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IBD & The Microbiome

The range of disorders cumulatively known as IBD affects many people across the UK, and the human microbiome is involved in more ways than one. The question is, what can we do to support our microbiome?

Around 1 in 210 people in the UK have inflammatory bowel disease (IBD), a range of disorders which involve chronic inflammation of the gastrointestinal tract. The most prevalent ones are known as ulcerative colitis (UC) and Crohn’s disease. 

IBD can cause debilitating gut symptoms, including severe diarrhoea, bloating and abdominal pain, and blood in stools. It can also drive health issues beyond the gut, ranging from weight loss and nutritional deficiencies to joint pain and depression. Effective management of IBD is essential to improving an individual’s quality of life and minimising their risk of long-term complications. The microbiome can play a role in the development and continuation of the disease, and interventions to change it are showing promise as support alongside regular medications.  


Testing for the amount of the protein, calprotectin, in the stool is a helpful screening tool for identifying gut inflammation. If the levels are high, this can help facilitate further internal investigations to distinguish IBD from other conditions which cause similar abdominal symptoms, including irritable bowel syndrome (IBS), coeliac disease, endometriosis, and ovarian cancer. The amount of hidden blood in the stool, known as occult blood or ‘FIT’, is also a helpful screening tool which can trigger further investigations for IBD or bowel cancer. 


Once an IBD diagnosis and the necessary medical care is in place, it can be helpful to take a step back and look beyond the diagnosis.  

Taking into account the person as a whole and their life up until the point of diagnosis can unravel the combination of genetic, environmental, and immune factors which led to the formation of their IBD in the first place. Factors influencing the formation of IBD include genetic susceptibility, sleep and stress levels, vitamin D level, smoking, diet, and microbiome disruption.

adapted from Dordevic et al., 2021


One of the key patterns of imbalance underlying IBD is disruption to the colonies of microbes, especially bacteria and fungi, living within the digestive tract, which is sometimes termed ‘dysbiosis’. Given the stressors of modern life, this typically develops following high exposure to factors which disrupt the human microbiome, notably antibiotics, pesticides, low fibre intake, alcohol, and high stress.  

The gut dysbiosis identified in IBD usually involves an overgrowth of pathogenic (disease-causing microbes) or pathobiont (commensals which become pathogenic in specific circumstances) microbes, creating an excessive amount of inflammatory traffic in the gut. These may include the bacteria Clostridium difficile, the fungi Malassezia restricta, and hydrogen sulphide-producing bacteria such as Desulfovibrio spp., as well as other pattern changes.  

Bacteria from the oral microbiome may also play a role. High levels of Fusobacterium nucleatum in the gut, a commensal bacterium from the mouth, has been linked to the progression of inflammatory bowel disorders.  

Dysbiosis in IBD often involves a ‘missing microbe’ picture too, characterised by a low diversity and abundance of protective commensal bacteria, especially those which produce anti-inflammatory compounds called short-chain fatty acids (SCFAs), such as butyrate or acetate, including Faecalibacterium prausnitzii, Roseburia homini, and Bifidobacterium. Butyrate, for example, helps the gut wall to repair and to modulate inflammation. If intestinal butyrate production is low, the gut wall can become hyperpermeable and chronically inflamed through the loss of this microbiome-mediated healing mechanism. 

The gut microbiome can further drive gut barrier dysfunction when colonies of ‘mucin-degrading’ bacteria start to overgrow, usually when there is a low fibre intake. If you think about the gut wall as an iced cake, the epithelial barrier is the sponge and the icing is the mucus layer. A thick, plump intestinal mucus layer cushions and protects the gut wall from the contents of the gut lumen.  

When mucin-degrading bacteria such as Ruminococcus gnavus and -torques, overgrow, the mucus layer starts to thin and the gut wall becomes more exposed to pro-inflammatory signals from the gut microbes. When this scenario becomes chronic, aberrant inflammatory responses in the gut wall appear to become the norm, contributing to the gut wall damage we see in IBD and the characteristic high faecal calprotectin and FIT. Chronic inflammation can then perpetuate gut dysbiosis and gut barrier dysfunction, creating a vicious cycle. 


1. Microbiome testing

Private stool testing for those with IBD, guided by a healthcare provider (HCP), is the ideal gateway to personalised support. It can identify which patterns of host-microbiome disruption are relevant for each individual with IBD, which then enables safe, effective personalised microbiome interventions. Given the complexity of IBD, being guided by an HCP is ideal to help you navigate the complexity and receive the tailored support you deserve. It is also possible to assess the oral microbiome to gauge how oral health might be contributing to poor gut health. 

Learn more about GI EcologiX

2. Reduce exposure to stressors

Reduce exposure to stressors of the commensal gut microbiota and gut barrier, especially high stress, pesticides, preservatives, alcohol, and a highly processed, high animal fat, low fibre typical Western diet, while increasing your exposure to nourishing microbiome influences: 

3. Fibre

Ample consumption of a wide diversity of fibre (soluble and insoluble) is the cornerstone of ensuring a healthy commensal gut microbiome and increasing intestinal SCFA production. Aim for at least 30 different types of plant each week.  

This can be optimised through prebiotic fibre supplementation, ideally guided by microbiome stool test results. For example, partially hydrolysed guar gum (PHGG) increases intestinal butyrate producers and normalises bowel motility. Other options include galactoligosaccharide (GOS) which is an important prebiotic for Bifidobacterium, as well as colostrum which is a rich source of antimicrobial and immunosupportive peptides. Increasing your fibre intake slowly is important with IBD.


Bio.Me Prebio PHGG

Bio.Prebio GOS

Bio.Revive Colostrum

4. Polyphenols

From brightly coloured plants such as pomegranate, aronia berry, and citrus peel can have a prebiotic property, support a healthy mucosal barrier in the gut, and modulate inflammation.  MicrobiomeX ® (found in Bio.Me Essential) patented bitter orange bioflavonoid extract reduced faecal calprotectin in a human clinical trial. 

5. Probiotics

A wealth of human clinical research is now available showing the functional benefit of specific probiotic strains for IBD. Please note that probiotics are best avoided when immunocompromised and best guided by an HCP. Some of the most promising strains include: 

  • Enterococcus faecium Rosell®- 26 (R0026) with Bacillus subtilis Rosell®-179 (R0179) has been extensively studied in humans, appearing in over 140 clinical studies for its impact on gut health, especially in relation to ulcerative colitis, as well as IBS, small intestinal bacterial overgrowth (SIBO), and reflux. This strain combination can be found in our recently launched Bio.Me IB+.

Bio.Me IB+

  • The probiotic yeast, Saccharomyces boulardii, has shown promise in human clinical trials as an adjunctive support for both Crohn’s and ulcerative colitis, especially by helping to reduce C. difficile, improve the balance of commensal bacteria, and modulate gut inflammatory markers. 

Bio.Me S.Boulardii

  • The Ecologic ® Barrier Probiotics blend of carefully selected strains (B. bifidum W23, B. lactis W51 and W52, L. acidophilus W37, L. brevis W63, L. casei W56, L. salivarius W24, L. lactis W19 and W58) can improve the integrity of the gut barrier in vitro with human clinical trials showing systemic health benefits, including for mental health.  

Bio.Me Barrier

Microbiome support provides an individual with the opportunity to better understand the underlying drivers of their IBD, which can then empower them to make simple changes to help modulate these. Such a root cause approach can help individuals to better manage their IBD alongside conventional care and have a transformative impact on their lives.  

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