Individuals with a genetic predisposition to Crohn’s disease develop aberrant immune responses to environmental triggers. The gastrointestinal microbiota is increasingly recognized to play an important role in the development of Crohn’s disease. Decrease in global gut microbial diversity and specific bacterial alterations have been implicated in Crohn’s disease. Advances in sequencing techniques and bioinformatics and correlation with host genetics continue to improve insight into the structure and function of the microbial community and interactions with the host immune system. This article summarizes the existing literature on the role of the gut microbiome and its manipulation in the development and management of Crohn’s disease.
Key points
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Patients with Crohn’s disease have decreased microbial diversity, which plays an important role in the pathogenesis of Crohn’s disease.
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Microbial restoration therapies are being studied for management of Crohn’s disease and may be an adjunct to standard therapies in the future.
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It may be feasible to modify the gut microbiota community structure or function to treat patients with Crohn’s disease with targeted therapies via individual agents, such as probiotics, bacterial consortia, or even dietary manipulation.
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Fecal microbiota transplantation should not be performed for Crohn’s disease other than in research settings.
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A better understanding of host-microbe interactions in patients with Crohn’s disease may help improve management of these patients.

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