SIBO — Small Intestinal Bacterial Overgrowth: When Bloating Builds Through the Day

Dipl. med. Charalampos Romanos, FMH-certified physician · Published: 17 June 2026 · Last medically reviewed: 17 June 2026 · 9 min read

A stomach that is flat in the morning and visibly distends over the course of the day. Bloating after almost every meal. Constipation or diarrhoea, often alternating, and a fatigue that worsens after eating. People who bring this to a doctor are frequently told it is irritable bowel syndrome and advised to reduce stress. In a proportion of these cases the underlying cause is small intestinal bacterial overgrowth — SIBO — which is measurable and treatable.

What SIBO means

SIBO stands for small intestinal bacterial overgrowth: a colonisation of the small intestine by bacteria that normally reside mainly in the colon. The small intestine is not sterile, but it is comparatively sparsely populated. When colonic bacteria migrate upwards or multiply excessively, they ferment carbohydrates in the small intestine — precisely where nutrient absorption is supposed to take place.

This fermentation produces gas, chiefly hydrogen and methane. That is where the characteristic pattern comes from: the abdomen is flat after a night's rest and distends further with every meal. In pronounced cases the absorption of iron, vitamin B12 and fat-soluble vitamins can suffer as well — which explains why some patients present primarily with exhaustion rather than abdominal complaints.

The typical clinical picture

No single symptom proves SIBO. It is the combination that stands out:

Bloating with marked increase over the course of the day. Fullness after small portions. Intolerance of onions, legumes, wheat or dairy, often newly acquired. Bowel irregularity in both directions. And frequently pronounced fatigue — partly from micronutrient deficiency, partly from the gas load itself.

Methane-dominant forms tend towards constipation, hydrogen-dominant forms towards diarrhoea. This distinction is not academic: it changes the treatment.

Why SIBO is regularly missed

Because the standard workup comes back normal. Full blood count, inflammatory markers, ultrasound and usually endoscopy show nothing. From this follows — understandably, but prematurely — the diagnosis of irritable bowel syndrome. The point is that SIBO is not detected by any of these investigations. It has to be looked for deliberately, and that requires a dedicated test.

The breath test — how it works

Detection is via a hydrogen-methane breath test. The principle is simple: human cells produce neither hydrogen nor methane. If these gases appear in exhaled air, they come from bacteria.

After a defined test solution is taken — usually lactulose or glucose — exhaled air is sampled at fixed intervals over two to three hours. An early rise points to overgrowth in the small intestine. Preparation and execution are decisive: a low-carbohydrate diet for 24 hours beforehand, fasting on the day, no smoking, no antibiotics in the preceding four weeks and no laxatives. If this is not observed, the result is not usable. We work with a specialised laboratory in Zurich for this test.

For context: the test is not perfect. Its sensitivity is limited, and the lactulose variant in particular is debated in the literature. A negative result does not reliably exclude SIBO, and a positive one must always be read against the clinical picture. A test without matching symptoms does not justify treatment.

What has to be excluded first

Before functional diagnostics become reasonable at all, the common and readily treatable causes need to be off the table. This is covered by basic insurance and generally includes coeliac serology, faecal calprotectin to exclude inflammatory bowel disease, full blood count and ferritin, inflammatory markers, TSH and — depending on the picture — pancreatic elastase.

This sequence is not a formality. Undiagnosed coeliac disease or hypothyroidism produces the same complaints and is treated differently.

The cause behind it

SIBO is rarely the actual diagnosis — usually it is the consequence of something else. Most commonly there is an underlying motility disorder: the migrating motor complex, which sweeps the small intestine between meals, is working too weakly. Other triggers include adhesions after abdominal surgery, a previous gastrointestinal infection, long-term use of acid blockers, ileocaecal valve dysfunction and underlying conditions such as diabetes mellitus.

Anyone who ignores this level is treating the relapse instead of the disease.

Treatment

Treatment rests on three pillars. First, reducing the overgrowth: the standard is a targeted, non-absorbed antibiotic course over roughly two weeks, with combination therapy considered in methane-dominant forms. Second, diet — a time-limited reduction of fermentable carbohydrates relieves symptoms, but is explicitly not a permanent state, since it degrades the diversity of the gut flora over time. Third, relapse prevention: treating the underlying motility disorder, adequate intervals between meals and, where possible, discontinuing unnecessary acid blockers.

What to realistically expect

A large proportion of patients respond clearly to the first course of treatment. It should be said just as plainly that the relapse rate is significant, and without addressing the cause it is high. SIBO responds well to treatment, but it is not a one-off intervention — it is a course that has to be followed.

Assessment for small intestinal bacterial overgrowth is part of our Extended Diagnostics in Zurich. The breath test is performed at a specialised laboratory in Zurich.