Autoimmune Reset Protocol

The science

Tight junction failure

Claudins, occludins and zonula occludens form the seals between intestinal cells. Zonulin — released by gliadin and certain bacteria — opens these junctions. Chronic opening makes the barrier permeable. Bacteria, food antigens and lipopolysaccharides (LPS) enter systemic circulation.

Dysbiosis

38 trillion microorganisms regulate immune tolerance and produce butyrate and other SCFAs that feed the gut lining. Loss of Akkermansia muciniphila — the keeper of the mucus layer — is documented across psoriasis, rheumatoid arthritis, Hashimoto's and lupus.

Molecular mimicry

Foreign antigens from the leaky gut trigger antibody production. Some of those antigens share structural sequences with your own tissue. The antibodies cross-react. The tissue being attacked is not the source of the problem — the gut is.

The LPS endotoxin loop

LPS binds TLR-4 and activates NFkB — the master switch of inflammation. Metabolic endotoxemia is documented in psoriasis, type 2 diabetes, MS and non-alcoholic fatty liver. Same broken barrier. Same fix.

The 3R framework

Phase 01 — Remove (days 1–14)

• Gluten — releases zonulin within minutes, even in non-celiac individuals.
• Refined sugar — feeds pathogenic bacteria, drives Candida, activates NFkB.
• Industrial seed oils — oxidised linoleic acid drives the arachidonic cascade.
• Alcohol — directly increases permeability, kills Lactobacillus colonies within hours.
• Ultra-processed foods — emulsifiers (polysorbate 80, CMC) disrupt the mucus layer.
• A1 dairy — beta-casomorphin-7 has documented immune-activating effects.

Phase 02 — Repair (days 15–45)

L-Glutamine, Zinc Carnosine, Bovine Colostrum, Quercetin + Bromelain, Slippery Elm, and Vitamin D3 + K2 rebuild the epithelium and restore tight junction proteins. Full stack and dosing in the supplement section below.

Phase 03 — Reinoculate (days 30–90)

Multi-strain probiotic + Saccharomyces boulardii + prebiotic fibre + daily fermented foods. Restore Akkermansia and Bifidobacterium colonies. The microbiome rebuild is what makes the changes permanent.

The supplement stack

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Lifestyle architecture

Supplements work. Lifestyle determines how fast. Chronic stress directly opens tight junctions and drives Th17 activity — the exact pathway the supplements are trying to calm. Non-negotiables:

• Breathwork — 10 min coherent breathing (5.5 breaths/min) morning and evening.
• Sleep — 7–9 hours, consistent wake time, no screens 60–90 min before bed.
• Movement — walking, yoga, swimming. Avoid high-intensity training during active flare.
• Fasting window — 12–16 hours overnight. Finish eating by 8pm.
• Cold finish — 30–60 second cold shower daily. Reduces TNF-alpha and IL-6.
• Vagus nerve — humming, gargling, cold face exposure. 5 minutes daily.