Genes Nutr (2011) 6:209–240 Jime´nez E, Mar´ın ML, Mart´ın R, Odriozola JM, Olivares M, Xaus J, Ferna´ndez L, Rodr´ıguez JM (2008) Is meconium from healthy newborns actually sterile? Res Microbiol 159(3):187–193 Johansson ME, Phillipson M, Petersson J, Velcich A, Holm L, Hansson GC (2008) The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci USA 105(39):15064–15069 Johansson ME, Holme´n Larsson JM, Hansson GC (2010) Microbes and Health Sackler Colloquium: The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc Natl Acad Sci USA. Epub Joossens M, Huys G, Cnockaert M, De Preter V, Verbeke K, Rutgeerts P, Vandamme P, Vermeire S (2011) Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives. Gut 60(5):631–637 Kajander K, Myllyluoma E, Rajilic´-Stojanovic´ M, Kyro¨npalo S, Rasmussen M, Ja¨rvenpa¨a¨ S, Zoetendal EG, De Vos WM, Vapaatalo H, Korpela R (2008) Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota. Aliment Pharmacol Ther 27(1):48–57 Kallioma¨ki M, Kirjavainen P, Eerola E, Kero P, Salminen S, Isolauri E (2001) Distinct patterns of neonatal gut microﬂora in infants in whom atopy was and was not developing. J Allergy Clin Immunol 107(1):129–134 Kallioma¨ki M, Collado MC, Salminen S, Isolauri E (2008) Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr 87(3):534–538 Kanazawa K, Konishi F, Mitsuoka T, Terada A, Itoh K, Narushima S, Kumemura M, Kimura H (1996) Factors inﬂuencing the development of sigmoid colon cancer. Bacteriologic and biochemical studies. Cancer 77(8 Suppl):1701–1706 Kang S, Denman SE, Morrison M, Yu Z, Dore´ J, Leclerc M, McSweeney CS (2010) Dysbiosis of fecal microbiota in Crohn’s disease patients as revealed by a custom phylogenetic micro- array. Inﬂamm Bowel Dis 16(12):2034–2042 Kankainen M, Paulin L, Tynkkynen S, von Ossowski I, Reunanen J, Partanen P, Satokari R, Vesterlund S, Hendrickx AP, Lebeer S, De Keersmaecker SC, Vanderleyden J, Ha¨ma¨la¨inen T, Laukka- nen S, Salovuori N, Ritari J, Alatalo E, Korpela R, Mattila- Sandholm T, Lassig A, Hatakka K, Kinnunen KT, Karjalainen H, Saxelin M, Laakso K, Surakka A, Palva A, Salusja¨rvi T, Auvinen P, De Vos WM (2009) Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc Natl Acad Sci USA 106(40): 17193–17198 Karantanos T, Markoutsaki T, Gazouli M, Anagnou NP, Karamanolis DG (2010) Current insights into the pathophysiology of Irritable Bowel Syndrome. Gut Pathog 2(1):3 Kassinen A, Krogius-Kurikka L, Ma¨kivuokko H, Rinttila¨ T, Paulin L, Corander J, Malinen E, Apajalahti J, Palva A (2007) The fecal microbiota of irritable bowel syndrome patients differs signif- icantly from that of healthy subjects. Gastroenterology 133(1):24–33 Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K, Akkermans LM (2009) Lower biﬁdobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World J Gastroenterol 15(23):2887–2892 Kerckhoffs AP, Ben-Amor K, Samsom M, van der Rest ME, de Vogel J, Knol J, Akkermans LM (2010) Molecular analysis of faecal and duodenal samples reveals signiﬁcantly higher prevalence and numbers of Pseudomonas aeruginosa in IBS. J Med Microbiol 60:236–245 235 Kim YS, Ho SB (2010) Intestinal goblet cells and mucins in health and disease: recent insights and progress. Curr Gastroenterol Rep 12(5):319–330 Kinross JM, Darzi AW, Nicholson JK (2011) Gut microbiome-host interactions in health and disease. Genome Med 3(3):14 Kirjavainen PV, Apostolou E, Arvola T, Salminen SJ, Gibson GR, Isolauri E (2001) Characterizing the composition of intestinal microﬂora as a prospective treatment target in infant allergic disease. FEMS Immunol Med Microbiol 32(1):1–7 Klaassens ES, De Vos WM, Vaughan EE (2007) Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl Environ Microbiol 73(4):1388–1392 Klaassens ES, Boesten RJ, Haarman M, Knol J, Schuren FH, Vaughan EE, De Vos WM (2009) Mixed-species genomic microarray analysis of fecal samples reveals differential tran- scriptional responses of biﬁdobacteria in breast- and formula-fed infants. Appl Environ Microbiol 75(9):2668–2676 Kleerebezem M, Vaughan EE (2009) Probiotic and gut lactobacilli and biﬁdobacteria: molecular approaches to study diversity and activity. Annu Rev Microbiol 63:269–290 Kleessen B, Kroesen AJ, Buhr HJ, Blaut M (2002) Mucosal and invading bacteria in patients with inﬂammatory bowel disease compared with controls. Scand J Gastroenterol 37(9):1034–1041 Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE (2010) Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA Epub Koide A, Yamaguchi T, Odaka T, Koyama H, Tsuyuguchi T, Kitahara H, Ohto M, Saisho H (2000) Quantitative analysis of bowel gas using plain abdominal radiograph in patients with irritable bowel syndrome. Am J Gastroenterol 95(7):1735–1741 Komanduri S, Gillevet PM, Sikaroodi M, Mutlu E, Keshavarzian A (2007) Dysbiosis in pouchitis: evidence of unique microﬂoral patterns in pouch inﬂammation. Clin Gastroenterol Hepatol 5(3):352–360 Koning CJ, Jonkers D, Smidt H, Rombouts F, Pennings HJ, Wouters E, Stobberingh E, Stockbru¨gger R (2010) The effect of a multispecies probiotic on the composition of the faecal micro- biota and bowel habits in chronic obstructive pulmonary disease patients treated with antibiotics. Br J Nutr 103(10):1452–1460 Kotlowski R, Bernstein CN, Sepehri S, Krause DO (2007) High prevalence of Escherichia coli belonging to the B2?D phylo- genetic group in inﬂammatory bowel disease. Gut 56(5):669–675 Kovatcheva-Datchary P, Egert M, Maathuis A, Rajilic´-Stojanovic´ M, De Graaf AA, Smidt H, De Vos WM, Venema K (2009) Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 11(4):914–926 Krogius-Kurikka L, Lyra A, Malinen E, Aarnikunnas J, Tuimala J, Paulin L, Ma¨kivuokko H, Kajander K, Palva A (2009) Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predom- inant irritable bowel syndrome sufferers. BMC Gastroenterol 9:95 Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M (2007) Comparative metage- nomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14(4):169–181 Lahtinen SJ, Tammela L, Korpela J, Parhiala R, Ahokoski H, Mykka¨nen H, Salminen SJ (2009) Probiotics modulate the Biﬁdobacterium microbiota of elderly nursing home residents. Age (Dordr) 31(1):59–66 123