Bacteria in the Wrong Place
The small intestine normally hosts relatively few bacteria — roughly 10³ to 10⁴ colony-forming units per millilitre — compared to 10¹¹ to 10¹² in the colon. Multiple defence mechanisms maintain this gradient: gastric acid kills ingested bacteria, bile acids have antimicrobial properties, the migrating motor complex (MMC) sweeps residual bacteria distally between meals, and the ileocaecal valve prevents retrograde colonic contamination. Small intestinal bacterial overgrowth (SIBO) occurs when these defences fail and bacterial populations in the small intestine reach abnormal levels.
Causes and Risk Factors
SIBO is not a primary disease but a secondary consequence of anatomical or functional disruption. Common predisposing conditions include: hypochlorhydria (from proton pump inhibitor use, atrophic gastritis, or post-gastrectomy), impaired motility (diabetic gastroparesis, scleroderma, opioid use, post-surgical adhesions), structural abnormalities (blind loops, strictures, small bowel diverticula), and immunodeficiency (IgA deficiency, HIV). The overlap with IBS is significant — some studies estimate 30 to 85 percent of IBS patients test positive for SIBO, though this wide range reflects disagreements about diagnostic thresholds.
Symptoms and Mechanisms
Excess bacteria in the small intestine ferment carbohydrates prematurely, producing hydrogen and methane gas (the latter now attributed to archaea, specifically Methanobrevibacter smithii, and termed intestinal methanogen overgrowth or IMO). This fermentation causes bloating, distension, flatulence, and abdominal pain. Bacterial deconjugation of bile acids impairs fat absorption, potentially causing steatorrhoea. Bacterial consumption of vitamin B12 and production of folate create a characteristic laboratory pattern. In severe cases, mucosal inflammation and villous blunting can mimic coeliac disease.
Testing: Breath Tests and Their Limitations
The most commonly used non-invasive test is the lactulose or glucose hydrogen breath test, which measures exhaled hydrogen and methane after ingesting a sugar substrate. A rise in hydrogen greater than 20 parts per million within 90 minutes is traditionally considered positive. However, breath testing has significant limitations: sensitivity ranges from 30 to 70 percent depending on the substrate and cut-off used, and specificity is similarly variable. The gold standard — quantitative culture of jejunal aspirate — is invasive and not routinely performed. This diagnostic uncertainty means SIBO is both over- and under-diagnosed depending on the clinical setting.
Treatment Beyond Antibiotics
Rifaximin (a non-absorbed antibiotic) is the most studied treatment, with meta-analyses showing normalisation of breath tests in approximately 50 to 70 percent of patients. However, recurrence rates are high — up to 45 percent within 9 months — because antibiotics treat the overgrowth without addressing the underlying predisposing condition. Successful long-term management requires identifying and treating the root cause: optimising motility (prokinetics), reviewing acid-suppressing medications, addressing structural issues, and dietary strategies (elemental diets, low-fermentation approaches) that reduce substrate availability.