Inflammatory bowel disease: Could your microbiome be involved?

Author: Bianca Maree-Harrington

11 January 2019 Health Conditions Inflammatory Bowel Disease
Women lying down suffering from irritable bowel disease

Until recently, inflammatory bowel diseases were primarily considered as autoimmune conditions, however emerging evidence now suggests that the gut microbiome plays a critical role in triggering Crohn’s disease and ulcerative colitis.

How is the gut microbiome involved in inflammatory bowel diseases (IBD)?

The two main forms of IBD, Crohn’s disease and Ulcerative Colitis, were previously thought to have their foundation in an immune-mediated response1. This line of thinking is shifting, as growing research indicates that changes to your gut microbiome may play a pivotal role in the presentation of IBD due to higher levels of localised inflammation which trigger the autoimmune response2.

How microbial changes and fibre are involved in the IBD inflammatory process

A healthy, balanced microbiome breaks down fibre into beneficial metabolites associated with good health outcomes. Not consuming sufficient dietary fibre can shift the composition of your microbiome unfavourably and promote species which produce pro-inflammatory compounds, as is the case in IBD.

When there is inadequate fibre in your diet, your microbiome reverts to protein as its main fuel source. The bacterial species that break down protein then set to work breaking down these proteins which results in the production of a variety of compounds, some of which promote inflammation in the body3,4. Also, while most protein is absorbed by your body, any excess protein will progress to feed your gut microbiome, which can further contribute to inflammation in the body.

Research supports this theory as low levels of Faecalibacterium and Roseburia species, which are well-known butyrate producers, are a common finding among patients who suffer from IBD5. The short chain fatty acid butyrate is the main fuel source for gut cells and has anti-inflammatory effects6. Furthermore, Akkermansia muciniphila, a well-researched bacterial species residing in the mucus lining of the gut can be observed at lower levels in IBD sufferers7. Mucus turnover is a normal part of our gut function and the Akkermansia muciniphila species plays an important role in regulating mucus turnover8.

How can we alter our gut microbiome composition?

A major factor that influences the composition and activity of our microbiome is our diet – what we eat fuels our microbiome and the different species that make up our microbial community.

Fibre plays an integral role in maintaining a healthy microbial balance – this is especially relevant in the case of IBD. This is because fibre-consuming bacteria are responsible for producing important by-products such as short-chain fatty acids, which play an important role in keeping your gut healthy3. Short-chain fatty acids, are involved in various bodily functions including:

  • reducing inflammation
  • regulating the immune system
  • maintaining the intestinal cell barrier
  • the absorption of nutrition from food
  • maintaining glucose stability
  • regulating appetite
  • providing fuel for intestinal cells

Fibre can be found in whole plant-based foods such as wholegrain cereals, fruit, vegetables, nuts, seeds, pulses and legumes. Studies have shown that dietary factors can influence the risk of developing IBD and contribute to the number of IBD presentations with intestinal inflammation9. One study found that participants consuming higher servings of vegetables and wholegrain cereals were less likely to have Crohn’s Disease while those consuming more servings of fruit and bean/legumes were less likely to have Ulcerative Collitis10.


Although further research is needed to fully understand the role of the microbiome and dietary interventions in the management of Inflammatory Bowel Diseases, these findings provide a positive outlook for IBD sufferers and the potential for earlier diagnosis and intervention. Furthermore, it raises the prospect that altering gut microbiome composition can reduce an individual’s risk of developing Crohn’s disease and ulcerative colitis.

If you’re interested in learning about the bacterial species in your gut and your personal microbiome’s potential to digest protein and fibre, a Microba InsightTM gut microbiome test will help you discover key insights into your unique gut microbiome and what this might mean for your health.


  1. Wen, Z., & Fiocchi, C. (2004). Inflammatory Bowel Disease: Autoimmune or Immune-mediated Pathogenesis? Clinical and Developmental Immunology, 11(3-4), 195–204.
  2. Matsuoka, K. & Kanai, T. The Gut Microbiota and Inflammatory Bowel Disease. Semin Immunopathol (2015) 37: 47.
  3. Makki, K., Deehan, E.C., Walter, J. and Backhed, F. (2018). The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host & Microbe, 23 (6): p705-715.
  1. Conlon, M.A. and Bird, A. R. (2015). The Impact of Diet and Lifestyle on Gut Microbiota and Human Health. Nutrients,7 (1): 17-44.
  2. Machiels, K., Joossens, M., Sabino, J., De Preter, V., Arijs, I., Eeckhaut, V., ... & Ferrante, M. (2014). A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut, 63(8), 1275-1283.
  3. Fava, F., & Danese, S. (2011). Intestinal microbiota in inflammatory bowel disease: friend of foe? World journal of gastroenterology, 17(5), 557-66.
  4. Ott, S. J., Musfeldt, M., Wenderoth, D. F., Hampe, J., Brant, O., Fölsch, U. R., ... & Schreiber, S. (2004). Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut, 53(5), 685-693.
  5. Everard, A., Belzer. C., Geurts, L., Ouwerkerk, J. P., Druart, C. et al., PNAS May 28, 2013 110 (22) 9066-9071;
  6. Knight-Sepulveda, K., Kais, S., Santaolalla, R., & Abreu, M. T. (2015). Diet and Inflammatory Bowel Disease. Gastroenterology & hepatology, 11(8), 511-20.
  7. Declercq, V., Langille, M. G., & Limbergen, J. V. (2018). Differences in adiposity and diet quality among individuals with inflammatory bowel disease in Eastern Canada. Plos One, 13(7).