Gut Reset Protocol
A full gut rehabilitation protocol targeting fungal overgrowth, pathogenic bacteria, biofilm, endotoxins, and gut lining repair — followed by deliberate repopulation with beneficial flora.
This protocol is assembled from the biohacking Twitter community's most repeated compounds and stacks. It is not a rigid linear sequence — phases overlap. Lining repair starts while you're still killing; repopulation begins after the kill phase settles.
Deworming sub-protocol
Antiparasitic clearance (ivermectin, fenbendazole, mebendazole) is an optional but frequently recommended first step before this protocol. See the Deworming Protocol for specifics. S. Boulardii must be run during deworming to protect native flora.
Phase 1 — Kill Fungus & Bad Bacteria
Goal: eradicate candida overgrowth, H. pylori, pathogenic bacterial overgrowths, mold/Aspergillus colonisation.
| Compound | Role | Sources |
|---|---|---|
| S. Boulardii (Florastor, CNCM I-745 strain) | Kills candida — 50% reduction vs nystatin's 18% in RCT. Antimicrobial. Anti-biofilm. Binds mycotoxins. SIBO control. 250mg 2×/day empty stomach | Gunnar · Ben Smith · Andra |
| Mastic gum | Eradicates H. pylori in 2 weeks (350mg 3×/day). Disrupts the biofilm that makes antibiotics fail 30–40% of the time | Gunnar |
| Lactoferrin | Antifungal (candida), antibacterial, antiparasitic (Giardia, Entamoeba). Chelates iron — the growth factor all pathogens depend on. 100–1000mg/day | Andra · Dalton |
| Propolis | 300+ active compounds. Kills bacteria, viruses, fungi on contact. Kills MRSA and candida | Gunnar (@FarvingCo) |
| Black seed oil | Antimicrobial, mast cell inhibition, gut-liver axis support | Fred Vine · GutOptimized · Sam |
| Coconut oil | Antifungal, membrane-disrupting | Sam |
| Itraconazole | Prescription antifungal for Aspergillus/mold colonisation. Case study: complete cognitive reversal post anti-mold protocol over 3 months | Andra |
| Nystatin | Antifungal for candida — outperformed by S. Boulardii in head-to-head RCT (18% vs 37%) | Gunnar |
Oral microbiome note
Two tweets (Gunnar · Andra) noted that brushing teeth 2–3×/day vs 1×/day reduced Candida albicans in stool — the oral and gut microbiomes are directly connected. Tongue scraping also mentioned (Fred Vine).
Phase 2 — Break Down Biofilm
Pathogens hide behind biofilm. Breaking it exposes them to antimicrobials and is often what unlocks a protocol that wasn't working.
| Compound | Role | Sources |
|---|---|---|
| NAC | Primary biofilm disruptor. Paired with selenium + molybdenum. 1000mg 2×/day | GutOptimized · Ross |
| Mastic gum | Specifically disrupts H. pylori biofilm | Gunnar |
| S. Boulardii | Anti-biofilm against candida specifically | Andra |
| Bismuth | Biofilm disruptor, used in H. pylori eradication protocols | Sam |
| Lactoferrin | Iron chelation starves biofilm communities | Andra · Dalton |
| Propolis | Broad-spectrum biofilm disruption | Gunnar (@FarvingCo) |
| Turpentine | "Removes biofilm" — causes parasites to flee. Controversial. Pure gum spirits of turpentine only | Victor Scott |
Phase 3 — Remove Endotoxins / LPS
Dead bacteria release endotoxins (LPS) into the bloodstream — the primary driver of visceral fat, systemic inflammation, brain fog, and hormonal disruption. Binding and clearing them is critical.
| Compound | Role | Sources |
|---|---|---|
| Enterogel | Direct endotoxin binder. Step 2 in gut-liver axis healing | Fred Vine |
| Raw carrots / carrot salad | Mechanical gut endotoxin cleanse (Ray Peat approach). Boiled mushrooms alongside | anabology |
| S. Boulardii | "Toxin binding (endotoxins, mycotoxins)" + reduces LPS + bile support | Andra |
| Lactoferrin | Direct LPS neutraliser. Binding endotoxins → stops visceral fat signal | Andra · Gunnar |
| Lactobacillus reuteri | "Reduces ENDOTOXIN" shown in study counteracting junk food diet | Dalton |
| Molybdenum | Oxidative stress support during die-off. Paired with NAC + selenium | GutOptimized |
| Selenium | Paired with NAC + molybdenum for die-off oxidative stress | GutOptimized |
| Pomegranate juice | Antioxidant support during die-off, GI oxidative stress | Fred Vine · GutOptimized |
| Bile flow support (taurine, glycine, folate, choline, B2, B12) | Restoring bile flow is the gut-liver axis endotoxin clearance pathway | GutOptimized |
| Castor oil packs | Gut-liver axis lymphatic support | Fred Vine |
Phase 4 — Heal & Seal the Gut Lining
Clearing pathogens without repairing the barrier leaves LPS translocation ongoing. These compounds rebuild the epithelium and restore tight junction proteins (Claudin-3).
| Compound | Role | Sources |
|---|---|---|
| BPC-157 | Rebuilds gut epithelium from the bottom up. 500mcg oral daily. Outperformed Pepcid in ulcer healing. Stops LPS translocation, reverses neuroinflammation | Gunnar · BasedBiohacker · Healthy Alfred |
| L-Glutamine | Gut barrier repair. 15g 2×/day (testimonial: decades of issues resolved in 2 months) | Michael · GutOptimized |
| Zinc L-Carnosine | Protects Claudin-3 (gut sealing protein) | Andra · Sam |
| Colostrum | Heals leaky gut — 500mg/day reversed all permeability markers (zonulin, L/M ratio) in athletes | Dalton · Andra |
| Lactoferrin | Restores gut barrier, Claudin-3 protection | Andra · Dalton |
| Butyrate / Sodium butyrate | Claudin-3 protection. SCFA fuel for colonocytes | Andra |
| Gelatin / Bone broth | Gut lining structural repair, collagen/glycine source | Gunnar · GutOptimized |
| Glycine | Gut lining support. Synergises with NAC for glutathione (+120% synthesis) | Dalton · Sam |
| Larazotide | Gut barrier peptide | GutOptimized · Sam |
| GHK-Cu | Healing peptide | Sam |
| Quercetin | Claudin-3 protection, anti-inflammatory | Andra |
| Curcumin (Meriva) | Anti-inflammatory, gut lining support. 1000mg 2×/day | GutOptimized · Ross · Sam |
| Apigenin | Claudin-3 protection | Andra |
| EGCG / Green tea | Claudin-3 protection | Andra |
| Vitamin D | Claudin-3 protection | Andra |
| Boswellia | Anti-inflammatory, mast cell inhibition | GutOptimized · Sam |
| TUDCA | Bile acid support, gut health | Sam · Ross |
| KPV peptide | Anti-inflammatory gut peptide | GutOptimized |
Phase 5 — Repopulate with Good Flora
The goal is not just adding probiotics — it's re-establishing extinct strains that modern life (antibiotics, diet, stress) has wiped out.
| Compound | Role | Sources |
|---|---|---|
| Lactobacillus reuteri | Most-cited repopulation strain. Extinct in most modern guts. Boosts oxytocin, antimicrobial, anti-inflammatory. Make homemade yogurt at 99°F for 36h | Noah Ryan · Gunnar · Hans Amato · Vance |
| Akkermansia muciniphila | Strengthens gut lining, insulin sensitivity, reduces visceral fat. "Extinct in most guts" | Noah Ryan |
| Lactobacillus rhamnosus | Gut barrier, reduces anxiety/depression, immune boost | Noah Ryan |
| VSL#3 | Broad-spectrum probiotic. Pair with S. Boulardii timed 4h apart during kill phase, continue after | Ben Smith |
| Spore-based probiotics | Survive stomach acid, robust colonisation | Sam |
| Kefir | L. Reuteri source, mood-enhancing, natural fermented flora | Vance |
| Colostrum | Modulates bacterial composition, HMO prebiotics | anabology · Dalton |
| Raw milk | Lactoferrin + beneficial bacteria + HMOs for recolonisation | anabology |
| Resistant starch | Prebiotic fuel to establish and sustain new colonies | GutOptimized |
| Butyrate | SCFA colonocyte fuel, supports healthy microbiome environment | Andra |
| Vitamin E | Increases relative abundance of Akkermansia, Bifidobacterium, Lachnospira (SCFA producers) | Morph (@doctormorphh) |
Most Repeated Compounds Across the Protocol
These appeared in the highest number of independent tweets and stacks:
S. Boulardii · Lactoferrin · BPC-157 · Lactobacillus reuteri · L-Glutamine · Zinc L-Carnosine · Colostrum · Mastic gum · NAC · Butyrate · Black seed oil · Curcumin (Meriva)
All information compiled from biohacking Twitter discussions. Educational purposes only. Not medical advice.