SIBO Repair-4
A doctor-formulated, 42-day clinical protocol to clear the bacterial overgrowth in your small intestine, repair the gut barrier, and restore the Migrating Motor Complex (MMC) function that keeps SIBO from coming back. Drawn from 30 years of clinical practice — sequenced to address all three SIBO types (hydrogen, methane, hydrogen sulphide).
SIBO is a small-intestine motility problem at its core.
Bloating that builds through the day. Pain after eating. Distension that makes your clothes feel tight by evening. Food sensitivities that seem to multiply. The hallmark symptoms of SIBO are the downstream consequence of bacteria overgrowing where they shouldn't be — in the normally low-bacteria environment of the small intestine.
Three SIBO types, one root cause. Hydrogen-dominant overgrowth (50-66% of cases, driving diarrhoea and pain), methane/IMO (~30%, driving constipation), and hydrogen sulphide (~25%, driving brain fog and sulphur-smelling gas) all stem from the same predisposing factor: impaired Migrating Motor Complex — the 90-minute cleansing wave that's supposed to sweep bacteria into the colon during fasting.
Compounded by 1,000-fold biofilm resistance, deconjugated bile acids, brush border damage, and the leaky gut barrier driving systemic symptoms — SIBO is a sequencing problem. The right antimicrobials in the wrong order won't work. This protocol is built around the sequence.
Four mechanisms. Forty-two days. The right sequence.
Biofilm Disruption
N-Acetyl Cysteine (600mg) — taken 30 minutes before antimicrobials
SIBO bacteria shield themselves in biofilms that may reduce antimicrobial penetration by up to 1,000-fold. NAC's sulfhydryl group cleaves the disulfide bonds holding the biofilm matrix together — physically weakening the shield before antimicrobials arrive. Recent studies show biofilm disruptors plus herbal antimicrobials achieve 60-100% SIBO eradication rates. NAC also supports glutathione synthesis for detoxification during die-off.
Phase 1 — strip the protective layer.
Antimicrobial Double-Strike
Enteric-coated essential oils + enhanced-absorption berberine (6× bioavailability)
Two complementary antimicrobial mechanisms hit the small intestine simultaneously. Enteric-coated oregano, clove, thyme, and phellodendron deliver concentrated essential oils past stomach acid — carvacrol creates pores in bacterial cell membranes. Lipid-delivery berberine achieves 6-fold greater absorption than standard supplements. The Johns Hopkins Chedid study found berberine-based herbal therapy outperformed rifaximin (46% vs 34% negative breath tests).
Phase 1 — eradicate exposed bacteria across all three SIBO types.
Endotoxin Neutralisation
Serum-derived bovine immunoglobulin (>50% IgG + IgA, IgM)
Bacterial die-off releases LPS endotoxins from gram-negative species — the primary driver of intestinal inflammation and barrier dysfunction in SIBO. These immunoglobulins bind LPS directly inside the gut lumen, neutralising them before they translocate. Protecting the gut barrier during the intensive 28-day eradication phase is critical to a tolerable die-off and a clean rebuild.
Phase 1 — shield the gut barrier through eradication.
Targeted Rebuild + MMC Restoration
L. reuteri DSM 35055 (10B CFU) + B. coagulans IS2 (4B CFU) + optional prokinetic
L. reuteri specifically colonises the upper GI — the SIBO terrain — and produces reuterin, a natural antimicrobial. B. coagulans is a spore-based probiotic that survives gastric acid and the residual antimicrobial environment of Phase 2. Where indicated, a prokinetic (5-HT4 agonist) restores the Migrating Motor Complex — the 90-minute cleansing wave whose impairment is the single most important predisposing factor for SIBO recurrence.
Phase 2 — rebuild into a receptive small intestine.
Backed by the MMC–biofilm–barrier axis.
From overgrowth to lasting remission.
SIBO breath test + Microbiome Doctor consult.
Complete a hydrogen and methane breath test to confirm overgrowth and identify your SIBO type (hydrogen-dominant 50-66%, methane/IMO ~30%, or hydrogen sulphide ~25%). A Microbiome Doctor reviews your results, personalises the protocol, and — where indicated — prescribes targeted antibiotics and/or a prokinetic to restore MMC function.
Phase 1 — Eradication (28 days).
NAC strips protective biofilms 30 minutes before antimicrobials arrive. Enteric-coated essential oils and lipid-delivery berberine deliver the antimicrobial double-strike directly to the small intestine. Immunoglobulin powder binds the LPS endotoxins released during die-off. Strict Low-Fermentation Restoration Protocol denies the overgrowth its fuel. Antibiotics, if prescribed, run for the first 14 days.
Phase 2 — Rebuild (14 days).
Bactrex continues as ongoing antimicrobial coverage, taken at least 2 hours before probiotics. L. reuteri re-colonises the upper GI tract with anti-inflammatory strains. Spore-based B. coagulans seeds the colon with antimicrobial-resistant beneficial flora. Low-Fermentation Protocol continues unchanged — fermentable foods stay out until your follow-up consult.
Maintain.
Transition to SIBO Maintain — daily probiotic plus prokinetic support — for a minimum of 6 months. 44% of SIBO patients relapse within 9 months without this step. Maintain 4-5 hour meal spacing and a 12-14 hour overnight fast to support ongoing MMC function. Guided FODMAP reintroduction begins under clinical oversight.
Re-test SIBO breath test.
Repeat your hydrogen and methane breath test at the 6-month mark to objectively confirm sustained eradication, identify any returning overgrowth, and decide whether continued intervention is warranted.
Questions, answered.
Who is this protocol for?
Adults with a positive SIBO breath test (hydrogen, methane/IMO, or hydrogen sulphide), or with clinical signs consistent with small intestinal bacterial overgrowth: persistent bloating that builds through the day, postprandial distension, alternating bowel habits, brain fog, fatigue, or food sensitivities that have multiplied. Also appropriate for patients with predisposing factors — impaired MMC, chronic PPI use, prior gastrointestinal infections, or ileocaecal valve dysfunction.
Do I need a Microbiome Doctor consult before starting?
Strongly recommended. A consult provides three things: a personalised review of your SIBO breath test results (confirming the type and severity of overgrowth), a protocol calibrated to your findings, and — where indicated — a prescription for targeted antibiotics and/or a prokinetic (Resotrans / Prucalopride) to restore MMC function. The protocol is designed to be used alongside clinical oversight.
Will I feel worse before I feel better?
Possibly — yes. A Jarisch-Herxheimer (die-off) reaction typically peaks in the first 7-10 days of Phase 1 as antimicrobials kill overgrown bacteria and toxins are released. Common: temporarily worse bloating, fatigue, brain fog, headaches, mild nausea. The immunoglobulin powder is specifically included to bind and neutralise these toxins. Stay hydrated (2-3L water daily). Contact the clinic if symptoms are severe or persist beyond 10 days.
Can I take this with my existing medications?
Generally yes, with one important consideration: berberine (Berb-Evail) may interact with the cytochrome P450 enzyme system — disclose all supplements to your prescribing doctor, particularly if you take medications metabolised by P450 (some statins, immunosuppressants, anticoagulants). No dangerous interactions documented with common SIBO-relevant medications (PPIs, prokinetics, antispasmodics, antibiotics). Separate supplement intake from prescription medications by 1-2 hours.
Can I take this if I'm pregnant or breastfeeding?
No. Two components carry explicit pregnancy warnings: the enteric-coated essential oil blend (Bactrex) and the enhanced-absorption berberine (Berb-Evail). Both are not to be taken if you are pregnant, breastfeeding, or planning to become pregnant. If this applies to you, please consult your Microbiome Doctor for an alternative protocol approach — do not start this program.
Are there any allergens I should know about?
Bovine: The immunoglobulin powder is derived from bovine serum (not milk) — generally fine for dairy-allergic patients, but disclose to your doctor. Sulphites + bovine gelatin: The enteric-coated essential oil blend contains sulphites and bovine gelatin. Halal-certified gelatin is used in the berberine capsule. Review allergen labels before starting.
Why is the diet so important for SIBO?
Bloating is the most stubborn SIBO symptom, and dietary compliance is the single strongest predictor of treatment success. The overgrown bacteria in your small intestine feed on fermentable carbohydrates — every high-FODMAP meal during the program directly fuels the overgrowth you're trying to eradicate. The Low-Fermentation Restoration Protocol (included with the program) is not optional. Nothing fermentable should be reintroduced until your follow-up Microbiome Doctor consult.
What happens after the 42 days?
Day 43 isn't the finish line — it's the start of the maintenance phase. Up to 44% of SIBO patients relapse within 9 months without a structured maintenance strategy. Transition to SIBO Maintain (daily probiotic + prokinetic support) for a minimum of 6 months. Continue 4-5 hour meal spacing and 12-14 hour overnight fasting to support MMC function. Re-test your SIBO breath test at the 6-month mark to objectively confirm sustained eradication.
Important — general advice only. Information presented on this page is general health information and is not personal medical advice. Always consult your treating practitioner before starting any new supplement.
Pregnancy: Two components of this protocol — the enteric-coated essential oil blend and enhanced-absorption berberine — carry explicit pregnancy warnings and are not to be taken if you are pregnant, breastfeeding, or planning to become pregnant. Consult your Microbiome Doctor for an alternative if this applies.
Allergens: The immunoglobulin powder is derived from bovine sources. The enteric-coated essential oil blend contains sulphites and bovine gelatin. Review allergen labels before starting.
These products are listed complementary medicines and are not intended to diagnose, treat, cure, or prevent any disease. The Microbiome Clinic has no commercial affiliation with any specific supplement brand included in this protocol — supplements are selected on the basis of clinical evidence alone, in line with the Microbiome Clinic Independence Guarantee.