Many people living with inflammatory bowel disease (IBD) know the frustration of ongoing bloating, wind, or loose stools even when blood tests and scans suggest their disease is quiet. One possible explanation, often overlooked, is small intestinal bacterial overgrowth (SIBO), a condition that can mimic or overlap with irritable bowel syndrome (IBS) and add an extra layer of symptoms on top of underlying gut disease.
What is SIBO?
The small intestine normally contains relatively few bacteria compared with the large intestine (colon). SIBO occurs when bacteria that usually live further down the digestive tract move upstream and multiply in the small intestine in excessive numbers. These bacteria ferment food, particularly carbohydrates, before the body has had a chance to digest and absorb it properly. This fermentation produces gas, most commonly hydrogen and sometimes methane, which contributes to bloating, abdominal discomfort, and altered bowel habit.
Why it matters for gut inflammation
SIBO is not, in itself, an inflammatory disease in the way Crohn’s disease or ulcerative colitis are. However, it can worsen how someone feels and can interact with an already sensitised gut. Excess bacteria in the small intestine can irritate the gut lining (the inner surface of the intestine that absorbs nutrients and forms a barrier against harmful substances), disrupt the balance of the gut microbiome (the community of bacteria and other microbes living in the digestive tract), and trigger low-grade immune activity. In people with IBD, this can make it harder to tell whether symptoms reflect active inflammation or a separate, overlapping problem, which matters because the two are managed very differently.
Key mechanisms
Bacterial fermentation and gas production
When bacteria ferment undigested sugars and fibres in the small intestine, they release gases that stretch the bowel wall. This stretching activates nerve endings, producing the bloating and cramping many people describe. Because these mechanisms are shared with IBS, a functional gut disorder defined by symptoms rather than visible damage, SIBO and IBS can look almost identical on the surface.
Altered gut motility
The small intestine relies on coordinated waves of muscle contraction, known as motility, to keep bacteria moving through and prevent them settling and multiplying. Conditions that slow this process, including some cases of IBD, previous bowel surgery, or nerve changes affecting the gut, can allow bacteria to accumulate. This is one reason SIBO is reported more often in people with Crohn’s disease, particularly after surgery involving the small intestine.
Structural changes in IBD
Crohn’s disease can cause strictures, narrowed sections of bowel caused by inflammation or scarring, which slow the transit of food and create pockets where bacteria can gather. Surgical removal of the ileocaecal valve (the valve between the small intestine and colon that normally limits bacteria moving backwards) can also make SIBO more likely, since this valve usually acts as a barrier.
Overlapping symptoms with IBS
Because bloating, wind, diarrhoea, and abdominal pain feature in both SIBO and IBS, clinicians often find it difficult to separate the two without specific testing, such as a hydrogen breath test that measures gas produced after drinking a sugar solution. Many people diagnosed with IBS, including some with quiescent IBD, may actually have undiagnosed SIBO contributing to their symptoms.
Malabsorption and nutrient impact
Bacterial overgrowth can interfere with the absorption of fats, vitamin B12, and certain carbohydrates, sometimes leading to unintentional weight loss or nutrient deficiencies. This is particularly relevant in IBD, where nutritional status is already a concern, and it reinforces the importance of accurate diagnosis rather than assuming all symptoms stem from disease flare.
It is important to stress that this article is not a substitute for medical assessment. Ongoing gut symptoms in someone with IBD do not automatically mean inflammation has returned. They may reflect SIBO, IBS-type symptoms, scar tissue, or another cause entirely, and distinguishing between these usually requires a clinician’s input and appropriate testing.
Practical Takeaways
- Keep a simple record of symptoms, including timing in relation to meals, to share with your gastroenterology team.
- Avoid self-diagnosing SIBO or IBS; ask your specialist about breath testing if symptoms persist despite controlled inflammation.
- Discuss any history of bowel surgery or strictures with your team, as these can raise SIBO risk.
- Do not start long-term antibiotics or restrictive diets without medical guidance, as both carry their own risks.
- Report unexplained weight loss or signs of nutrient deficiency promptly rather than assuming they relate to diet alone.
Conclusion
SIBO and IBS share overlapping symptoms that can complicate the picture for people already managing IBD, making it harder to know whether a flare, a functional issue, or bacterial overgrowth is behind ongoing discomfort. Recognising this overlap encourages a more measured, investigative approach rather than assuming every symptom means active disease. Long-term stability in IBD depends on accurate diagnosis alongside consistent monitoring, and SIBO is one of several factors worth ruling out when symptoms persist despite quiet inflammation. As always, any change in symptoms should be discussed with a gastroenterology team rather than managed alone.
References
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- Shah A, Talley NJ, Jones M, et al. Small intestinal bacterial overgrowth in irritable bowel syndrome: a systematic review and meta-analysis of case-control studies. Am J Gastroenterol. 2020;115(2):190-201. doi:10.14309/ajg.0000000000000504.
- Klaus J, Spaniol U, Adler G, et al. Small intestinal bacterial overgrowth mimicking acute flare as a pitfall in patients with Crohn’s disease. BMC Gastroenterol. 2009;9:61. doi:10.1186/1471-230X-9-61.
- Rana SV, Bhardwaj SB. Small intestinal bacterial overgrowth. Scand J Gastroenterol. 2008;43(9):1030-1037. doi:10.1080/00365520801947074.
- Ricci JER Junior, Chebli LA, Ribeiro TCDR, et al. Small-intestinal bacterial overgrowth is associated with concurrent intestinal inflammation but not with systemic inflammation in Crohn’s disease patients. J Clin Gastroenterol. 2018;52(6):530-536. doi:10.1097/MCG.0000000000000803.
- Bushyhead D, Quigley EMM. Small intestinal bacterial overgrowth: pathophysiology and its implications for clinical practice. Clin Gastroenterol Hepatol. 2022;20(2):219-230. doi:10.1016/j.cgh.2021.02.031.
This article is intended for informational and educational purposes only. It does not constitute medical advice and should not be used as a substitute for professional medical guidance, diagnosis, or treatment.