The onset of inflammatory bowel disease: could your microbiome be involved?

Author: Bianca Maree Harrington and Dr Alena Pribyl

03 May 2019 Health Conditions Inflammatory Bowel Disease
Women lying down suffering from irritable bowel disease

Emerging evidence suggests the gut microbiome may play a role in triggering the onset of inflammatory bowel diseases such as Ulcerative colitis and Crohn’s disease.

What is Inflammatory Bowel Disease (IBD)?

Crohn’s and Colitis Australia describes Inflammatory Bowel Disease (also known as IBD), as a group of conditions in which the intestines become chronically inflamed due to an abnormal immune response. The two main types of IBD are Ulcerative colitis and Crohn’s disease. Ulcerative colitis predominately impacts the lining of the large intestine (or colon), whereas Crohn’s disease can occur in any part of the intestines and can impact all layers of the intestinal wall. These conditions are deemed to be lifelong and can present themselves at any age.

Australia has one of the highest incidences of IBD worldwide, affecting 1 in 250 people, which is over 80,000 total. Currently, there is no cure for IBD, but it can be managed effectively under the supervision of a specialist medical practitioner to provide symptom relief and prevent future flare-ups1.

We see a healthier future for the many Australians affected by IBD. Find out how we're making a difference.

How could the gut microbiome be involved in the onset of IBD?

Although the exact cause of IBD is still unclear, it is thought that a combination of factors including genetics, environment, and lifestyle choices are involved. However, these factors do not completely explain IBD risk and recent research is now indicating that changes to the gut microbiome may also play a role in the onset of IBD2.

According to this research, compared to healthy people, the gut microbiome in those with IBD seem to have:

  • An increased potential to produce substances that promote inflammation, such as lipopolysaccharides3,4.
  • A reduced potential to produce substances that suppress inflammation, such as short chain fatty acids, known as butyrate3-5 and acetate4.
  • A lower microbial diversity5,.
  • And fewer gut microorganisms that can break down fibre4.

These findings seem to suggest that a lack of fibre in the diet may be involved in the changes to the gut microbiome of those with IBD. When gut microbes break down fibre, they primarily produce inflammation suppressing short chain fatty acids which are beneficial for many disease states including, but not limited to IBD. Specifically, butyrate assists by not only being the main fuel source for our gut cells, but also by helping to maintain the intestinal cell barrier, suppressing inflammation and regulating appetite6.

What role does diet play in the inflammatory process?

Foods we eat, that our body is not able to absorb, get passed to our large intestine where they fuel the various species in our gut microbiome. These fuel sources include excess protein and dietary fibre.

While most protein that we consume can be absorbed by our body, eating excessive amounts means that it cannot be completely absorbed and will then progress to the large intestine, where it feeds our protein digesting bacteria. Fibre follows a similar path, where fibre digesting bacteria end up producing beneficial short chain fatty acids, which contributes to a healthy gut. This makes fibre an integral part in maintaining a healthy microbial balance between protein digesting microbes and fibre digesting microbes.

fibre intake
Illustration of the how fibre relates to the production of short chain fatty acids and inflammation.

When there is an inadequate amount of fibre in our diet, the composition of our gut microbiome can shift unfavourably to species that use protein. These bacterial species that break down protein produce a variety of compounds, some of which promote inflammation in the body3,4. Subsequently, diet is a critical component of the composition and activity of our gut microbiome.

Our gut microbiome plays a fundamental role in our wellbeing. Learn More about your microbiome's digestion potential.

How can we alter our gut microbiome composition?

A diet full of diverse sources of fibre can maximise our gut bacteria’s potential to produce short chain fatty acids, which potentially increase our microbial diversity and are beneficial to our health6. These sources of fibre include:

  • Wholegrains
  • Fruits
  • Vegetables
  • Nuts
  • Seeds
  • Pulses
  • Legumes

One study in particular, found that participants consuming higher servings of vegetables and wholegrain cereals were less likely to have Crohn’s disease and those consuming more servings of fruit and beans/legumes were less likely to have Ulcerative colitis7.

However, while increasing fibre consumption may help reduce the risk of developing IBD, there is currently no evidence to suggest increasing fibre intake will alleviate symptoms in people already diagnosed with IBD. Due to the complexities of each individual case of IBD, we suggest consulting with a treating specialist before making any modifications to diet.


Although further study is required to fully understand the role of the gut microbiome in Inflammatory Bowel Disease, emerging research suggests that by manipulating the gut microbiome through diet, it may be possible to reduce an individual’s risk of developing IBD in the future. Additionally, these associations suggest that the gut microbiome has the potential to be a possible source for new therapeutics and diagnostics.

We aim to investigate the role the microbiome may play in the onset of IBD. Find out more about the research Microba is undertaking.


If you’re interested in learning about the bacterial species in your gut, along with your personal microbiome’s ability to digest fibre and produce short chain fatty acids, a Microba Insight™ test could help you discover these key insights.


This microbiome test is not intended to be used to diagnose or treat medical conditions. A full disclaimer is available here.


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