What is the treatment for Small Intestine Bacterial Overgrowth (SIBO)?

Treatment of Small Intestinal Bacterial Overgrowth (SIBO)

Rifaximin 550 mg twice daily for 1-2 weeks is the first-line treatment for proven SIBO, achieving 60-80% efficacy in eradicating bacterial overgrowth. 1

Diagnostic Approach Before Treatment

The 2025 British Society of Gastroenterology guidelines now recommend testing rather than empirical treatment to improve antibiotic stewardship and avoid treating patients who don't actually have SIBO. 1

Preferred Diagnostic Methods:

• Combined hydrogen and methane breath testing is more accurate than hydrogen-only testing for identifying SIBO 1
• Glucose or lactulose breath tests should be used when available 1
• Qualitative small bowel aspiration during upper endoscopy is an alternative when breath testing is unavailable (flush 100 mL sterile saline into duodenum, aspirate ≥10 mL into sterile trap, send to microbiology) 1

Common pitfall: Lack of response to empirical antibiotics may indicate resistant organisms, absence of SIBO, or coexisting disorders causing similar symptoms—this is why testing first is now preferred. 1

First-Line Antibiotic Treatment

Primary Option:

• Rifaximin 550 mg twice daily for 1-2 weeks 1
• This non-absorbed antibiotic is preferred because it reduces systemic resistance risk 1
• Effective for both hydrogen-dominant and methane-dominant SIBO 1

Equally Effective Alternatives:

• Doxycycline 1
• Ciprofloxacin 1
• Amoxicillin-clavulanic acid 1
• Cefoxitin 1

Avoid metronidazole as first-line—it has documented lower efficacy. 1

Critical warning: If using metronidazole long-term, stop immediately if numbness or tingling develops in feet (early reversible peripheral neuropathy). 2 With ciprofloxacin, monitor for tendonitis and use the lowest effective dose. 2

Management of Recurrent SIBO

For patients with recurrent SIBO after initial successful treatment, use one of these strategies: 1

1. Cyclical antibiotics (rotating antibiotics with 1-2 week antibiotic-free periods) 2, 3
2. Low-dose long-term antibiotics 1
3. Recurrent short courses of antibiotics 1

Key distinction: Patients with reversible causes (e.g., immunosuppression during chemotherapy) typically need only one antibiotic course. 1 Those with persistent underlying causes require ongoing management strategies. 1

Adjunctive Dietary Management

While antibiotics eradicate bacteria, dietary modifications help manage symptoms and prevent recurrence:

• Low-FODMAP diet for 2-4 weeks reduces fermentable carbohydrates that feed bacterial overgrowth 4
• Adequate protein intake while reducing fat consumption minimizes steatorrhea 4
• Complex carbohydrates and fiber from non-cereal plant sources support gut motility 4, 3
• 4-6 small meals daily rather than 3 large meals 4

Role of Probiotics

The evidence on probiotics is mixed and modest:

• A 2014 study showed probiotics added to maintenance antibiotic therapy improved outcomes (93.3% negative breath tests vs 66.7% in controls) 5
• However, a 2024 trial found probiotics during active treatment may counteract therapeutic effects by introducing bacteria while trying to reduce overgrowth 6
• The 2013 Rome Foundation report concluded probiotics have a "positive, albeit modest, effect" in functional bowel disorders 1

Practical approach: Consider probiotics after completing antibiotic therapy for maintenance, not during active treatment. 6, 5

Monitoring for Complications

Nutritional Deficiencies to Monitor:

• Fat-soluble vitamins (A, D, E, K) due to bile salt deconjugation 4
• Vitamin B12 and iron are commonly depleted 4
• Vitamin D deficiency occurs in 20% of patients if bile acid sequestrants are needed 1

Managing Persistent Steatorrhea:

If fatty, foul-smelling stools persist after SIBO treatment:

• Consider bile salt sequestrants (cholestyramine or colesevelam) 1, 4
• Start at low doses (¼ sachet colestyramine) at mealtimes, titrate slowly 1
• Monitor closely for worsening vitamin deficiencies 1, 4

Addressing Underlying Causes:

• Pancreatic exocrine insufficiency: Add pancreatic enzyme replacement therapy if faecal elastase <500 μg/g 1
• Impaired gut motility: Consider prokinetic agents to prevent recurrence 7, 8

Important caveat: If patients don't tolerate pancreatic enzyme replacement therapy, this often indicates underlying SIBO; once SIBO is eradicated, enzymes are usually better tolerated. 2

Special Considerations for Methane-Dominant SIBO

Methane-producing archaea cause constipation-predominant symptoms and may be more resistant:

• Rifaximin remains first-line (60-80% effective) 3
• Combination therapy (antibiotics plus probiotics after treatment) showed 55% eradication vs 33% for probiotics alone or 25% for antibiotics alone in one study 3
• Herbal antimicrobials are sometimes used as alternatives but require caution 3, 9

Treatment Algorithm Summary

1. Confirm diagnosis with combined hydrogen/methane breath testing or small bowel aspiration 1
2. Initiate rifaximin 550 mg twice daily for 1-2 weeks (or alternative if contraindicated) 1
3. Implement low-FODMAP diet during treatment 4
4. Monitor for nutritional deficiencies (vitamins A, D, E, K, B12, iron) 4
5. Reassess symptoms after completing antibiotics 7
6. For recurrence: Use cyclical antibiotics, address underlying causes (motility, pancreatic insufficiency), consider maintenance probiotics 1, 3, 7
7. If steatorrhea persists: Add bile salt sequestrants with close vitamin monitoring 1, 4