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SIBO Protocol: What We Actually Use in Clinic (and What's Overhyped)

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Most SIBO treatments fail for one reason: they only focus on killing bacteria — not preventing it from coming back. We see patients who have: • been misdiagnosed as IBS • tried multiple antibiotics • spent hundreds on probiotics that made symptoms wo...
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PHASE 1 — KILL (Reduce Overgrowth)

Phase 1 is reducing the bacterial overgrowth in the small intestine. We use botanical antimicrobials over antibiotics for most patients because the research shows comparable efficacy with lower recurrence rates and less microbiome damage. This phase ...

 
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One of the most studied herbal antimicrobials for SIBO. Used for hydrogen-dominant SIBO and mixed infections. ✔ Helps reduce bacterial overgrowth ✔ Supports blood sugar balance ✔ Anti-inflammatory effects in gut Clinic use: 500mg, 2–3x daily with mea...
THORNE Berberine Dual Action Formula
 
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The key herb for methane SIBO (constipation-type SIBO). Most treatments fail methane cases — this is why. ✔ Targets methane-producing organisms ✔ Reduces bloating + constipation ✔ Works where standard antimicrobials fail Important: only stabilized al...
Allicin Supplement 100% Stabilized Garlic
 
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Broad-spectrum antimicrobial for mixed infections. ✔ Targets bacteria + yeast ✔ Useful in Candida + SIBO overlap ✔ Enteric-coated for small intestine delivery Cycle use: 4 weeks on, 2 weeks off Strong antimicrobial — not for long-term continuous use.
Micro Ingredients Oil of Oregano Softgels, 150ct

PHASE 2 — MOVE (Fix Gut Motility)

This is the phase 90% of practitioners skip, and it's why SIBO comes back. The migrating motor complex (MMC) is the cleansing wave that sweeps bacteria out of the small intestine between meals. When the MMC is broken (from food poisoning, stress, ant...

 
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One of the simplest and most effective prokinetics. Fixes impaired migrating motor complex (MMC), which is the #1 reason SIBO comes back. ✔ Supports gut clearance between meals ✔ Reduces recurrence risk ✔ Improves digestion and nausea Use: 500–1000mg...
Pure Encapsulations Ginger Extract Supplement
 
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Multi-pathway prokinetic formula for stubborn motility issues. ✔ Supports MMC signaling ✔ Combines ginger + amino acids + cofactors ✔ Used when ginger alone isn’t enough Use: 1–2 capsules at bedtime Best for post-infection or chronic SIBO cases.
Pure Encapsulations MotilPro Hypoallergenic Supplement

Restore — Rebuild the Right Way

Phase 3 is where most patients want to start, and it's exactly why they fail. You don't add probiotics to an active SIBO gut, you'd be feeding the overgrowth. Once the small intestine is clear and motility is moving, then we rebuild, strategically. T...

 
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Safe probiotic yeast used during and after SIBO treatment. ✔ Does NOT feed bacterial overgrowth ✔ Helps crowd out pathogens ✔ Supports gut recovery phase Dose: 1–2 capsules daily This is usually the only probiotic used during active treatment.
Klaire Labs SFI Saccharomyces Boulardii Probiotics
 
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Spore-based probiotic used after SIBO is cleared. ✔ Reconditions microbiome safely ✔ Less risk of feeding SIBO recurrence ✔ Helps rebalance gut ecosystem Start low: 1 capsule every other day Slow ramp-up is important — reactions are common early on.
MegaSporeBiotic - Microbiome Labs
 
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Rebuilds gut lining after SIBO damage. ✔ Repairs intestinal barrier ✔ Reduces new food sensitivities ✔ Supports post-infection healing Dose: 5g daily, empty stomach Critical for full recovery — not optional in most cases.
Amazon.com: Pure Encapsulations L-Glutamine Powder
 
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Soothes inflamed intestinal tissue during recovery. ✔ Calms irritation + reflux ✔ Supports gut lining healing ✔ Fast symptom relief support Use before meals as needed during recovery phase.
4 Soothing Herbs For An Irritated Gi Tract - Thorne