How do you diagnose small intestinal bacterial overgrowth (SIBO)?

How to Diagnose SIBO

Begin with combined hydrogen and methane breath testing using glucose substrate as the first-line diagnostic approach, as this is non-invasive, cost-effective, and more accurate than hydrogen testing alone for detecting both bacterial and archaeal overgrowth. 1, 2

First-Line Diagnostic Testing

• Perform combined hydrogen-methane breath testing rather than hydrogen alone, as this detects both hydrogen-producing bacteria and methane-producing archaea (Methanobrevibacter smithii), which are missed by hydrogen-only testing 1, 2, 3
• Use glucose as the preferred substrate for breath testing, with lactulose as an alternative if glucose is unavailable 1
• Avoid lactulose breath testing in patients with rapid small bowel transit, as this causes false positives due to early colonic fermentation 1

Important caveat: The British Society of Gastroenterology explicitly states that both glucose and lactulose hydrogen breath tests have poor sensitivity and specificity and are not recommended for SIBO diagnosis 4. However, the American Gastroenterological Association and American College of Gastroenterology recommend combined hydrogen-methane breath testing as first-line, representing more recent consensus 1, 2. This discrepancy reflects evolving understanding that combined hydrogen-methane testing is superior to hydrogen-only testing.

When to Suspect SIBO Clinically

Test patients presenting with:

• Abdominal pain, bloating, distension, diarrhea, and flatulence 1
• Fat-soluble vitamin deficiencies (particularly vitamins A and E) from bacterial deconjugation of bile salts 1
• Vitamin B12 malabsorption 4

Identify predisposing conditions before testing:

• Gastric acid suppression (proton pump inhibitors) 1, 2
• Intestinal dysmotility or absent migrating motor complex (diabetes with autonomic neuropathy) 2
• Absent ileocecal valve, surgical blind loops, or fistulae 1, 2
• Severe chronic small intestinal dysmotility with gut stasis or dilated bowel 1
• Crohn's disease with stricturing/fistulizing phenotype (up to 30% prevalence) 1

Small Bowel Aspiration and Culture (Gold Standard)

Reserve small bowel aspiration for:

• Confirming methane-dominant SIBO when breath testing is unavailable 5
• Differentiating SIBO from fungal overgrowth, enteric infections, or graft-versus-host disease in immunocompromised patients 5
• Patients with suspected structural abnormalities requiring endoscopic evaluation 5

Proper aspiration technique to avoid contamination:

• Avoid aspirating on intubation during upper endoscopy 5
• Flush 100 mL sterile saline into the duodenum, then flush the channel with 10 mL air 5
• Turn down suction, allow fluid to settle for seconds, then aspirate ≥10 mL into a sterile trap 5
• Send immediately to microbiology for culture 5

Diagnostic thresholds:

• Traditional threshold: ≥10⁵ CFU/mL 6, 7
• Modern threshold: ≥10³ CFU/mL with colonic-type bacteria may indicate SIBO, as the traditional threshold is overly restrictive 1
• Positive result shows growth of colonic bacteria in small intestine sample 5

Supporting Laboratory Findings

Check for indirect evidence of SIBO:

• Fat-soluble vitamin deficiencies (A, D, E, K) 1, 5
• High anion gap acidosis from D-lactic acid production 1
• Raised urinary indicans, blood D-lactate, or alcohol levels 4

Critical Pitfalls to Avoid

• Do not rely on breath testing alone in patients with rapid transit, as this produces false positives 1
• Do not use elevated fecal calprotectin to diagnose SIBO—elevated levels indicate inflammatory bowel disease or other inflammatory conditions, not SIBO 2
• Do not treat empirically without testing, as this undermines antibiotic stewardship and fails to establish the true cause of symptoms 1, 2
• Ensure local microbiology services agree on appropriate processing and reporting before performing aspiration 5

Diagnostic Algorithm Summary

1. Identify predisposing risk factors (PPI use, dysmotility, anatomical abnormalities) 1, 2
2. Perform combined hydrogen-methane breath testing with glucose as first-line 1, 2
3. If breath testing unavailable or equivocal, consider small bowel aspiration with proper technique 5
4. Check supporting labs (vitamin deficiencies, D-lactate) to strengthen diagnosis 1
5. If positive, investigate and address underlying causes before or concurrent with treatment 2