IBD is an immune-mediated condition that causes chronic inflammation in the digestive tract. The two main types are ulcerative colitis (UC) and Crohn’s disease (CD). There’s no single cause. Genetics, immune dysregulation, gut dysbiosis, a Western-style diet low in fibre and high in ultra-processed food, antibiotic use, smoking (for Crohn’s), stress and poor sleep can all play a part.

Research is also showing that UC may have a true autoimmune component. People who go on to develop UC can carry antibodies against integrin αvβ6, a protein that helps hold the gut barrier together, and these antibodies can appear up to 10 years before diagnosis. It’s another sign of how central the gut barrier is in IBD.

Ulcerative colitis and Crohn’s disease

UC and Crohn’s share many symptoms, including abdominal pain and cramping, diarrhoea, urgency, a feeling of incomplete emptying, blood or mucus in the stool, fatigue, poor appetite, weight loss and sometimes fever. Both follow a pattern of flares and remission, and both can range from mild to severe. They are still quite different conditions.

Ulcerative colitis affects the inner lining of the large intestine. It starts in the rectum and spreads upwards in one continuous stretch. The ulcers can bleed and produce mucus or pus, and ongoing blood loss can lead to iron deficiency anaemia.

Crohn’s disease can affect any part of the digestive tract, from the mouth to the anus, but most often involves the end of the small intestine (the ileum) and the colon. Inflammation can go through the full thickness of the bowel wall and appears in patches, with healthy sections in between. When the small intestine is affected, it can interfere with absorbing nutrients such as iron, vitamin B12, vitamin D and fats.

The gut microbiome in IBD

The gut microbiome is one of the most studied areas in IBD research, and the patterns are consistent. People with Crohn’s and UC tend to have:

• Lower diversity. Fewer different types of bacteria, which makes the gut ecosystem less resilient.
• Fewer butyrate producers. Bacteria like Faecalibacterium prausnitzii turn fibre into butyrate, which feeds the cells lining the bowel and helps calm the immune system. F. prausnitzii is often low in Crohn’s, and lower levels have been linked with a higher risk of the disease coming back after surgery.
• More inflammatory bacteria. Some species thrive in an inflamed gut and keep the immune system switched on.
• A weaker gut barrier. The protective mucus layer thins and the gut lining becomes more permeable, so bacteria come into closer contact with immune cells.

It becomes a cycle. Dysbiosis drives inflammation, and inflammation changes the environment in a way that favours more dysbiosis. I explain this process in more detail in How Your Gut Microbiome Drives Inflammation in Autoimmune Disease.

SIBO is common too. A 2025 analysis found around 31% of people with IBD had small intestinal bacterial overgrowth, much higher than in healthy people. The risk was higher after bowel surgery and in stricturing Crohn’s. SIBO can cause bloating, gas and diarrhoea that look a lot like a flare, so it’s worth testing when symptoms don’t match your inflammation markers.

Is IBD different from IBS?

Yes. The symptoms can look similar, but they are very different conditions.

IBD is driven by the immune system. It causes inflammation and damage to the gut lining that can be seen on colonoscopy and biopsy, and inflammation markers in the blood and stool are usually raised.

IBS is a disorder of gut-brain interaction. There’s no visible damage on colonoscopy and inflammation markers are usually normal. Gut sensitivity, motility changes, dysbiosis, SIBO, food triggers, stress and past gut infections can all play a part.

It’s possible to have both. Some people with IBD in remission still have IBS-type symptoms, which is why Microbiome testing is so important. Microbiome testing shows where the imbalance of bacteria is and we can then use selective prebiotics and probiotics to favourably change the composition of the gut microbiota.

How is IBD diagnosed and what happens next?

Diagnosis is done by your gastroenterologist who will use a combination of tests:

• Blood tests to check for inflammation (such as CRP), anaemia and nutrient deficiencies like iron, vitamin B12 and vitamin D
• Faecal calprotectin, a stool test that measures inflammation in the bowel and helps tell IBD apart from IBS
• PCR Stool tests to rule out infection
• Colonoscopy with biopsy, the main test for confirming IBD and telling UC and Crohn’s apart
• Gastroscopy if Crohn’s may be affecting the upper digestive tract
• MRI, CT, bowel ultrasound or capsule endoscopy to look at the small intestine, which a colonoscopy can’t fully reach

Gut testing

Once IBD is diagnosed, the next question is what’s driving the inflammation in your gut. This is what I look at starting with a detailed history: when your symptoms began, how severe they are, and what makes them better or worse. I then use:

• Microbiome stool testing to see your diversity, which beneficial bacteria are missing or low, which inflammatory species are overgrown, and markers of gut barrier health
• SIBO breath testing if bloating, gas or diarrhoea don’t match your inflammation markers
• A review of your pathology, especially iron, B12, vitamin D and zinc

Managing IBD with AIP

There’s no cure for IBD, but diet, targeted supplements and lifestyle changes can ease symptoms, reduce the severity of flares and help you stay in remission for longer. This works alongside your medical treatment, not instead of it.

The Autoimmune Protocol (AIP) is an elimination and reintroduction diet that can be very effective at reducing inflammation. Foods that can trigger an immune response in some people (gluten and other grains, dairy, eggs, legumes, nightshades, nuts, seeds, refined sugar, alcohol and processed foods) are removed for a short period of time. The focus is on nutrient-dense fruit and vegetables, quality protein and healthy fats. Foods are then brought back one at a time to see what you actually react to. Stress management, sleep and movement are part of the protocol too.

IBD was the first condition AIP was studied in. In a pilot study of 15 people with active Crohn’s or UC, 73% were in clinical remission by week 6, and they stayed in remission through the rest of the study. Most participants were still on their usual medication, so AIP was used as an add-on.

Reintroduction and fibre

AIP is a short-term tool, and the reintroduction phase is the most important part. Your microbiome results show which beneficial bacteria are missing or low, which helps me prioritise the foods to bring back first. Fibre is usually the most important, because it feeds the bacteria that make butyrate, and butyrate is one of the main things that helps settle inflammation in the bowel. We start with gentle, cooked and soluble fibres and build up slowly.

A note on strictures. If you have Crohn’s with a narrowed section of bowel, high amounts of insoluble fibre (raw vegetables, skins, seeds, nuts and tough fibrous foods) can raise the risk of a blockage. International IBD dietary guidance recommends limiting insoluble fibre in this situation, so your plan needs to be adjusted around it.

Other things that help

International dietary guidance for IBD also suggests:

• Eating more oily fish such as salmon and sardines for omega-3s
• Eating plenty of fruit and vegetables
• Cutting back on ultra-processed foods, especially those containing emulsifiers like carrageenan, carboxymethylcellulose and polysorbate-80
• Reducing red and processed meat

It’s also important to correct nutrient deficiencies, especially iron, vitamin B12, selenium, vitamin D and zinc, which are common in IBD.

Ready to look deeper?

If you’ve been diagnosed with Crohn’s or ulcerative colitis and you’re still dealing with flares, bloating, fatigue or unpredictable bowels, your microbiome is a good place to start. In my Gut Program, we combine microbiome testing, SIBO breath testing when needed and a review of your pathology, then build a plan around what your gut actually needs.

Living with IBD and want support? Book a consultation with me here: https://dashboard.healthbank.io/practitioner/vicky-ellenport

References

Feng X, Hu J, Zhang X. Prevalence and predictors of small intestinal bacterial overgrowth in inflammatory bowel disease: a meta-analysis. Front Med (Lausanne). 2025;11:1490506. doi:10.3389/fmed.2024.1490506. https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2024.1490506/full

Konijeti GG, Kim N, Lewis JD, et al. Efficacy of the autoimmune protocol diet for inflammatory bowel disease. Inflamm Bowel Dis. 2017;23(11):2054-2060. doi:10.1097/MIB.0000000000001221. https://doi.org/10.1097/MIB.0000000000001221

Levine A, Rhodes JM, Lindsay JO, et al. Dietary guidance from the International Organization for the Study of Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2020;18(6):1381-1392. doi:10.1016/j.cgh.2020.01.046. https://doi.org/10.1016/j.cgh.2020.01.046

Livanos AE, Dunn A, Fischer J, et al. Anti-integrin αvβ6 autoantibodies are a novel biomarker that antedate ulcerative colitis. Gastroenterology. 2023;164(4):619-629. doi:10.1053/j.gastro.2022.12.042. https://pubmed.ncbi.nlm.nih.gov/36634824/

Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A. 2008;105(43):16731-16736. doi:10.1073/pnas.0804812105

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