The intestinal microbiota and chronic disorders of the gut (original) (raw)

• Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Zoetendal, E. G., Akkermans, A. D. & De Vos, W. M. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64, 3854–3859 (1998).
  CAS PubMed PubMed Central Google Scholar
• Mariat, D. et al. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol. 9, 123 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Dethlefsen, L., Huse, S., Sogin, M. L. & Relman, D. A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6, e280 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Jernberg, C., Lofmark, S., Edlund, C. & Jansson, J. K. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156, 3216–3223 (2010).
  Article CAS PubMed Google Scholar
• Nikkila, J. & de Vos, W. M. Advanced approaches to characterize the human intestinal microbiota by computational meta-analysis. J. Clin. Gastroenterol. 44 (Suppl. 1), S2–S5 (2010).
  Article PubMed CAS Google Scholar
• Kinross, J. M., Darzi, A. W. & Nicholson, J. K. Gut microbiome-host interactions in health and disease. Genome Med. 3, 14 (2011).
  Article PubMed PubMed Central Google Scholar
• Bouskra, D. et al. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 456, 507–510 (2008).
  Article CAS PubMed Google Scholar
• Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S. & Medzhitov, R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118, 229–241 (2004).
  Article CAS PubMed Google Scholar
• Lee, J. et al. Maintenance of colonic homeostasis by distinctive apical TLR9 signalling in intestinal epithelial cells. Nat. Cell Biol. 8, 1327–1336 (2006).
  Article CAS PubMed Google Scholar
• Bauer, H., Horowitz, R. E., Levenson, S. M. & Popper, H. The response of the lymphatic tissue to the microbial flora. Studies on germfree mice. Am. J. Pathol. 42, 471–483 (1963).
  CAS PubMed PubMed Central Google Scholar
• Bauer, H., Paronetto, F., Burns, W. A. & Einheber, A. The enhancing effect of the microbial flora on macrophage function and the immune response. A study in germfree mice. J. Exp. Med. 123, 1013–1024 (1966).
  Article CAS PubMed PubMed Central Google Scholar
• Tsuda, M. et al. Intestinal commensal bacteria promote T cell hyporesponsiveness and down-regulate the serum antibody responses induced by dietary antigen. Immunol. Lett. 132, 45–52 (2010).
  Article CAS PubMed Google Scholar
• Vijay-Kumar, M. et al. Deletion of TLR5 results in spontaneous colitis in mice. J. Clin. Invest. 117, 3909–3921 (2007).
  CAS PubMed PubMed Central Google Scholar
• Abraham, C. & Medzhitov, R. Interactions between the host innate immune system and microbes in inflammatory bowel disease. Gastroenterology 140, 1729–1737 (2011).
  Article CAS PubMed Google Scholar
• Macpherson, A. J., McCoy, K. D., Johansen, F. E. & Brandtzaeg, P. The immune geography of IgA induction and function. Mucosal Immunol. 1, 11–22 (2008).
  Article CAS PubMed Google Scholar
• Jackson, R. J., Smith, S. D., Wadowsky, R. M., DePudyt, L. & Rowe, M. I. The effect of E coli virulence on bacterial translocation and systemic sepsis in the neonatal rabbit model. J. Pediatr. Surg. 26, 483–485 (1991).
  Article CAS PubMed Google Scholar
• Mahjoub-Messai, F. et al. Escherichia coli isolates causing bacteremia via gut translocation and urinary tract Infection in young infants exhibit different virulence genotypes. J. Infect. Dis. 203, 1844–1849 (2011).
  Article CAS PubMed Google Scholar
• Katayama, M., Xu, D., Specian, R. D. & Deitch, E. A. Role of bacterial adherence and the mucus barrier on bacterial translocation: effects of protein malnutrition and endotoxin in rats. Ann. Surg. 225, 317–326 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Merlini, E. et al. Evidence for polymicrobic flora translocating in peripheral blood of HIV-infected patients with poor immune response to antiretroviral therapy. PLoS ONE 6, e18580 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• DuPont, H. L. The search for effective treatment of Clostridium difficile infection. N. Engl. J. Med. 364, 473–475 (2011).
  Article CAS PubMed Google Scholar
• Khoruts, A., Dicksved, J., Jansson, J. K. & Sadowsky, M. J. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent _Clostridium difficile_-associated diarrhea. J. Clin. Gastroenterol. 44, 354–360 (2010).
  PubMed Google Scholar
• Grehan, M. J. et al. Durable alteration of the colonic microbiota by the administration of donor fecal flora. J. Clin. Gastroenterol. 44, 551–561 (2010).
  Article PubMed Google Scholar
• Poppe, C. et al. Characterization of antimicrobial resistance of Salmonella Newport isolated from animals, the environment, and animal food products in Canada. Can. J. Vet. Res. 70, 105–114 (2006).
  CAS PubMed PubMed Central Google Scholar
• Varma, J. K. et al. Highly resistant Salmonella Newport-MDRAmpC transmitted through the domestic US food supply: a FoodNet case-control study of sporadic Salmonella Newport infections, 2002–2003. J. Infect. Dis. 194, 222–230 (2006).
  Article CAS PubMed Google Scholar
• Neill, M. A. et al. Failure of ciprofloxacin to eradicate convalescent fecal excretion after acute salmonellosis: experience during an outbreak in health care workers. Ann. Intern. Med. 114, 195–199 (1991).
  Article CAS PubMed Google Scholar
• Effler, P. et al. Sporadic Campylobacter jejuni infections in Hawaii: associations with prior antibiotic use and commercially prepared chicken. J. Infect. Dis. 183, 1152–1155 (2001).
  Article CAS PubMed Google Scholar
• Moore, J. E., McLernon, P., Wareing, D., Xu, J. & Murphy, P. G. Characterisation of fluoroquinolone-resistant Campylobacter species isolated from human beings and chickens. Vet. Rec. 150, 518–520 (2002).
  Article CAS PubMed Google Scholar
• Dibaise, J. K., Young, R. J. & Vanderhoof, J. A. Enteric microbial flora, bacterial overgrowth, and short-bowel syndrome. Clin. Gastroenterol. Hepatol. 4, 11–20 (2006).
  Article PubMed Google Scholar
• Corazza, G. R. et al. The diagnosis of small bowel bacterial overgrowth. Reliability of jejunal culture and inadequacy of breath hydrogen testing. Gastroenterology 98, 302–309 (1990).
  Article CAS PubMed Google Scholar
• Riordan, S. M., McIver, C. J., Duncombe, V. M. & Bolin, T. D. Bacteriologic analysis of mucosal biopsy specimens for detecting small-intestinal bacterial overgrowth. Scand. J. Gastroenterol. 30, 681–685 (1995).
  Article CAS PubMed Google Scholar
• Bratten, J. R., Spanier, J. & Jones, M. P. Lactulose breath testing does not discriminate patients with irritable bowel syndrome from healthy controls. Am. J. Gastroenterol. 103, 958–963 (2008).
  Article CAS PubMed Google Scholar
• Sahakian, A. B., Jee, S. R. & Pimentel, M. Methane and the gastrointestinal tract. Dig. Dis. Sci. 55, 2135–2143 (2010).
  Article PubMed Google Scholar
• Khoshini, R., Dai, S. C., Lezcano, S. & Pimentel, M. A systematic review of diagnostic tests for small intestinal bacterial overgrowth. Dig. Dis. Sci. 53, 1443–1454 (2008).
  Article PubMed Google Scholar
• Bauer, T. M. et al. Small intestinal bacterial overgrowth in human cirrhosis is associated with systemic endotoxemia. Am. J. Gastroenterol. 97, 2364–2370 (2002).
  Article PubMed Google Scholar
• Morencos, F. C. et al. Small bowel bacterial overgrowth in patients with alcoholic cirrhosis. Dig. Dis. Sci. 41, 552–556 (1996).
  Article Google Scholar
• Gunnarsdottir, S. A. et al. Small intestinal motility disturbances and bacterial overgrowth in patients with liver cirrhosis and portal hypertension. Am. J. Gastroenterol. 98, 1362–1370 (2003).
  Article PubMed Google Scholar
• Morencos, F. C. et al. Small bowel bacterial overgrowth in patients with alcoholic cirrhosis. Dig. Dis. Sci. 40, 1252–1256 (1995).
  Article CAS PubMed Google Scholar
• Gupta, A. et al. Role of small intestinal bacterial overgrowth and delayed gastrointestinal transit time in cirrhotic patients with minimal hepatic encephalopathy. J. Hepatol. 53, 849–855 (2010).
  Article PubMed Google Scholar
• Pande, C., Kumar, A. & Sarin, S. K. Small-intestinal bacterial overgrowth in cirrhosis is related to the severity of liver disease. Aliment. Pharmacol. Ther. 29, 1273–1281 (2009).
  Article CAS PubMed Google Scholar
• Bjarnason, I., Peters, T. J. & Wise, R. J. The leaky gut of alcoholism: possible route of entry for toxic compounds. Lancet 1, 179–182 (1984).
  Article CAS PubMed Google Scholar
• Lorenzo-Zuniga, V. et al. Oral bile acids reduce bacterial overgrowth, bacterial translocation, and endotoxemia in cirrhotic rats. Hepatology 37, 551–557 (2003).
  Article CAS PubMed Google Scholar
• Campillo, B. Intestinal permeability in liver cirrhosis: relationship with severe septic complications. Eur. J. Gastroenterol. Hepatol. 11, 755–759 (1999).
  Article CAS PubMed Google Scholar
• Parlesak, A., Schafer, C., Schutz, T., Bode, J. C. & Bode, C. Increased intestinal permeability to macromolecules and endotoxemia in patients with chronic alcohol abuse in different stages of alcohol-induced liver disease. J. Hepatol. 32, 742–747 (2000).
  Article CAS PubMed Google Scholar
• Sanchez, E., Casafont, F., Guerra, A., de Benito, I. & Pons-Romero, F. Role of intestinal bacterial overgrowth and intestinal motility in bacterial translocation in experimental cirrhosis. Rev. Esp. Enferm. Dig. 97, 805–814 (2005).
  CAS PubMed Google Scholar
• Drossman, D. A., Camilleri, M., Mayer, E. A. & Whitehead, W. E. AGA technical review on irritable bowel syndrome. Gastroenterology 123, 2108–2131 (2002).
  Article PubMed Google Scholar
• Kassinen, A. et al. The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133, 24–33 (2007).
  Article CAS PubMed Google Scholar
• Krogius-Kurikka, L. et al. Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. BMC Gastroenterol. 9, 95 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• Lyra, A. et al. Diarrhoea-predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification. World J. Gastroenterol. 15, 5936–5945 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Tana, C. et al. Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. Neurogastroenterol. Motil. 22, 512–519, e114–e3115 (2010).
  CAS PubMed Google Scholar
• McKernan, D. P., Gaszner, G., Quigley, E. M., Cryan, J. F. & Dinan, T. G. Altered peripheral toll-like receptor responses in the irritable bowel syndrome. Aliment. Pharmacol. Ther. 33, 1045–1052 (2011).
  Article CAS PubMed Google Scholar
• Schoepfer, A. M., Schaffer, T., Seibold-Schmid, B., Muller, S. & Seibold, F. Antibodies to flagellin indicate reactivity to bacterial antigens in IBS patients. Neurogastroenterol. Motil. 20, 1110–1118 (2008).
  Article CAS PubMed Google Scholar
• Spiller, R. & Garsed, K. Postinfectious irritable bowel syndrome. Gastroenterology 136, 1979–1988 (2009).
  Article PubMed Google Scholar
• Lee, K. J. & Tack, J. Altered intestinal microbiota in irritable bowel syndrome. Neurogastroenterol. Motil. 22, 493–498 (2010).
  Article CAS PubMed Google Scholar
• Esposito, I. et al. Breath test for differential diagnosis between small intestinal bacterial overgrowth and irritable bowel disease: an observation on non-absorbable antibiotics. World J. Gastroenterol. 13, 6016–6021 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Lupascu, A. et al. Hydrogen glucose breath test to detect small intestinal bacterial overgrowth: a prevalence case–control study in irritable bowel syndrome. Aliment. Pharmacol. Ther. 22, 1157–1160 (2005).
  Article CAS PubMed Google Scholar
• Pimentel, M., Chow, E. J. & Lin, H. C. Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. Am. J. Gastroenterol. 95, 3503–3506 (2000).
  Article CAS PubMed Google Scholar
• Shah, E. D., Basseri, R. J., Chong, K. & Pimentel, M. Abnormal breath testing in IBS: a meta-analysis. Dig. Dis. Sci. 55, 2441–2449 (2010).
  Article PubMed Google Scholar
• Posserud, I., Stotzer, P. O., Bjornsson, E. S., Abrahamsson, H. & Simren, M. Small intestinal bacterial overgrowth in patients with irritable bowel syndrome. Gut 56, 802–808 (2007).
  Article PubMed Google Scholar
• Pimentel, M. et al. Rifaximin therapy for patients with irritable bowel syndrome without constipation. N. Engl. J. Med. 364, 22–32 (2011).
  Article CAS PubMed Google Scholar
• Brown, E. L., Xue, Q., Jiang, Z. D., Xu, Y. & Dupont, H. L. Pretreatment of epithelial cells with rifaximin alters bacterial attachment and internalization profiles. Antimicrob. Agents Chemother. 54, 388–396 (2010).
  Article CAS PubMed Google Scholar
• Kerlin, P. & Phillips, S. Variability of motility of the ileum and jejunum in healthy humans. Gastroenterology 82, 694–700 (1982).
  Article CAS PubMed Google Scholar
• Vantrappen, G., Janssens, J., Hellemans, J. & Ghoos, Y. The interdigestive motor complex of normal subjects and patients with bacterial overgrowth of the small intestine. J. Clin. Invest. 59, 1158–1166 (1977).
  Article CAS PubMed PubMed Central Google Scholar
• Pimentel, M., Soffer, E. E., Chow, E. J., Kong, Y. & Lin, H. C. Lower frequency of MMC is found in IBS subjects with abnormal lactulose breath test, suggesting bacterial overgrowth. Dig. Dis. Sci. 47, 2639–2643 (2002).
  Article CAS PubMed Google Scholar
• Barbara, G. et al. New pathophysiological mechanisms in irritable bowel syndrome. Aliment. Pharmacol. Ther. 20 (Suppl. 2), 1–9 (2004).
  Article PubMed Google Scholar
• Lin, H. C. Small intestinal bacterial overgrowth: a framework for understanding irritable bowel syndrome. JAMA 292, 852–858 (2004).
  Article CAS PubMed Google Scholar
• Salonen, A., de Vos, W. M. & Palva, A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology 156, 3205–3215 (2010).
  Article CAS PubMed Google Scholar
• Andoh, A. et al. Comparison of the fecal microbiota profiles between ulcerative colitis and Crohn's disease using terminal restriction fragment length polymorphism analysis. J. Gastroenterol. 46, 479–486 (2011).
  Article PubMed Google Scholar
• Manichanh, C. et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55, 205–211 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Ott, S. J. et al. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53, 685–693 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Onderdonk, A. B., Hermos, J. A. & Bartlett, J. G. The role of the intestinal microflora in experimental colitis. Am. J. Clin. Nutr. 30, 1819–1825 (1977).
  Article CAS PubMed Google Scholar
• Lal, S. & Steinhart, A. H. Antibiotic therapy for Crohn's disease: a review. Can. J. Gastroenterol. 20, 651–655 (2006).
  Article PubMed PubMed Central Google Scholar
• Rutgeerts, P. et al. Effect of faecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum. Lancet 338, 771–774 (1991).
  Article CAS PubMed Google Scholar
• Mow, W. S. et al. Association of antibody responses to microbial antigens and complications of small bowel Crohn's disease. Gastroenterology 126, 414–424 (2004).
  Article CAS PubMed Google Scholar
• Sartor, R. B. Microbial influences in inflammatory bowel diseases. Gastroenterology 134, 577–594 (2008).
  Article CAS PubMed Google Scholar
• Martin, H. M. et al. Enhanced Escherichia coli adherence and invasion in Crohn's disease and colon cancer. Gastroenterology 127, 80–93 (2004).
  Article CAS PubMed Google Scholar
• Subramanian, S. et al. Characterization of epithelial IL-8 response to inflammatory bowel disease mucosal, E. coli and its inhibition by mesalamine. Inflamm. Bowel Dis. 14, 162–175 (2008).
  Article PubMed Google Scholar
• Swidsinski, A. et al. Mucosal flora in inflammatory bowel disease. Gastroenterology 122, 44–54 (2002).
  Article PubMed Google Scholar
• Chassaing, B. & Darfeuille-Michaud, A. The commensal microbiota and enteropathogens in the pathogenesis of inflammatory bowel diseases. Gastroenterology 140, 1720–1728 e3 (2011).
  Article PubMed Google Scholar
• Gewirtz, A. T. Flag in the crossroads: flagellin modulates innate and adaptive immunity. Curr. Opin. Gastroenterol. 22, 8–12 (2006).
  Article CAS PubMed Google Scholar
• Wullaert, A. Role of NF-kappaB activation in intestinal immune homeostasis. Int. J. Med. Microbiol. 300, 49–56 (2010).
  Article CAS PubMed Google Scholar
• Pruteanu, M., Hyland, N. P., Clarke, D. J., Kiely, B. & Shanahan, F. Degradation of the extracellular matrix components by bacterial-derived metalloproteases: implications for inflammatory bowel diseases. Inflamm. Bowel Dis. 17, 1189–1200 (2010).
  Article PubMed Google Scholar
• Maccaferri, S. et al. Rifaximin modulates the colonic microbiota of patients with Crohn's disease: an in vitro approach using a continuous culture colonic model system. J. Antimicrob. Chemother. 65, 2556–2565 (2010).
  Article CAS PubMed Google Scholar
• Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl Acad. Sci. USA 104, 13780–13785 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Ott, S. J. & Schreiber, S. Reduced microbial diversity in inflammatory bowel diseases. Gut 55, 1207 (2006).
  CAS PubMed PubMed Central Google Scholar
• Mondot, S. et al. Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm. Bowel Dis. 17, 185–192 (2011).
  Article CAS PubMed Google Scholar
• Bibiloni, R., Mangold, M., Madsen, K. L., Fedorak, R. N. & Tannock, G. W. The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients. J. Med. Microbiol. 55, 1141–1149 (2006).
  Article PubMed Google Scholar
• Seksik, P. et al. Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 52, 237–242 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Chassaing, B. et al. Crohn disease--associated adherent-invasive, E. coli bacteria target mouse and human Peyer's patches via long polar fimbriae. J. Clin. Invest. 121, 966–975 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Darfeuille-Michaud, A. et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127, 412–421 (2004).
  Article PubMed Google Scholar
• Jia, W. et al. Is the abundance of Faecalibacterium prausnitzii relevant to Crohn's disease? FEMS Microbiol. Lett. 310, 138–144 (2010).
  Article CAS PubMed Google Scholar
• Willing, B. et al. Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease. Inflamm. Bowel Dis. 15. 653–660 (2009).
  Article PubMed Google Scholar
• Schippa, S. et al. Dominant genotypes in mucosa-associated Escherichia coli strains from pediatric patients with inflammatory bowel disease. Inflamm. Bowel Dis. 15, 661–672 (2009).
  Article PubMed Google Scholar
• Petersen, A. M. et al. A phylogenetic group of Escherichia coli associated with active left-sided inflammatory bowel disease. BMC Microbiol. 9, 171 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• Mitchell, D. N. & Rees, R. J. Agent transmissible from Crohn's disease tissue. Lancet 2, 168–171 (1970).
  Article CAS PubMed Google Scholar
• Dessein, R., Rosenstiel, P. & Chamaillard, M. Debugging the intestinal microbiota in IBD. Gastroenterol. Clin. Biol. 33 (Suppl. 3), S131–S136 (2009).
  Article PubMed Google Scholar
• Hollander, D. et al. Increased intestinal permeability in patients with Crohn's disease and their relatives. A possible etiologic factor. Ann. Intern. Med. 105, 883–885 (1986).
  Article CAS PubMed Google Scholar
• Keita, A. V. et al. Increased uptake of non-pathogenic, E. coli via the follicle-associated epithelium in longstanding ileal Crohn's disease. J. Pathol. 215, 135–144 (2008).
  Article CAS PubMed Google Scholar
• Heazlewood, C. K. et al. Aberrant mucin assembly in mice causes endoplasmic reticulum stress and spontaneous inflammation resembling ulcerative colitis. PLoS Med. 5, e54 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Swidsinski, A., Weber, J., Loening-Baucke, V., Hale, L. P. & Lochs, H. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J. Clin. Microbiol. 43, 3380–3389 (2005).
  Article PubMed PubMed Central Google Scholar
• Achkar, J. P. & Duerr, R. The expanding universe of inflammatory bowel disease genetics. Curr. Opin. Gastroenterol. 24, 429–434 (2008).
  Article PubMed Google Scholar
• Sydora, B. C., McFarlane, S. M., Doyle, J. S. & Fedorak, R. N. Neonatal exposure to fecal antigens reduces intestinal inflammation. Inflamm. Bowel Dis. 17, 899–906 (2011).
  Article PubMed Google Scholar
• Singhal, S. et al. The role of oral hygiene in inflammatory bowel disease. Dig. Dis. Sci. 56, 170–175 (2011).
  Article PubMed Google Scholar
• Matricon, J., Barnich, N. & Ardid, D. Immunopathogenesis of inflammatory bowel disease. Self Nonself 1, 299–309 (2010).
  Article PubMed PubMed Central Google Scholar
• Sobhani, I. et al. Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS ONE 6, e16393 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Swidsinski, A. et al. Association between intraepithelial Escherichia coli and colorectal cancer. Gastroenterology 115, 281–286 (1998).
  Article CAS PubMed Google Scholar
• de Martel, C. & Franceschi, S. Infections and cancer: established associations and new hypotheses. Crit. Rev. Oncol. Hematol. 70, 183–194 (2009).
  Article PubMed Google Scholar
• Chung, K. T., Stevens, S. E. Jr & Cerniglia, C. E. The reduction of azo dyes by the intestinal microflora. Crit. Rev. Microbiol. 18, 175–190 (1992).
  Article CAS PubMed Google Scholar
• Walker, A. W. et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 5, 220–230 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Candela, M. et al. Human intestinal microbiota: cross-talk with the host and its potential role in colorectal cancer. Crit. Rev. Microbiol. 37, 1–14 (2011).
  Article CAS PubMed Google Scholar
• Breuer, N. & Goebell, H. The role of bile acids in colonic carcinogenesis. Klin. Wochenschr. 63, 97–105 (1985).
  Article CAS PubMed Google Scholar
• Hope, M. E., Hold, G. L., Kain, R. & El-Omar, E. M. Sporadic colorectal cancer—role of the commensal microbiota. FEMS Microbiol. Lett. 244, 1–7 (2005).
  Article CAS PubMed Google Scholar
• Zhang, M. M., Cheng, J. Q., Xia, L., Lu, Y. R. & Wu, X. T. Monitoring intestinal microbiota profile: a promising method for the ultraearly detection of colorectal cancer. Med. Hypotheses 76, 670–672 (2011).
  Article PubMed Google Scholar
• Fallani, M. et al. Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres. Microbiology 157, 1385–1392 (2011).
  Article CAS PubMed Google Scholar
• Shen, Q., Chen, Y. A., Tuohy, K. M. A comparative in vitro investigation into the effects of cooked meats on the human faecal microbiota. Anaerobe 16, 572–577 (2010).
  Article CAS PubMed Google Scholar
• Vulevic, J., Rastall, R. A. & Gibson, G. R. Developing a quantitative approach for determining the in vitro prebiotic potential of dietary oligosaccharides. FEMS Microbiol. Lett. 236, 153–159 (2004).
  Article CAS PubMed Google Scholar
• Bodera, P. Influence of prebiotics on the human immune system (GALT). Recent Pat. Inflamm. Allergy Drug Discov. 2, 149–153 (2008).
  Article CAS PubMed Google Scholar
• Schley, P. D. & Field, C. J. The immune-enhancing effects of dietary fibres and prebiotics. Br. J. Nutr. 87 (Suppl. 2), S221–S230 (2002).
  Article CAS PubMed Google Scholar
• Pothoulakis, C. Review article: anti-inflammatory mechanisms of action of Saccharomyces boulardii. Aliment. Pharmacol. Ther. 30, 826–833 (2009).
  Article CAS PubMed Google Scholar
• D'Inca, R. et al. Rectal administration of Lactobacillus casei DG modifies flora composition and Toll-like receptor expression in colonic mucosa of patients with mild ulcerative colitis. Dig. Dis. Sci. 56, 1178–1187 (2011).
  Article PubMed Google Scholar
• Gareau, M. G., Sherman, P. M. & Walker, W. A. Probiotics and the gut microbiota in intestinal health and disease. Nat. Rev. Gastroenterol. Hepatol. 7, 503–514 (2010).
  Article PubMed PubMed Central Google Scholar
• Oelschlaeger, T. A. Mechanisms of probiotic actions—a review. Int. J. Med. Microbiol. 300, 57–62 (2010).
  Article CAS PubMed Google Scholar
• Damaskos, D. & Kolios, G. Probiotics and prebiotics in inflammatory bowel disease: microflora 'on the scope'. Br. J. Clin. Pharmacol. 65, 453–467 (2008).
  Article PubMed PubMed Central Google Scholar
• Silverman, M. S., Davis, I. & Pillai, D. R. Success of self-administered home fecal transplantation for chronic Clostridium difficile infection. Clin. Gastroenterol. Hepatol. 8, 471–473 (2010).
  Article PubMed Google Scholar
• Sproule-Willoughby, K. M. et al. In vitro anaerobic biofilms of human colonic microbiota. J. Microbiol. Methods 83, 296–301 (2010).
  Article CAS PubMed Google Scholar