The Principle
Breath tests exploit a simple biological fact: when carbohydrates are fermented by bacteria, they produce gases — hydrogen (H₂) and methane (CH₄) — that are absorbed into the bloodstream, transported to the lungs, and exhaled in measurable quantities. By giving a patient a defined sugar substrate and measuring exhaled gases over 2 to 3 hours, clinicians can infer bacterial fermentation patterns in the gut.
SIBO Breath Testing
The most common application is diagnosing small intestinal bacterial overgrowth (SIBO). Patients fast overnight and then ingest either glucose or lactulose. Exhaled hydrogen and methane are measured at regular intervals. A rise in hydrogen greater than 20 parts per million (ppm) above baseline within 90 minutes is traditionally considered suggestive of SIBO — indicating bacterial fermentation of the substrate in the small intestine before it reaches the colon.
Glucose is absorbed in the proximal small intestine, so a positive glucose breath test localises fermentation to the upper small bowel with reasonable specificity. Lactulose is not absorbed anywhere, so it always reaches the colon and produces a late hydrogen rise — the challenge is distinguishing an early (small intestinal) rise from a colonic rise, which is notoriously difficult.
Carbohydrate Malabsorption Testing
Breath tests also diagnose specific carbohydrate malabsorption. Lactose breath test: a hydrogen rise after ingesting 25 to 50 grams of lactose indicates lactase deficiency and lactose malabsorption. Fructose breath test: a hydrogen rise after 25 grams of fructose suggests fructose malabsorption. Sorbitol breath tests follow the same principle. These tests help identify specific dietary triggers in patients with IBS-like symptoms.
Limitations and Pitfalls
Breath testing has significant limitations that clinicians and patients must understand. Sensitivity for SIBO ranges from 30 to 70 percent depending on substrate, cut-off values, and reference standard. Specificity is similarly variable. Up to 15 to 30 percent of the population are "non-hydrogen producers" — their colonic bacteria produce methane instead of hydrogen. If methane is not measured alongside hydrogen, these patients will produce false-negative results. Preparation is critical: antibiotics within 4 weeks, probiotics within 2 weeks, and prokinetics can all affect results. Rapid small intestinal transit can deliver substrate to the colon quickly, producing a false-positive "early" peak.
Methane: A Different Story
Methane is produced not by bacteria but by archaea — primarily Methanobrevibacter smithii. Elevated methane production (greater than 10 ppm at any point) is now termed intestinal methanogen overgrowth (IMO) rather than SIBO, reflecting the distinct biology. Methane is associated with constipation-predominant symptoms, as methane slows intestinal transit. Treatment for IMO differs from hydrogen-dominant SIBO — rifaximin alone is often insufficient, and combination therapy with neomycin or metronidazole is recommended.
The Right Context
Breath tests are most useful when interpreted in clinical context — correlated with symptoms, medication history, and response to treatment — rather than as standalone diagnostic verdicts. A negative breath test does not exclude SIBO, and a positive test does not prove it. The test shifts clinical probability, just like any other investigation.