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The Gut Microbiome as a Target for IBD Treatment: Are We There Yet?


Purpose of review

This review aims to highlight recent research on the gut microbiome in IBD and the application of microbiome-modulating therapies for the treatment of IBD including the use of the microbiome as an indicator for disease severity and treatment response.

Recent findings

Despite the high number of gut microbiome studies and emerging evidence supporting the gut microbiome’s involvement in disease pathogenesis, no single microorganism has been identified as a pathogenic agent in IBD. Retrospective studies and meta-analyses on antibiotic use in ulcerative colitis and Crohn’s disease and long-term outcomes are conflicting. Similarly, the use of probiotics for the treatment of IBD remains inconclusive; however, some encouraging results are emerging as microbial concoctions are optimized to include beneficial bacterial strains. Fecal microbial transplantation (FMT) is currently emerging as one of the more promising microbiome-modulating IBD therapies. FMT studies in ulcerative colitis have shown improved remission rates compared to placebo; however, relatively small study sample sizes and varied treatment methods, limit definitive conclusions.


With clear evidence of an IBD gut dysbiosis, novel therapies to treat and prevent disease relapse will undoubtedly require a microbiome-modulating approach. The complexity and variability of IBD disease pathogenesis (disease phenotype, gut microbiome, host genetic susceptibility, and environmental factors) will likely require a personalized and multidimensional treatment approach where microbiome-modulating therapy is coupled with other therapies to target other IBD disease components.

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Crohn’s disease


Clostridium difficile infection


exclusive enteral nutrition (EEN)


inflammatory bowel disease


fecal microbiota transplantation


microbial dysbiosis index


specific carbohydrate diet


ulcerative colitis


Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

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Gary Van Domselaar receives operational funding from the Public Health Agency of Canada and has also received research support from the Multiple Sclerosis Society of Canada, the Canadian Institutes of Health Research, The National Sciences and Engineering Research Council, and Genome Canada.

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Correspondence to Charles N. Bernstein MD.

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Charles Bernstein is supported in part by the Bingham Chair in Gastroenterology. He has served on advisory boards of Abbvie Canada, Ferring Canada, Janssen Canada, Pfizer Canada, Shire Canada, Takeda Canada, Napo Pharmaceuticals, and has consulted to 4D Pharm and Mylan Pharmaceuticals. He has received educational grants from Abbvie Canada, Janssen Canada, Pfizer Canada, Shire Canada, and Takeda Canada.

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Knox, N.C., Forbes, J.D., Van Domselaar, G. et al. The Gut Microbiome as a Target for IBD Treatment: Are We There Yet?. Curr Treat Options Gastro 17, 115–126 (2019).

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  • Inflammatory bowel disease
  • Gut microbiota
  • Fecal microbiota transplant
  • Antibiotics
  • Probiotics
  • Prebiotics
  • Gut microbiome
  • Microbiota-modifying treatment