The gut microbiota in IBD


IBD—ulcerative colitis and Crohn's disease—is emerging as a worldwide epidemic. An association between the increased incidence of IBD and environmental factors linked to socioeconomic development has been persistently detected in different parts of the world. The lifestyle in developed countries might impair the natural patterns of microbial colonization of the human gut. The interaction of microbes with mucosal immune compartments in the gut seems to have a major role in priming and regulating immunity. In IBD, mucosal lesions are generated by an excessive or dysregulated immune response against commensal microbes in the gut. In individuals with a genetic susceptibility to IBD, abnormal microbial colonization of the gastrointestinal tract might be the origin of such dysregulation. Developments in gene-sequencing technologies, as well as increased availability of powerful bioinformatic tools, have enabled novel insights into the microbial composition of the human gut microbiota and the effect of microbial communities on human physiology and disease. Studies that used these technologies indicate that dysbiosis (that is, abnormal microbiota composition) and decreased complexity of the gut microbial ecosystem are common features in patients with Crohn's disease or ulcerative colitis. Whether such changes are a cause or a consequence of the disease remains to be elucidated.

Key Points

  • Environmental factors are necessary contributors to the pathogenesis of IBD—most individuals with genetic susceptibility do not develop the disease—and are primarily responsible for its growing incidence around the globe

  • The lifestyle in developed countries can be linked with alterations in the microbial colonization of the human gut

  • Microbial colonization has an important effect on the instruction and regulation of the immune system

  • The gut microbiota is an essential factor in driving inflammation and the development of mucosal lesions in IBD; certain microbes exacerbate inflammation, but some others mitigate inflammation

  • Dysbiosis and decreased complexity of the gut microbial ecosystem are common features in patients with IBD

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Figure 1: Suggested model of perpetuation of intestinal inflammation in IBD.
Figure 2: Technologies to investigate the gut microbiota.
Figure 3: Dysbiosis in ulcerative colitis based on data by Lepage et al.57 from 62 participants.
Figure 4: Reduction of bacterial diversity in patients with Crohn's disease based on data by Manichanh et al.71 from 12 participants.


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The authors received funding from the European Commission Seventh Framework Programme (MetaHIT, grant agreement HEALTH-F4-2007-201052), and Fondo de Investigaciones Sanitarias (FIS PI10/00902, Ministerio de Ciencia e Innovacion, Spain). CIBEREHD is funded by the Instituto de Salud Carlos III (Madrid, Spain).

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All authors contributed equally to all aspects of this article.

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Correspondence to Francisco Guarner.

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Manichanh, C., Borruel, N., Casellas, F. et al. The gut microbiota in IBD. Nat Rev Gastroenterol Hepatol 9, 599–608 (2012).

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