Microbiota in Inflammatory Bowel Disease Pathogenesis and Therapy: Is It All About Diet?

Nutr Clin Pract. 2015 Dec;30(6):760-79. doi: 10.1177/0884533615606898. Epub 2015 Oct 9.


Inflammatory bowel disease (IBD), including ulcerative colitis, Crohn's disease, and unclassified IBD, continues to cause significant morbidity. While its incidence is increasing, no clear etiology and no cure have yet been discovered. Recent findings suggest that IBD may have a multifactorial etiology, where complex interactions between genetics, epigenetics, environmental factors (including diet but also infections, antibiotics, and sanitation), and host immune system lead to abnormal immune responses and chronic inflammation. Over the past years, the role of altered gut microbiota (in both composition and function) in IBD pathogenesis has emerged as an outstanding area of interest. According to new findings, gut dysbiosis may appear as a key element in initiation of inflammation in IBD and its complications. Moreover, complex metagenomic studies provide possibilities to distinguish between IBD types and appreciate severity and prognosis of the disease, as well as response to therapy. This review provides an updated knowledge of recent findings linking altered bacterial composition and functions, viruses, and fungi to IBD pathogenesis. It also highlights the complex genetic, epigenetic, immune, and microbial interactions in relation to environmental factors (including diet). We overview the actual options to manipulate the altered microbiota, such as modified diet, probiotics, prebiotics, synbiotics, antibiotics, and fecal transplantation. Future possible therapies are also included. Targeting altered microbiota could be the next therapeutic personalized approach, but more research and well-designed comparative prospective studies are required to formulate adequate directions for prevention and therapy.

Keywords: antibiotics; diet; enteral nutrition; epigenetics; fecal transplantation; genetics; inflammatory bowel disease; microbiome; microbiota; mycobiome; probiotics; virome.

Publication types

  • Review

MeSH terms

  • Gastrointestinal Microbiome*
  • Humans
  • Inflammatory Bowel Diseases / microbiology*
  • Inflammatory Bowel Diseases / therapy*
  • Prebiotics*
  • Probiotics / therapeutic use*


  • Prebiotics