How should I test for small intestinal bacterial overgrowth (SIBO)?

Testing for Small Intestinal Bacterial Overgrowth (SIBO)

In patients with high pretest probability of SIBO—those with anatomical abnormalities, prior small bowel surgery, dysmotility, diverticulosis, or pseudo-obstruction—proceed directly to empirical antibiotic therapy without testing. 1, 2

When to Test vs. Treat Empirically

Proceed Directly to Empirical Treatment (No Testing Needed):

• Documented intestinal dysmotility or pseudo-obstruction 2
• Prior small bowel surgery or resection 1
• Small bowel diverticulosis 1
• Anatomical abnormalities causing dilation or stasis 1
• Structural abnormalities like strictures or fistulas 3

The rationale is that breath testing adds minimal value when pretest probability is high—a positive test reinforces your suspicion, but a negative test does not exclude SIBO. 1

Test When Pretest Probability is Low to Moderate:

• Nonspecific symptoms (bloating, diarrhea, abdominal pain) without clear predisposing factors 1
• Need to establish diagnosis for antibiotic stewardship 3
• Atypical presentations requiring diagnostic confirmation 1

First-Line Testing: Hydrogen-Methane Breath Testing

When testing is indicated, combined hydrogen and methane breath testing using glucose or lactulose substrate is the recommended first-line approach. 3, 2, 4

Test Protocol:

• Use glucose (75g) or lactulose (10g) as substrate 2, 4
• Glucose provides greater testing accuracy than lactulose 4
• Measure both hydrogen AND methane—hydrogen-only testing misses methane-dominant cases 3, 2, 4
• Lactulose has approximately 68% sensitivity and 70% specificity 2
• Glucose has <50% sensitivity with positive/negative predictive values <70% 1, 2

Critical Limitations to Recognize:

• Breath tests assume fixed orocecal transit time, causing false positives in patients with rapid transit 1, 2
• False negatives occur in 3-25% of individuals whose gut flora don't produce measurable hydrogen 1, 2
• Particularly unreliable after intestinal resection, with enteric fistulas, or in dysmotility 2
• A negative breath test does NOT rule out SIBO 2

Second-Line Testing: Small Bowel Aspirate and Culture

Small bowel aspirate with quantitative culture is the most sensitive test for SIBO, but is reserved for cases where breath testing is inconclusive or unavailable. 1, 3, 2

Procedure Technique:

• During upper endoscopy, avoid aspirating on intubation to prevent oropharyngeal contamination 3
• Flush 100 mL sterile saline into duodenum, then flush channel with 10 mL air 3
• Turn down suction, allow fluid to settle, then aspirate ≥10 mL into sterile trap 3
• Send to microbiology for quantitative culture 3

Interpretation:

• Bacterial load >10⁵ CFU/mL defines clinically significant overgrowth (normal is <10⁴ CFU/mL) 2, 5, 6
• Most frequently isolated organisms: Bacteroides, Enterococcus, and Lactobacillus 2

Major Limitations:

• Most pathogenic bacteria implicated in SIBO cannot be cultured with standard techniques 2
• Prone to contamination from oropharyngeal flora causing false positives 1, 2
• Sampling error—only tests one location in small bowel 2, 4
• Requires endoscopy, dedicated microbiology infrastructure, and is poorly standardized 1
• Positive results may not reflect clinically significant SIBO 1

When to Use Aspirate/Culture:

• Post-stem cell transplant patients with diarrhea to differentiate SIBO from fungal overgrowth, enteric infections, or graft-versus-host disease 3
• Suspected structural abnormalities requiring endoscopic visualization 3
• When breath testing unavailable or results conflict with clinical picture 3, 2

Common Pitfalls to Avoid

• Do not use lactose, fructose, or sorbitol as breath test substrates—they are inappropriate for SIBO diagnosis 4
• Do not rely solely on symptoms to diagnose SIBO—bloating, gas, distension, and diarrhea do not predict positive diagnosis 6
• Do not assume breath test accuracy is high—it requires careful patient selection, proper preparation, and cautious interpretation 4
• Ensure local microbiology lab can appropriately process and report small bowel aspirates before performing the procedure 3
• Remember that qualitative assessment (presence of colonic bacteria) is easier than quantitative culture and may be sufficient 3

After Diagnosis: Treatment Considerations

Once SIBO is confirmed, rifaximin 550 mg twice daily for 1-2 weeks achieves 60-80% efficacy and is first-line therapy. 3, 2, 7 Alternative antibiotics include doxycycline, ciprofloxacin, amoxicillin-clavulanic acid, and cefoxitin, while metronidazole should be avoided due to lower efficacy. 3, 2, 7

For recurrent SIBO, address underlying predisposing factors (discontinue unnecessary proton pump inhibitors, treat dysmotility) rather than simply repeating antibiotics. 2, 7 Consider rotating antibiotics with 1-2 week antibiotic-free intervals, or use cyclical/long-term low-dose regimens. 3, 2