garcia- Gil LJ (2006) Abnormal microbiota composition in the ileoco- lonic mucosa of Crohn’s disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophore- sis. Inﬂamm Bowel Dis 12(12):1136–1145 Marzotto M, Maffeis C, Paternoster T, Ferrario R, Rizzotti L, Pellegrino M, Dellaglio F, Torriani S (2006) Lactobacillus paracasei A survives gastrointestinal passage and affects the fecal microbiota of healthy infants. Res Microbiol 157(9):857–866 Matsuki T, Watanabe K, Fujimoto J, Kado Y, Takada T, Matsumoto K, Tanaka R (2004) Quantitative PCR with 16S rRNA-gene- targeted species-speciﬁc primers for analysis of human intestinal biﬁdobacteria. Appl Environ Microbiol 70(1):167–173 Ma¨tto¨ J, Maunuksela L, Kajander K, Palva A, Korpela R, Kassinen A, Saarela M (2005) Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome—a longitudinal study in IBS and control subjects. FEMS Immunol Med Microbiol 43(2):213–222 Maukonen J, Satokari R, Ma¨tto¨ J, So¨ derlund H, Mattila-Sandholm T, Saarela M (2006) Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. J Med Microbiol 55(Pt 5):625–633 McFarland LV (1998) Epidemiology, risk factors and treatments for antibiotic-associated diarrhea. Dig Dis 16(5):292–307 Medina M, Izquierdo E, Ennahar S, Sanz Y (2007) Differential immunomodulatory properties of Biﬁdobacterium longum strains: relevance to probiotic selection and clinical applications. Clin Exp Immunol 150(3):531–538 Meijerink M, van Hemert S, Taverne N, Wels M, De Vos P, Bron PA, Savelkoul HF, van Bilsen J, Kleerebezem M, Wells JM (2010) Identiﬁcation of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using compar- ative genome hybridization. PLoS One 5(5):e10632 Merritt ME, Donaldson JR (2009) Effect of bile salts on the DNA and membrane integrity of enteric bacteria. J Med Microbiol 58(Pt 12):1533–1541 Mihajlovski A, Alric M, Bruge`re JF (2008) A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene. Res Microbiol 159(7–8): 516–521 Mohan R, Koebnick C, Schildt J, Schmidt S, Mueller M, Possner M, Radke M, Blaut M (2006) Effects of Biﬁdobacterium lactis Bb12 supplementation on intestinal microbiota of preterm infants: a double-blind, placebo-controlled, randomized study. J Clin Microbiol 44(11):4025–4031 Mondot S, Kang S, Furet JP, Aguirre de Carcer D, McSweeney C, Morrison M, Marteau P, Dore´ J, Leclerc M (2011) Highlighting new phylogenetic speciﬁcities of Crohn’s disease microbiota. Inﬂamm Bowel Dis 17(1):185–192 Montesi A, Garc´ıa-Albiach R, Pozuelo MJ, Pintado C, Gon˜i I, Rotger R (2005) Molecular and microbiological analysis of caecal microbiota in rats fed with diets supplemented either with prebiotics or probiotics. Int J Food Microbiol 98(3):281–289 Moore WE, Moore LH (1995) Intestinal ﬂoras of populations that have a high risk of colon cancer. Appl Environ Microbiol 61(9):3202–3207 Mortensen PB, Andersen JR, Arffmann S, Krag E (1987) Short-chain fatty acids and the irritable bowel syndrome: the effect of wheat bran. Scand J Gastroenterol 22(2):185–192 Mshvildadze M, Neu J, Shuster J, Theriaque D, Li N, Mai V (2010) Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J Pediatr 156(1):20–25