Who this is for
You bloat within 30–90 minutes of eating, not hours. Worse with fibre, worse with probiotics, worse with the “healthy” foods everyone told you to eat more of. You have maybe done a round of something, felt genuinely better for six weeks, and watched it all come back.
The thing this whole protocol turns on
Your small intestine stays sparse because of the migrating motor complex — a sweeping wave that clears it between meals. When that wave weakens, bacteria that belong downstream colonise upstream and ferment your food before you absorb it. That is the entire reason recurrence is the norm. You can sterilise the small bowel, and if the wave is still broken you have reset a clock, not fixed a problem.
This is not a theory you have to take on faith. Adding a low-dose nightly prokinetic after successful treatment delayed symptom recurrence compared with treatment alone. (PMID 20574504)
- Reduce the overgrowth
- Restore the sweep — the one people skip
- Repair the barrier and the absorption
Anyone selling you arm one alone is selling you a repeat customer.
Why it broke — find yours
- Post-infectious. Food poisoning triggers antibodies (anti-CdtB, anti-vinculin) that cross-react with the nerve tissue driving the sweep. The most common cause, and validated as a human biomarker. (PMID 25970536)
- Hypothyroidism. Slows transit directly. A cause, not a coincidence — check TSH, free T4 and free T3.
- PPIs and low stomach acid. Acid is a barrier. Remove it and things survive the trip.
- Opioids, anticholinergics, some antidepressants. All slow the sweep.
- Structural. Adhesions from surgery, strictures, diverticula, ileocecal valve dysfunction.
- Diabetes or autonomic neuropathy. The nerves that drive the wave are the nerves that get damaged.
Know your phenotype before you buy anything
Treating all three the same is the second most common reason this fails. The breath test is what tells you which one you have, and the ACG guideline puts it at the centre of diagnosis. (PMID 32023228)
| Phenotype | Presents as | What it is |
|---|---|---|
| Hydrogen-dominant | Diarrhoea, bloating | Bacteria |
| Methane-dominant (IMO) | Constipation, hard stool | Archaea, not bacteria |
| Hydrogen sulfide | Rotten-egg gas, diarrhoea, sulfur reactions | Sulfate-reducing bacteria |
What your labs are telling you
| What to look at | Why it matters here |
|---|---|
| Vitamin B12 + MMA | Bacteria consume B12. MMA catches tissue-level deficiency while serum B12 still reads “normal.” |
| Folate | The counter-intuitive one — gut bacteria make folate, so overgrowth can push serum folate high. Low B12 sitting next to high folate is the pattern worth noticing. |
| Ferritin + full iron panel | Iron is absorbed in the duodenum and proximal jejunum — exactly where the overgrowth sits. |
| Vitamin D (and A, E, K if available) | Fat malabsorption from bacterial bile-salt deconjugation shows in the fat-soluble vitamins first. |
| Zinc, copper, selenium | Depleted by malabsorption — and zinc is required for the barrier repair in arm three. |
| Albumin and liver enzymes | Albumin is a crude but honest read on whether you are absorbing protein. |
| hs-CRP and ESR | Normal rules nothing out, but meaningfully raised points at IBD rather than SIBO. |
| TSH, free T4, free T3 | Because hypothyroidism is a cause of the motility failure. |
| tTG-IgA + total IgA | Coeliac. Total IgA matters — IgA deficiency makes the coeliac test falsely negative. |
| Lipase and amylase | Pancreatic insufficiency mimics this almost perfectly. |
Test before you treat
You cannot tell which phenotype you have, or whether you are actually malabsorbing, without numbers. This is the Gut Health & Absorption panel — 11 markers, loaded into the cart in one click with Cam’s code already applied.
Drawn at Quest. Results in days, not weeks. Paste them into the Bloodwork Vault when they land.
Reduce the overgrowth
A herbal antimicrobial protocol performed equivalently to rifaximin for breath-test normalisation in a head-to-head trial. One study — strong enough to build on, not strong enough to call settled. Rifaximin itself has real randomised evidence, and for methane it underperforms unless paired with neomycin. Both are prescriptions; that conversation is with your doctor.
PMID 24891990 PMID 21208106 PMID 19996983
The sulphur compound responsible for most of garlic's biological activity — and it is chemically unstable, which is the entire practical problem with this category.
A potent antimicrobial essential oil (carvacrol/thymol) used short-term for gut-flora balance and immune defense.
A plant alkaloid that activates AMPK — the same energy-sensing pathway as exercise and metformin — with powerful effects on glucose and lipid metabolism.
Tree resin from the Greek island of Chios with a small but real evidence base in upper-GI symptoms.
Innate-immune antimicrobial peptide — disrupts microbial membranes and modulates inflammation and wound healing.
If your test said hydrogen sulfide
The phenotype almost nobody addresses, and there is one tool with direct human data. Bismuth subsalicylate markedly decreases hydrogen sulfide release in the human colon — measured in people, not modelled. The black tongue is the sulfide-binding reaction, not a side effect to fear. The honest caveat: binding sulfide did not protect rats from colitis. It reduces the gas; whether that fixes your disease is not established.
PMID 9558280 PMID 10961726 PMID 29767695
An essential trace mineral cofactor for enzymes that detoxify sulfites and process amino acids — useful for sulfite sensitivity.
Restore the sweep — the arm that decides whether this comes back
Ginger and artichoke together beat placebo in a randomised, double-blind trial and improved gastric motility in healthy volunteers — the best-evidenced natural prokinetic pair you can buy. Iberogast’s nine-herb preparation has a positive meta-analysis behind it, which is better human evidence than most of this page.
PMID 25954317 PMID 26813467 PMID 15606389 PMID 20413719
A root with strong evidence for nausea (motion sickness, pregnancy, chemo) plus digestion and anti-inflammatory support.
A nine-herb liquid preparation (bitter candytuft, angelica, chamomile, caraway, milk thistle, lemon balm, peppermint, celandine, liquorice) developed in Germany for functional gut symptoms.
Direct serotonin precursor derived from Griffonia seed — one step closer to serotonin than tryptophan.
Repair the barrier and the absorption
Zinc carnosine has human evidence for stabilising small bowel integrity and stimulating gut repair — the best-evidenced item in this section. Larazotide has the best human data of the peptides, from Phase 3 in coeliac; it is a tight-junction regulator, which is the actual mechanism people mean when they say “leaky gut.”
A zinc-and-carnosine complex that adheres to and heals the stomach and gut lining — excellent for ulcers, gastritis and leaky gut.
Zonulin antagonist — tightens intestinal tight junctions to reduce 'leaky gut' permeability; furthest-along gut-barrier drug (celiac trials).
Cytoprotective peptide from gastric juice — upregulates VEGFR2/angiogenesis, nitric-oxide and growth-factor pathways to accelerate tendon, gut, muscle and nerve repair.
Anti-inflammatory tripeptide from α-MSH — calms NF-κB signaling systemically and in the gut.
The most abundant amino acid in the body and a primary fuel for gut and immune cells.
The nutrient- and antibody-rich 'first milk,' packed with immunoglobulins, lactoferrin and growth factors for gut-lining and immune support.
An iron-binding immune protein that supports gut and systemic immunity, regulates iron, and has antimicrobial/antiviral activity.
The primary short-chain fatty acid that fuels colon cells — the postbiotic your gut bacteria normally make from fiber, supplied directly.
Digestion and symptom control
None of this clears an overgrowth. It makes the months while you do liveable, and it supports absorption while absorption is still poor. Enteric-coated peppermint oil has two independent meta-analyses behind it in IBS.
Enteric-coated peppermint oil that relaxes gut smooth muscle — one of the best-evidenced natural tools for IBS.
Supplemental stomach acid (with the enzyme pepsin) for people with low gastric acid, which impairs protein and mineral absorption.
Supplemental bile salts for people who cannot make or release enough of their own — most relevantly after gallbladder removal.
A blend of digestive enzymes plus betaine HCl and bile support to help break down protein, fat and carbohydrate — useful when digestion is sluggish.
A demulcent bark that forms a soothing gel to coat and calm an irritated digestive tract — classic support for reflux, IBS and sore throat.
A demulcent — its mucilage forms a slippery gel that physically coats irritated mucous membranes.
Licorice with the blood-pressure-raising glycyrrhizin removed — soothes the stomach and supports the mucosal lining for reflux and ulcers.
A soothing inner-leaf gel for gut-lining comfort, regularity and (topically) skin — used internally for reflux and IBS.
What to stop wasting money on
- Probiotics during the antimicrobial phase. You are taking bacteria for a bacterial overgrowth. Saccharomyces boulardii is the sensible exception — a yeast, it does not colonise. Reintroduce bacterial probiotics after the sweep is working, if at all.
- “Leaky gut” stool panels. Poorly validated, expensive, and they will not change what you do.
- Food sensitivity IgG panels. IgG is an exposure marker. It tells you what you eat.
- Elimination diets as a permanent home. Low-FODMAP is a diagnostic and symptom-control tool for weeks, not a life. Starving your microbiome long-term makes the underlying problem worse.
- Glutamine megadoses as a standalone cure. It supports the lining. It does not clear an overgrowth.
- A fourth round of the same antimicrobial. If three did not hold, the answer is upstream — motility, thyroid, structure — not another bottle.
The 16-week protocol is inside Skool
Everything above is yours free — what it is, why it recurs, what to test, and every compound by name. What is inside is what to actually do with them.
- Which compounds go with which phenotype — the pairing that decides whether this works
- The phenotype-matched arsenal with doses — hydrogen, methane and sulfide each get their own
- The 16-week schedule, week by week, including when each arm starts and stops
- The sequencing rules — what must not overlap, and why
- The decision tree for “it is not working” at week 4, week 8 and week 12
- How to read the retest, and what counts as actually fixed
Retest, and what “working” looks like
At 10–12 weeks, re-run the panel above.
Working:
- MMA falling and B12 rising
- Folate coming down toward mid-range if it was high
- Ferritin and transferrin saturation climbing
- Albumin stable or up
- Fibre tolerated without 90-minute bloating
- Meals spaced 4–5 hours without distress
Not working: Symptoms returning within 4–6 weeks of stopping the antimicrobials. That is a motility answer, not a stronger-antimicrobial answer.
Where to go next
The SIBO goal pathways map the same territory by mechanism rather than by condition, and the gut blueprint is the broader stack this protocol sits inside.
Not getting anywhere on your own?
This page is a template, and a template cannot see your history, your labs or the three things you already tried. Tell Cam where you are now and he will build the version of this that fits you.
Questions people actually ask
Why does SIBO keep coming back?
Because SIBO is a motility failure, not an infection. A sweeping wave called the migrating motor complex is supposed to clear the small intestine between meals; when it weakens, bacteria colonise upstream. Killing them without restoring that wave resets a clock rather than fixing the problem, which is why recurrence is the norm rather than the exception. In one trial, adding a low-dose nightly prokinetic after successful treatment measurably delayed relapse.
What are the three types of SIBO?
Hydrogen-dominant, which usually presents as diarrhoea; methane-dominant (properly called intestinal methanogen overgrowth), which usually presents as constipation and is caused by archaea rather than bacteria; and hydrogen sulfide, which presents with rotten-egg gas and sulfur reactions. They need different treatment, and treating all three the same is one of the most common reasons people fail to get better.
Can a blood test diagnose SIBO?
No. SIBO is diagnosed on a breath test measuring hydrogen and methane. Blood work is still worth running, because it shows the consequences — B12 and iron depletion, low fat-soluble vitamins, sometimes a raised folate from bacterial production — and because it rules out coeliac disease, inflammatory bowel disease, pancreatic insufficiency and thyroid disease, which mimic SIBO and are frequently missed for years.
Should you take probiotics with SIBO?
Not during the antimicrobial phase — you would be adding bacteria to a bacterial overgrowth, and the evidence is genuinely mixed with many people feeling worse. Saccharomyces boulardii is the sensible exception because it is a yeast and does not colonise. Bacterial probiotics are better reintroduced later, once motility is working, and only if they are tolerated.
How long does it take to treat SIBO?
Plan on around sixteen weeks, not four. Roughly four weeks to reduce the overgrowth, then at least three months of prokinetic support to restore the sweep, with barrier repair running alongside. The single most common mistake is stopping after the antimicrobial phase, which is the point at which most people feel better and most relapses begin.
Does bismuth help hydrogen sulfide SIBO?
Bismuth subsalicylate has been shown in humans to markedly reduce hydrogen sulfide release in the colon, and the black tongue and stool it causes are that sulfide-binding reaction. What has not been established is whether reducing the gas changes the disease — in a rat colitis model, binding sulfide did not protect the animals. It is a reasonable, well-evidenced tool for the symptom, not a proven cure for the condition.
Sources
Every reference below was resolved against the NCBI PubMed API on 23 August 2026 — title, journal and year read back from NCBI rather than from memory.
- PMID 32023228 — Pimentel M. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Am J Gastroenterol, 2020.
- PMID 24891990 — Chedid V. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med, 2014.
- PMID 21208106 — Pimentel M. Rifaximin therapy for patients with irritable bowel syndrome without constipation. N Engl J Med, 2011.
- PMID 19996983 — Low K. A combination of rifaximin and neomycin is most effective in treating IBS patients with methane on lactulose breath test. J Clin Gastroenterol, 2010.
- PMID 20574504 — Pimentel M. Low-dose nocturnal tegaserod or erythromycin delays symptom recurrence after treatment of IBS based on presumed bacterial overgrowth. Gastroenterol Hepatol, 2009.
- PMID 25970536 — Pimentel M. Development and validation of a biomarker for diarrhea-predominant IBS in human subjects. PLoS One, 2015.
- PMID 9558280 — Suarez FL. Bismuth subsalicylate markedly decreases hydrogen sulfide release in the human colon. Gastroenterology, 1998.
- PMID 10961726 — Furne JK. Binding of hydrogen sulfide by bismuth does not prevent dextran sulfate-induced colitis in rats. Dig Dis Sci, 2000.
- PMID 29767695 — Novotny JA. Molybdenum. Adv Nutr, 2018.
- PMID 25954317 — Giacosa A. The effect of ginger and artichoke extract supplementation on functional dyspepsia: a randomised, double-blind, placebo-controlled clinical trial. eCAM, 2015.
- PMID 26813467 — Lazzini S. The effect of ginger and artichoke extract supplementation on gastric motility: a pilot randomized study in healthy volunteers. Eur Rev Med Pharmacol Sci, 2016.
- PMID 15606389 — Melzer J. Meta-analysis: phytotherapy of functional dyspepsia with the herbal drug preparation STW 5 (Iberogast). Aliment Pharmacol Ther, 2004.
- PMID 20413719 — Dickson EJ. Critical role of 5-HT1A, 5-HT3 and 5-HT7 receptor subtypes in the initiation, generation and propagation of the murine colonic migrating motor complex. Am J Physiol Gastrointest Liver Physiol, 2010.
- PMID 16777920 — Mahmood A. Zinc carnosine, a health food supplement that stabilises small bowel integrity and stimulates gut repair processes. Gut, 2007.
- PMID 25683116 — Leffler DA. Larazotide acetate for persistent symptoms of celiac disease despite a gluten-free diet: a randomized controlled trial. Gastroenterology, 2015.
- PMID 24100754 — Khanna R. Peppermint oil for the treatment of irritable bowel syndrome: a systematic review and meta-analysis. J Clin Gastroenterol, 2014.
- PMID 35942669 — Ingrosso MR. Systematic review and meta-analysis: efficacy of peppermint oil in irritable bowel syndrome. Aliment Pharmacol Ther, 2022.
- PMID 16716248 — Dürr UH. LL-37, the only human member of the cathelicidin family of antimicrobial peptides. Biochim Biophys Acta, 2006.
- PMID 29589544 — Chieosilapatham P. Tissue-specific regulation of innate immune responses by human cathelicidin LL-37. Curr Pharm Des, 2018.