The Gut Microbiota in Inflammatory Bowel Disease

Gastroenterology Clinics of North America

Volumn 46, Issue 1, 2017, Pages 143-154

  Sheehan, Donal ^a   Shanahan, Fergus ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Crohn's disease; Fecal microbial transplantation; Inflammatory bowel disease; Microbiota; Ulcerative colitis

Indexed keywords

PREBIOTIC AGENT; PROBIOTIC AGENT;

ASPERGILLUS; AUTOPHAGY; BACTERIOPHAGE; BIFIDOBACTERIACEAE; CROHN DISEASE; ENTEROBACTERIACEAE; ENVIRONMENTAL FACTOR; ESCHERICHIA COLI; FAECALIBACTERIUM PRAUSNITZII; FECAL MICROBIOTA TRANSPLANTATION; FUSOBACTERIACEAE; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HUMAN; IMMUNE RESPONSE; IMMUNOREGULATION; INFLAMMATORY BOWEL DISEASE; INTESTINE FLORA; LIFESTYLE; MICROBIAL DIVERSITY; MYCOBIOME; NONHUMAN; NOROVIRUS; PASTEURELLA; PATHOGENESIS; RANDOMIZED CONTROLLED TRIAL (TOPIC); REGULATORY T LYMPHOCYTE; REVIEW; RISK ASSESSMENT; RISK FACTOR; TREATMENT DURATION; TREATMENT OUTCOME; TREATMENT RESPONSE; ULCERATIVE COLITIS; ENVIRONMENTAL EXPOSURE; GASTROINTESTINAL TRACT; GENETICS; IMMUNOLOGY; MICROBIOLOGY; PHYSIOLOGY; VIROLOGY;

ENVIRONMENTAL EXPOSURE; FECAL MICROBIOTA TRANSPLANTATION; GASTROINTESTINAL MICROBIOME; GASTROINTESTINAL TRACT; HUMANS; INFLAMMATORY BOWEL DISEASES;

EID: 85008502005     PISSN: 08898553     EISSN: 15581942     Source Type: Journal    
DOI: 10.1016/j.gtc.2016.09.011     Document Type: Review

References (50)

1. 1 Kostic, A.D., Xavier, R.J., Gevers, D., The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 146 (2014), 1489–1499.
2. 2 Huttenhower, C., Kostic, A.D., Xavier, R.J., Inflammatory bowel disease as a model for translating the microbiome. Immunity 40 (2014), 843–854.
3. 3 Dalal, S.R., Chang, E.B., The microbial basis of inflammatory bowel diseases. J Clin Invest 124 (2014), 4190–4196.
4. 4 de Souza, H.S., Fiocchi, C., Immunopathogenesis of IBD: current state of the art. Nat Rev Gastroenterol Hepatol 13 (2016), 13–27.
5. 5 Shanahan, F., The gut microbiota-a clinical perspective on lessons learned. Nat Rev Gastroenterol Hepatol 9 (2012), 609–614.
6. 6 Buttớ, L.F., Haller, D., Dysbiosis in intestinal inflammation: cause or consequence. Int J Med Microbiol 306:5 (2016), 302–309.
7. 7 Gensollen, T., Iyer, S.S., Kasper, D.L., et al. How colonization by microbiota in early life shapes the immune system. Science 352:6285 (2016), 539–544.
8. 8 Bernstein, C.N., Shanahan, F., Disorders of a modern lifestyle: reconciling the epidemiology of inflammatory bowel diseases. Gut 57:9 (2008), 1185–1191.
9. 9 Shanahan, F., Sheehan, D., Microbial contributions to chronic inflammation and metabolic disease. Curr Opin Clin Nutr Metab Care 19 (2016), 257–262.
10. 10 Bloomfield, S.F., Rook, G.A., Scott, E.A., et al. Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene. Perspect Public Health 136 (2016), 213–224.
11. 11 Quévrain, E., Maubert, M.A., Michon, C., et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease. Gut 65 (2016), 415–425.
12. 12 Chu, H., Khosravi, A., Kusumawardhani, I.P., et al. Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science 352 (2016), 1116–1120.
13. 13 Cadwell, K., Liu, J.Y., Brown, S.L., et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 456 (2008), 259–263.
14. 14 Hand, T.W., Dos Santos, L.M., Bouladoux, N., et al. Acute gastrointestinal infection induces long-lived microbiota-specific T cell responses. Science 337:6101 (2012), 1553–1556.
15. 15 Fonseca, D.M., Hand, T.W., Han, S.J., et al. Microbiota-dependent sequelae of acute infection compromise tissue-specific immunity. Cell 163:2 (2015), 354–366.
16. 16 Shanahan, F., Quigley, E.M., Manipulation of the microbiota for treatment of IBS and IBD-challenges and controversies. Gastroenterology 146 (2014), 1554–1563.
17. 17 Bothin, C., Midtvedt, T., The role of gastrointestinal microflora in postsurgical adhesion formation–a study in germfree rats. Eur Surg Res 24 (1992), 309–312.
18. 18 Mourelle, M., Salas, A., Guarner, F., et al. Stimulation of transforming growth factor beta1 by enteric bacteria in the pathogenesis of rat intestinal fibrosis. Gastroenterology 114 (1998), 519–526.
19. 19 Van Tol, E.A.F., Holt, L., Ling Li, F., et al. Bacterial cell wall polymers promote intestinal fibrosis by direct stimulation of myofibroblasts. Am J Physiol 277 (1999), G245–G255.
20. 20 Rigby, R.J., Hunt, M.R., Scull, B.P., et al. A new animal model of postsurgical bowel inflammation and fibrosis: the effect of commensal microflora. Gut 58 (2009), 1104–1112.
21. 21 Shanahan, F., The colonic microbiota in health and disease. Curr Opin Gastroenterol 29 (2013), 49–54.
22. 22 Gevers, D., Kugathasan, S., Denson, L.A., et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15 (2014), 382–392.
23. 23 Darfeuille-Michaud, A., Boudeau, J., Bulois, P., et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127 (2004), 412–421.
24. 24 Morgan, X.C., Tickle, T.L., Sokol, H., et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol, 13, 2012, R79.
25. 25 Martinez-Medina, M., Aldeguer, X., Lopez-Siles, M., et al. Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn's disease. Inflamm Bowel Dis 15 (2009), 872–882.
26. 26 Chassaing, B., Rolhion, N., de Vallee, A., 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 (2011), 966–975.
27. 27 Lapaquette, P., Glasser, A.L., Huett, A., et al. Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly. Cell Microbiol 12 (2010), 99–113.
28. 28 Sadaghian Sadabad, M., Regeling, A., de Goffau, M.C., et al. The ATG16L1-T300A allele impairs clearance of pathosymbionts in the inflamed ileal mucosa of Crohn's disease patients. Gut 64 (2015), 1546–1552.
29. 29 Sokol, H., Pigneur, B., Watterlot, L., et al. 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 (2008), 16731–16736.
30. 30 Sonnenburg, E.D., Smits, S.A., Tikhonov, M., et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529 (2016), 212–215.
31. 31 Dalmasso, M., Hill, C., Ross, R.P., Exploiting gut bacteriophages for human health. Trends Microbiol 22 (2014), 399–405.
32. 32 Kernbauer, E., Ding, Y., Cadwell, K., An enteric virus can replace the beneficial function of commensal bacteria. Nature 516 (2014), 94–98.
33. 33 Weinbauer, M.G., Ecology of prokaryotic viruses. FEMS Microbiol Rev 28 (2004), 127–181.
34. 34 Rodriguez-Valera, F., Martin-Cuadrado, A.B., Rodriguez-Brito, B., et al. Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7 (2009), 828–836.
35. 35 Lepage, P., Colombet, J., Marteau, P., et al. Dysbiosis in inflammatory bowel disease: a role for bacteriophages?. Gut 57 (2008), 424–425.
36. 36 Wagner, J., Maksimovic, J., Farries, G., et al. Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing. Inflamm Bowel Dis 19 (2013), 1598–1608.
37. 37 Norman, J.M., Handley, S.A., Baldridge, M.T., et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160 (2015), 447–460.
38. 38 Minot, S., Sinha, R., Chen, J., et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res 21 (2011), 1616–1625.
39. 39 Modi, S.R., Lee, H.H., Spina, C.S., et al. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499 (2013), 219–222.
40. 40 Mukherjee, P.K., Sendid, B., Hoarau, G., et al. Mycobiota in gastrointestinal diseases. Nat Rev Gastroenterol Hepatol 12 (2015), 77–87.
41. 41 Dollive, S., Peterfreund, G.L., Sherrill-Mix, S., et al. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol, 13, 2012, R60.
42. 42 Hoffmann, C., Dollive, S., Grunberg, S., et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One, 8, 2013, e66019.
43. 43 Ott, S.J., Kuhbacher, T., Musfeldt, M., et al. Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scand J Gastroenterol 43 (2008), 831–841.
44. 44 Moayyedi, P., Surette, M.G., Kim, P.T., et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology 149 (2015), 102–109.e6.
45. 45 Rossen, N.G., Fuentes, S., van der Spek, M.J., et al. findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology 149 (2015), 110–118.e4.
46. 46 Suskind, D.L., Brittnacher, M.J., Wahbeh, G., et al. Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn's disease. Inflamm Bowel Dis 21 (2015), 556–563.
47. 47 Gough, E., Shaikh, H., Manges, A.R., Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis 53 (2011), 994–1002.
48. 48 Kelly, C.R., Kahn, S., Kashyap, P., et al. Update on fecal microbiota transplantation 2015: indications, methodologies, mechanisms, and outlook. Gastroenterology 149 (2015), 223–237.
49. 49 Vermeire, S., Joossens, M., Verbeke, K., et al. Donor species richness determines faecal microbiota transplantation success in inflamm bowel disease. J Crohns Colitis 10 (2016), 387–394.
50. 50 Petrof, E.O., Gloor, G.B., Vanner, S.J., et al. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome, 1, 2013, 3.