SIBO and Ulcerative Colitis: Could Bacterial Overgrowth Be Part of Your Picture?

Living with ulcerative colitis (UC) is already demanding enough. The unpredictability, the flares, the ongoing management, it takes considerable energy. So when symptoms such as bloating, excessive gas, and abdominal discomfort appear or worsen, the assumption is usually straightforward: it must be the UC.

That assumption is understandable, but it isn’t always correct. Research increasingly shows that people with UC carry a significantly elevated risk of developing Small Intestinal Bacterial Overgrowth (SIBO), and that the two conditions can produce symptoms so similar that one is routinely mistaken for the other. (Feng et al. 2025) For someone whose UC appears well managed on paper but who continues to experience daily digestive symptoms, SIBO as a complicating factor deserves serious consideration.

This piece explores what the research tells us about the UC-SIBO connection, why UC creates conditions that predispose to bacterial overgrowth, how the two conditions can be distinguished, and what a comprehensive assessment might look like.

A brief note on SIBO

Small Intestinal Bacterial Overgrowth occurs when bacteria — which should largely be confined to the large intestine — migrate into and multiply within the small intestine in excessive numbers. This disrupts normal digestion and absorption, and produces symptoms including bloating, abdominal pain, flatulence, diarrhoea, constipation, and fatigue. These symptoms overlap significantly with those of ulcerative colitis, which is precisely what makes the co-existence of the two conditions so easy to miss. 

SIBO is not a single, uniform condition. Breath testing can identify three types based on the gas produced — hydrogen-dominant, methane-dominant (now formally classified as Intestinal Methanogen Overgrowth, or IMO), and hydrogen sulphide-dominant — each presenting with a somewhat different symptom profile. Understanding which type is present matters for treatment selection.

How common is SIBO in people with ulcerative colitis?

A systematic review and meta-analysis by Shah et al. (2019), which analysed 11 studies comprising over 1,500 IBD patients and 407 controls, found that UC patients had nearly eight times the odds of developing SIBO compared to healthy controls.

A more recent and larger meta-analysis by Feng et al. (2025), incorporating 29 studies and over 3,000 IBD patients, reported a pooled SIBO prevalence of 27.8% specifically in UC patients — meaning more than one in four people with UC may have concurrent SIBO.

These are not minor statistical associations. They represent a clinically significant and under-recognised complication that, in our experience, remains largely undetected in NHS pathways where SIBO testing is not routinely offered to UC patients.

Why does ulcerative colitis increase the risk of SIBO?

The small intestine has several overlapping defence mechanisms that ordinarily prevent bacterial overgrowth. In people with UC, a number of these mechanisms become compromised — both as a direct consequence of the disease itself, and as a result of the medical and surgical management often required to control it.

Impaired gut motility and the migrating motor complex

The migrating motor complex (MMC) is the gut’s housekeeping system — a series of coordinated muscular contractions that sweep bacteria and debris from the small intestine into the large intestine during fasting periods. The chronic inflammation associated with UC disrupts normal gastrointestinal motility and can extend oral-caecal transit time, impairing MMC function and creating an environment in which bacteria accumulate in the small bowel.(Feng et al. 2025)

Mucosal damage and compromised innate defences

Healthy intestinal mucosal cells play an active role in limiting bacterial populations through the production of secretory IgA, antimicrobial peptides, and an intact gut barrier. UC causes chronic inflammation and ulceration of the mucosal lining — predominantly in the colon and rectum — which can compromise these innate defence mechanisms and reduce the gut’s ability to maintain normal microbial boundaries.

Medication use – particularly PPIs and corticosteroids

Long-term proton pump inhibitor (PPI) use — common in UC patients managing reflux symptoms alongside their IBD (Fossmark et al. 2023) — reduces gastric acid production, weakening one of the gut’s primary antimicrobial barriers, and increasing susceptibility to SIBO (Khurmatullina et al. 2025). Corticosteroids, frequently used to manage UC flares, can alter the composition of the gut microbiome and impair local immune defences, potentially creating conditions more favourable to overgrowth (Okafuji et al. 2022).

Surgical interventions affecting the ileocaecal valve

The ileocecal valve (ICV) sits at the junction between the small and large intestine and acts as a one-way barrier, preventing bacteria-rich colonic contents from flowing back into the small bowel. Surgical procedures that alter or remove the ICV — used in some cases of severe or refractory UC — can impair this mechanism, potentially allowing colonic bacteria to migrate into the small intestine and directly seed an overgrowth (Feng et al. 2025).

Dysbiosis as both cause and consequence

UC is associated with significant dysbiosis — an alteration in the composition and diversity of the gut ecology (microbiome). This dysbiosis is thought to be both a feature of the disease and a driver of ongoing inflammation, creating a self-reinforcing cycle in which the microbial environment of the gut becomes progressively more disrupted (Kaur & Thakur 2026). SIBO, as a specific form of microbial dysbiosis affecting the small intestine, sits within this broader picture.

UC and SIBO — how do the symptoms overlap, and how can you tell them apart?

This is perhaps the most clinically important question for someone living with UC. The symptom overlap between the two conditions is substantial:

• Abdominal bloating and distension
• Abdominal pain and cramping
• Diarrhoea or loose stools
• Excessive flatulence
• Fatigue
• Nausea

All of these can be features of either active UC or SIBO. This creates a genuine diagnostic challenge — and a practically significant one, because the treatment for a UC flare (typically immunosuppression or corticosteroids) is entirely different from the treatment for SIBO (antimicrobial protocols, motility support, dietary modification).

A 2019 meta-analysis found that UC patients with concurrent SIBO showed significantly higher levels of abdominal bloating, flatulence, loose stools and increased stool frequency compared to UC patients without SIBO — suggesting that when bloating and gas are disproportionately prominent in a UC patient’s symptom picture, SIBO warrants investigation (Shah et al. 2019).

Features that may point more specifically towards SIBO

While no symptom pattern definitively distinguishes SIBO from a UC flare, certain features may increase clinical suspicion for SIBO as a contributing factor:

• Bloating and gas as the dominant symptoms, particularly if worse after eating and improving with fasting
• Symptoms that persist during periods when UC appears otherwise well-controlled — normal calprotectin, stable endoscopy findings
• A clear relationship between symptoms and specific foods, particularly fermentable carbohydrates
• Symptoms that have not responded as expected to standard UC management
• A history of food poisoning or gastroenteritis preceding the onset or worsening of symptoms

It is important to emphasise that these observations are clinical pointers rather than diagnostic criteria. Confirmation of SIBO requires breath testing, and any changes to UC management should always involve the treating gastroenterologist.

How is SIBO diagnosed in someone with ulcerative colitis?

The gold standard for SIBO diagnosis is jejunal aspirate and culture — a direct sampling of small intestinal fluid that can quantify bacterial populations with precision. However, this procedure is highly invasive, expensive, and rarely performed outside specialist centres.

In clinical practice, the hydrogen and methane breath test (HMBT) is the standard diagnostic tool for SIBO. The test involves ingesting a sugar substrate — typically lactulose or glucose (with the former preferential for UC) — and then measuring the gases produced by bacterial fermentation in the small intestine via breath samples taken at regular intervals. A positive result, indicating abnormal gas production in the small bowel, supports a SIBO diagnosis.

Breath testing carries particular relevance for UC patients because it is non-invasive, can be performed at home, and does not require any alteration to existing UC medications. It provides an objective measure that can help clinicians — and patients — understand whether SIBO is contributing to the overall symptom burden.

One important caveat: interpretation of breath test results in people with IBD requires clinical expertise. Altered gut transit, the effects of IBD medications, and the underlying dysbiosis associated with UC can all influence breath test patterns and require careful contextualisation. Results should always be interpreted alongside a full clinical history.

SIBO breath testing is not routinely offered on the NHS for UC patients. Private testing, available through specialist clinics, provides access to this diagnostic tool without the need for a GP or gastroenterology referral.

Can SIBO make ulcerative colitis worse?

This is an area of active research and the evidence, while not yet definitive, points in a clinically significant direction. The relationship between SIBO and UC appears to be bi-directional — each condition can create conditions that perpetuate or worsen the other.

Bacterial overgrowth in the small intestine produces an increased bacterial load and elevated levels of bacterial metabolites — including lipopolysaccharides (LPS) — that can drive systemic and local inflammation. In someone with UC, where the mucosal barrier is already compromised and the immune system is in a state of chronic activation, this additional inflammatory input from the small bowel may compound the overall inflammatory burden and potentially contribute to flare activity.

Research has also shown that treating SIBO in IBD patients produces meaningful clinical improvement. A 2018 study found significant symptom improvement in IBD patients following SIBO treatment, with the majority achieving breath test normalisation after antibiotic therapy. This suggests that in at least a subset of UC patients, SIBO is not merely a passenger condition but an active contributor to symptoms (Cohen-Mekelburg et al. 2018).

It is important to note that this does not mean SIBO causes UC, or that treating SIBO will resolve UC. What the evidence does suggest is that in people with UC who have concurrent SIBO, addressing the overgrowth may reduce symptom burden and potentially support a more stable disease course — and that leaving it undiagnosed and untreated represents a missed clinical opportunity.

How we approach SIBO in the context of ulcerative colitis at IBS & SIBO Clinics

We work with clients who have complex, multi-layered digestive conditions — and UC with suspected concurrent SIBO is a clinical picture we encounter regularly. Our approach is built on a clear principle: SIBO does not exist in isolation, and neither does UC. Understanding how the two interact in any individual requires a thorough clinical assessment, not a one-size-fits-all treatment protocol.

We want to be explicit about the scope of what we do in this context. We are nutritional therapists and functional medicine practitioners, not gastroenterologists. We do not manage UC as a condition, and we would never advise a client to alter their UC medication or gastroenterology care plan without direct consultation with their specialist. What we offer is complementary to — not a replacement for — the medical management of UC.

Where SIBO is identified as a complicating factor in someone with UC, our work typically involves:

• A thorough case review
• SIBO breath testing to confirm and identify the type of overgrowth present
• A targeted antimicrobial protocol appropriate to the SIBO type and the individual’s broader clinical picture
• Motility support to address the underlying MMC impairment that commonly drives SIBO
• Dietary guidance that manages SIBO symptoms without unnecessarily restricting the diet of someone already managing a complex digestive condition
• Nutritional assessment and support for deficiencies commonly associated with both UC and SIBO — including B12, iron, vitamin D, and fat-soluble vitamins
• Close communication with the treating gastroenterologist where appropriate, and clear guidance on which symptoms warrant prompt medical review

Our goal is to reduce the symptom burden associated with SIBO, support the best possible gut environment, and help our clients feel more in control of a condition that can otherwise feel relentlessly unpredictable.

FAQ

Can you have SIBO and ulcerative colitis at the same time?

Yes. Research shows that people with ulcerative colitis carry a significantly elevated risk of developing SIBO compared to the general population. A 2025 meta-analysis found that more than one in four people with UC may have concurrent SIBO (Feng et al., 2025). The two conditions can co-exist and, in some cases, each can create conditions that make the other more difficult to manage. Identifying whether SIBO is present alongside UC requires specific testing — it is not something that standard UC monitoring will detect.

How do I know if my symptoms are from UC or SIBO?

This is genuinely difficult to determine without testing, because the symptom overlap is considerable. Both conditions can cause bloating, abdominal pain, diarrhoea, flatulence, and fatigue. Some patterns — such as bloating and gas that are disproportionately prominent, or symptoms that persist during periods when UC appears otherwise well controlled — may raise clinical suspicion for SIBO as a contributing factor. However, a SIBO breath test is required to confirm the diagnosis, and any changes to UC management should always involve your gastroenterologist.

Will treating SIBO improve my ulcerative colitis?

Treating SIBO is unlikely to resolve UC, and we would never suggest otherwise. What the emerging research does indicate is that in people with UC who have concurrent SIBO, addressing the overgrowth may help reduce the overall symptom burden — particularly bloating, gas, and altered bowel habits. For some people, this can make a meaningful difference to daily quality of life. It is important to approach this as a complementary step alongside, not instead of, ongoing gastroenterological care.

Is SIBO breath testing safe if I have ulcerative colitis?

Yes — the hydrogen and methane breath test is non-invasive, involves no medication changes, and does not interfere with existing UC treatment. It can be completed at home using a postal testing kit. It is worth noting that interpretation of breath test results in people with IBD requires clinical expertise, as altered gut transit and the effects of IBD medications can influence results. We always review breath test findings within the full context of your clinical history.

Can my GP or gastroenterologist test me for SIBO?

SIBO testing is not routinely available on the NHS, and most gastroenterology pathways do not currently include SIBO breath testing as part of standard UC monitoring. Some gastroenterologists working privately will arrange testing, but access varies considerably. Private testing through a specialist clinic provides a straightforward route to investigation without the need for a referral.

Do I need to stop my UC medications before being tested or treated for SIBO?

No — and we would never advise stopping or altering UC medication without direct guidance from your gastroenterologist. Breath testing does not require any changes to existing medication. When it comes to SIBO treatment, we take your full medication history into account when developing a plan, and we work in a way that is complementary to your medical management rather than in conflict with it. Any clinical concerns that arise during our work together that we feel warrant medical review will always be communicated clearly.

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