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The Gut Microbiome in Inflammatory Bowel Disease

Lessons Learned From Other Immune-Mediated Inflammatory Diseases

Knox, Natalie C. PhD1,2; Forbes, Jessica D. PhD3,4; Peterson, Christy-Lynn BSc1; Van Domselaar, Gary PhD1,2; Bernstein, Charles N. MD4,5

American Journal of Gastroenterology: July 2019 - Volume 114 - Issue 7 - p 1051–1070
doi: 10.14309/ajg.0000000000000305

There is a growing appreciation for the role of the gut microbiome in human health and disease. Aided by advances in sequencing technologies and analytical methods, recent research has shown the healthy gut microbiome to possess considerable diversity and functional capacity. Dysbiosis of the gut microbiota is believed to be involved in the pathogenesis of not only diseases that primarily affect the gastrointestinal tract but also other less obvious diseases, including neurologic, rheumatologic, metabolic, hepatic, and other illnesses. Chronic immune-mediated inflammatory diseases (IMIDs) represent a group of diseases that share many underlying etiological factors including genetics, aberrant immunological responses, and environmental factors. Gut dysbiosis has been reported to be common to IMIDs as a whole, and much effort is currently being directed toward elucidating microbiome-mediated disease mechanisms and their implications for causality. In this review, we discuss gut microbiome studies in several IMIDs and show how these studies can inform our understanding of the role of the gut microbiome in inflammatory bowel disease.

1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada;

2Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada;

3Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada;

4IBD Clinical and Research Centre, University of Manitoba, Winnipeg, Manitoba, Canada;

5Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.

Correspondence: Charles N. Bernstein, MD. E-mail:

SUPPLEMENTARY MATERIAL accompanies this paper at and

Received September 09, 2018

Accepted May 13, 2019

© The American College of Gastroenterology 2019. All Rights Reserved.
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