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1 AW Walker , J Ince & SH Duncan (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5, 220–230.
2 BS Wostmann (1981) The germfree animal in nutritional studies. Annu Rev Nutr 1, 257–279.
3 AM O'Hara & F Shanahan (2006) The gut flora as a forgotten organ. EMBO Rep 7, 688–693.
4 F Guarner & JR Malagelada (2003) Gut flora in health and disease. Lancet 361, 512–519.
5 NA Moran (2006) Symbiosis. Curr Biol 16, R866–R871.
7 EM Kiely , NA Ajayi , RA Wheeler , et al. (2001) Diversion procto-colitis: response to treatment with short-chain fatty acids. J Pediatr Surg 36, 1514–1517.
8 MF Kagnoff (2006) Microbial–epithelial cell crosstalk during inflammation: the host response. Ann N Y Acad Sci 1072, 313–320.
9 P Brandtzaeg (2009) Mucosal immunity: induction, dissemination, and effector functions. Scand J Immunol 70, 505–515.
12 Y Umesaki & H Setoyama (2000) Structure of the intestinal flora responsible for development of the gut immune system in a rodent model. Microbes Infect 2, 1343–1351.
13 G Eberl & M Lochner (2009) The development of intestinal lymphoid tissues at the interface of self and microbiota. Mucosal Immunol 2, 478–485.
14 J Handelsman , MR Rondon , SF Brady , et al. (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5, R245–R249.
15 DN Frank & NR Pace (2008) Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol 24, 4–10.
16 PJ Turnbaugh , RE Ley , M Hamady , et al. (2007) The human microbiome project. Nature 449, 804–810.
17 PB Eckburg , EM Bik , CN Bernstein , et al. (2005) Diversity of the human intestinal microbial flora. Science 308, 1635–1638.
18 J Qin , R Li , J Raes , et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65.
19 M Arumugam , J Raes , E Pelletier , et al. (2011) Enterotypes of the human gut microbiome. Nature 473, 174–180.
20 SM Huse , Y Ye , Y Zhou , et al. (2012) A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One 7, e34242.
21 M Gatt , BS Reddy & J MacFie (2007) Review article: bacterial translocation in the critically ill – evidence and methods of prevention. Aliment Pharmacol Ther 25, 741–757.
22 RE Ley , PJ Turnbaugh , S Klein , et al. (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023.
23 M Blaut & S Klaus (2012) Intestinal microbiota and obesity. Handb Exp Pharmacol 209, 251–273.
24 F Guarner (2008) What is the role of the enteric commensal flora in IBD? Inflamm Bowel Dis 14, S83–S84.
25 H Sokol , B Pigneur , L Watterlot , 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.
26 DN Frank , AL St Amand , RA Feldman , 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.
27 FA Van Nimwegen , J Penders , EE Stobberingh , et al. (2011) Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy. Allergy Clin Immunol 128, 948–955.e1–3.
28 J Penders , C Thijs , PA van den Brandt , et al. (2007) Gut microbiota composition and development of atopic manifestations in infancy: the KOALA Birth Cohort Study. Gut 56, 661–667.
29 H Duboc (2012) Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome. Neurogastroenterol Motil 24, 513–520.
30 Y Song , C Liu & SM Finegold (2004) Real-time PCR quantitation of clostridia in feces of autistic children. Appl Environ Microbiol 70, 6459–6465.
31 SM Finegold , SE Dowd , V Gontcharova , et al. (2010) Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16, 444–453.
33 M Roberfroid , GR Gibson , L Hoyles , et al. (2010) Prebiotic effects: metabolic and health benefits. Br J Nutr 104, Suppl. 2, S1–S63.
34 GV Coppa , S Bruni , L Morelli , et al. (2004) The first prebiotics in humans: human milk oligosaccharides. J Clin Gastroenterol 38, Suppl. 6, S80–S83.
35 C Grüber , M van Stuijvenberg & F Mosca (2010) Reduced occurrence of early atopic dermatitis because of immunoactive prebiotics among low-atopy-risk infants. J Allergy Clin Immunol 126, 791–797.
36 J Landy (2011) Review article: faecal transplantation therapy for gastrointestinal disease. Aliment Pharmacol Ther 34, 409–415.