SIBO: The Hidden Cause of Your Bloating

Your abdomen expands like a balloon after every meal. You look six months pregnant by dinner time, regardless of what you eat. The gas is relentless, the cramping unpredictable, and your bowel habits swing between diarrhoea and constipation without any discernible pattern. You have tried the low-FODMAP diet, probiotics, digestive enzymes, and every supplement your naturopath recommended. Nothing has made a lasting difference.

If this sounds familiar, there is a strong chance that Small Intestinal Bacterial Overgrowth — SIBO — is the cause. And the good news is that once it is diagnosed, it is treatable.

What Is SIBO?

SIBO occurs when bacteria that normally reside predominantly in the large intestine migrate into and colonise the small intestine in abnormal numbers. The small intestine is designed to be a relatively low-bacteria zone — its primary function is nutrient absorption, and it relies on a combination of gastric acid, bile salts, intestinal motility, and the ileocaecal valve to keep bacterial populations in check.

When these defence mechanisms fail — due to factors such as reduced gastric acid (often from long-term PPI use), impaired intestinal motility, anatomical abnormalities, or previous abdominal surgery — bacteria from the colon can establish themselves in the small bowel. Once there, they ferment food as it passes through, producing hydrogen and/or methane gas. This gas production is the direct cause of the bloating, distension, pain, and altered bowel habits that characterise SIBO.

Hydrogen vs Methane: Why the Gas Type Matters

Not all SIBO is the same, and understanding which gas is being produced is critical for effective treatment. Hydrogen-dominant SIBO is typically associated with diarrhoea. The excess hydrogen produced by small bowel bacteria draws water into the intestinal lumen and accelerates transit, resulting in loose, frequent stools.

Methane-dominant overgrowth — sometimes called Intestinal Methanogen Overgrowth or IMO — presents differently. Methane actually slows intestinal transit, leading to constipation rather than diarrhoea. Patients with methane-dominant overgrowth often describe severe bloating with infrequent, hard stools that are difficult to pass. This subtype is frequently misdiagnosed as constipation-predominant IBS.

The treatment approach differs between the two types. Hydrogen-dominant SIBO typically responds to rifaximin alone, while methane-dominant overgrowth often requires a combination of rifaximin and neomycin or metronidazole to target the methane-producing archaea (which are technically not bacteria but a separate domain of microorganisms called methanogens).

How SIBO Is Diagnosed

The gold standard for diagnosing SIBO in clinical practice is the lactulose breath test. Lactulose is a non-absorbable sugar that passes through the entire small intestine without being digested. If bacteria are present in the small bowel, they ferment the lactulose as it passes through, producing hydrogen and/or methane gas that is absorbed into the bloodstream and exhaled in the breath.

During the test, breath samples are collected every 15 to 20 minutes over a two to three hour period after ingesting the lactulose solution. A characteristic early rise in hydrogen or methane — occurring before the lactulose would have reached the colon — indicates bacterial overgrowth in the small intestine.

At our clinic, we perform lactulose breath testing with measurement of both hydrogen and methane, ensuring that neither hydrogen-dominant nor methane-dominant SIBO is missed. The test is non-invasive, requires no sedation, and provides results that directly guide treatment decisions.

What Causes SIBO?

Understanding the underlying cause of SIBO is just as important as diagnosing it, because without addressing the root cause, recurrence is common. The most frequent contributing factors include long-term proton pump inhibitor use (which reduces gastric acid, one of the body's key defences against bacterial overgrowth), impaired intestinal motility (which can result from diabetes, hypothyroidism, scleroderma, or post-surgical adhesions), anatomical factors such as small bowel diverticula or a deficient ileocaecal valve, and previous abdominal or pelvic surgery.

Chronic stress, which impairs both gastric acid production and intestinal motility via the vagus nerve, is also increasingly recognised as a contributing factor. Many patients with SIBO describe a period of significant stress preceding the onset of their symptoms.

We also assess for underlying conditions that impair nutrient absorption or that may predispose to SIBO. Coeliac disease, which damages small bowel mucosa and impairs absorption, frequently co-occurs with SIBO. Similarly, inflammatory bowel disease can predispose to bacterial overgrowth. Pancreatic insufficiency (whether from chronic pancreatitis or cystic fibrosis) reduces the amount of antimicrobial pancreatic secretions, increasing SIBO risk. For each patient, understanding these underlying factors allows us to address them — whether through PPI reduction, prokinetic therapy, treatment of diabetes, or management of other primary conditions.

The migrating motor complex (MMC) is a critical physiological process that we assess when investigating SIBO. The MMC is a wave of muscular contractions that occurs in the fasting state, sweeping bacteria and food debris from the small intestine into the colon. When the MMC is impaired — by PPI use, by strictures, by dysmotility disorders, or by post-surgical adhesions — bacteria accumulate. Understanding the integrity of a patient's MMC allows us to target prokinetic therapy appropriately and to counsel about recurrence risk.

Treatment: More Than Just Antibiotics

The cornerstone of SIBO treatment is targeted antibiotic therapy. Rifaximin is the most extensively studied antibiotic for SIBO and has the advantage of being minimally absorbed — meaning it acts locally in the gut with very few systemic side effects. For methane-dominant overgrowth, we typically add a second agent to target the methanogens.

However, antibiotics alone are often not sufficient for long-term management. Addressing the underlying cause is essential. For patients on long-term PPIs, we work to reduce or eliminate acid suppression where clinically appropriate. For patients with impaired motility, prokinetic agents can help restore the migrating motor complex — the cyclical wave of intestinal contractions that sweeps bacteria and debris from the small bowel during fasting.

Dietary modifications play a supporting role. While the low-FODMAP diet can help manage symptoms during and after treatment, it is not a treatment for SIBO itself — it merely reduces the substrate available for bacterial fermentation. A more nuanced dietary approach, guided by breath test results and the patient's specific triggers, is typically more effective and sustainable.

The choice of antibiotic depends on the pattern revealed by breath testing. Hydrogen-dominant SIBO typically responds to rifaximin monotherapy, a minimally absorbed antibiotic that acts locally in the small bowel with virtually no systemic side effects. Methane-dominant overgrowth requires additional agents — either neomycin or metronidazole — because the methane-producing organisms are archaea (methanogens) that require different targets than standard bacteria.

Recurrence: The Ongoing Challenge

SIBO has a well-documented tendency to recur, particularly if the underlying predisposing factor has not been addressed. Recurrence rates of 40 to 50 percent within 12 months are reported in the literature. This is why our approach to SIBO management extends well beyond the initial antibiotic course — we work with patients on long-term strategies to minimise the risk of recurrence, including prokinetic therapy, dietary optimisation, and regular monitoring.

For patients with methane-dominant overgrowth — which typically carries higher recurrence rates than hydrogen-dominant SIBO — we often recommend repeat breath testing at three to six months post-treatment to assess for early recurrence. Similarly, for patients whose SIBO is driven by profound dysmotility (such as those with diabetes or scleroderma), or for those with anatomical factors like adhesions or strictures, we work with a longer treatment horizon. Some patients benefit from extended courses of prokinetic agents after initial antibiotic therapy, using agents such as prucalopride or low-dose domperidone to maintain improved intestinal motility.

Post-treatment dietary management is also critical. Rather than maintaining restrictive FODMAP avoidance indefinitely, we work with patients to gradually reintroduce foods as tolerance improves, guided by symptoms and in partnership with a specialist dietitian. This prevents the nutritional depletion and quality-of-life impact that can result from prolonged restrictive dieting.

If your abdomen expands like a balloon after meals despite every dietary restriction imaginable, SIBO may be the reason — and a simple breath test can tell you for certain.

SIBO is common, underdiagnosed, and treatable. If you have been battling chronic bloating that no one has been able to explain, we encourage you to ask about breath testing. The answer may be simpler than you think.