A client came to me last year with a familiar story. She'd been told she had IBS years ago, had cut out gluten, then dairy, then half of FODMAPs and was still waking up with a swollen stomach most mornings. She'd done "everything right" and nothing had really shifted. When we dug into her history together - slow digestion, constipation that worsened with fibre, bloating that built through the day rather than easing - it became clear IBS wasn't the whole picture. What she was actually dealing with was SIBO: small intestinal bacterial overgrowth.
This mix-up happens more than people realise. IBS and SIBO share so many of the same symptoms - abdominal pain, excess gas, irregular bowel habits - that it's easy for one to be treated as the other for years. Knowing the difference matters clinically, because the right approach for IBS isn't always the right approach for SIBO, and sometimes it can even make things worse.
What's actually going on in SIBO
The small intestine is responsible for around 90% of how we absorb calories and nutrients from food, and under normal conditions it hosts relatively few bacteria. SIBO occurs when bacteria that typically dominate in the large intestine overgrow in the small intestine instead - most commonly types such as Streptococci, Escherichia coli and Klebsiella.
This overgrowth is often driven by low stomach acid. Adequate stomach acid is needed to trigger the release of pancreatic enzymes once food empties into the small intestine, allowing carbohydrates to be digested efficiently. When stomach acid is insufficient, undigested carbohydrates linger in the small intestine for longer, creating exactly the environment an overgrowth of bacteria needs to establish itself. Disordered gut motility plays an equally important role: consistent, rhythmic movement through the small intestine is what normally clears bacteria along and prevents them from accumulating. Vagus nerve dysfunction, along with chronic stress, can disrupt this motility, slowing transit and creating the stagnant conditions that allow overgrowth to take hold.
Once established, this bacterial population ferments food before the body has had the chance to properly digest and absorb it and in doing so, the bacteria effectively "steal" nutrients from food as it passes through the intestine. This is a key reason why so many people with SIBO describe a frustrating cycle of continual hunger alongside digestive discomfort: the body isn't being properly nourished by the food that's being eaten, even when intake is adequate. Over time, this malabsorption can also affect levels of B12, the fat-soluble vitamins (A, D and E), iron and calcium.
So how is this different from IBS?
IBS is a broader, symptom-based diagnosis - a way of describing a cluster of digestive symptoms once other conditions have been ruled out. SIBO is a specific, identifiable driver of digestive symptoms, and a meaningful proportion of people who carry an IBS diagnosis are found to have SIBO underlying it. In other words, SIBO can sit underneath an existing IBS diagnosis as one of its actual root causes, rather than being a separate, unrelated condition.
A few clues that point more towards SIBO than "general" IBS:
- Symptoms that worsen with fibre or prebiotic foods, rather than improving
- Constipation that's stubborn and methane-driven, not responding to the usual "eat more fibre" advice
- A history of acid reflux, low stomach acid, or long-term use of acid-suppressing medication (PPIs are linked to SIBO in roughly half of long-term users)
- Bloating that builds steadily through the day rather than coming and going randomly
- Ongoing fatigue or hunger that doesn't make sense given food intake
None of these confirm SIBO in isolation, but together they form a strong clinical picture that's worth investigating rather than continuing to manage symptoms generically.
Why "just eat more fibre" can make things worse
This is one of the more frustrating parts of receiving a generic IBS label without further investigation. Standard gut health advice leans heavily on fibre and prebiotics and for a lot of people, that's genuinely the right approach. But if SIBO is the underlying issue, feeding more fermentable fibre to an already-overgrown population of bacteria in the small intestine can intensify bloating and constipation rather than ease it. It's a clear example of why generic advice so often falls short: the advice itself isn't wrong, it's simply being applied to the wrong problem.
A different lens: looking at the whole gut picture
It's worth saying clearly: NHS guidance is cautious about breath testing for SIBO, particularly in people who already have an IBS diagnosis, and that caution is well-founded - breath tests can produce false positives even in people with no symptoms at all, and a positive result doesn't reliably predict whether treatment will work.
This is part of why, rather than relying on a single breath test in isolation to chase a yes/no SIBO answer, I focus on gut microbiome testing as part of a wider picture. The aim isn't to diagnose SIBO as a standalone label, but to understand how the gut is functioning as a whole - what's thriving, what's depleted, what patterns of fermentation, motility and imbalance are showing up - and where SIBO-type overgrowth might be sitting within that broader picture rather than treated as an isolated event.
This matters because, as covered above, SIBO rarely shows up on its own. It's typically connected to low stomach acid, sluggish motility, vagus nerve function, stress, or an underlying gluten sensitivity and addressing the overgrowth without addressing what allowed it to take hold in the first place tends to mean symptoms simply return. Working with a nutritionist to look at this holistically (rather than chasing a single test result) means the support strategy can be built around your gut specifically: what's driving things, what needs calming, what needs rebuilding, and in what order.
What actually helps
Management isn't a single fix or a single test result - it's typically a personalised combination based on what your gut picture shows: addressing low stomach acid, supporting motility and the MMC so the small intestine clears properly, considering vagus nerve and stress regulation where relevant, and in some cases working with targeted antimicrobial approaches alongside dietary strategies such as a low FODMAP or specific carbohydrate approach — used strategically, rather than as a long-term default. Probiotics can also play a role, although evidence on strain-specific benefit is still developing; some research points to Bifido species being particularly useful in reducing bacterial burden, while methane-dominant presentations may respond differently to probiotic support, making this an area where individualised guidance matters.
If any of this sounds familiar - years of "doing everything right" with little to show for it - it's worth getting a proper, personalised look at what's actually going on across your whole gut, rather than chasing a single test result. That's exactly what we work through together in the Thrive Gut Blueprint, starting with a complimentary, low-pressure strategy call to talk through your history, symptoms and what testing (if any) makes sense for you. Book your strategy call here.
The bottom line
IBS and SIBO can look almost identical from the outside, but they don't always respond to the same approach, and the gas-type distinction alone can change the entire treatment pathway. If standard IBS advice hasn't shifted your symptoms, it doesn't mean you're doing something wrong — it may mean the underlying driver hasn't been correctly identified yet. Understanding what's actually happening in your gut is the first real step toward symptoms that don't just keep circling back.
References
- Anderson, S., Cryan, J. and Dinan, T., 2019. The Psychobiotic Revolution. 1st ed. Washington D.C.: National Geographic Partners.
- Guts UK. Small Intestinal Bacterial Overgrowth (SIBO). Available at: gutscharity.org.uk