Gut Healing Protocol

Testing: Know Your Baseline

Before starting, consider testing to identify what you're working with:

• Intestinal permeability: lactulose/mannitol test measures how much large-molecule lactulose leaks through tight junctions. Elevated ratio confirms increased permeability.
• Zonulin: serum or stool zonulin is a biomarker for tight junction integrity. Elevated in celiac disease, gluten sensitivity, and other barrier dysfunction.
• Stool testing (GI-MAP): identifies pathogens, commensal balance, digestive markers (elastase, steatocrit), and inflammatory markers (calprotectin).

Phase 1: Remove (Weeks 1-4)

Remove everything that irritates the gut lining. This is the most impactful step and the one most people skip or do halfway.

• Food triggers identified by elimination diet (gluten, dairy, soy, corn, eggs, sugar at minimum)
• NSAIDs (ibuprofen, aspirin) -- directly damage gut lining within hours of use
• Alcohol -- increases intestinal permeability dose-dependently
• Identified pathogens (bacterial, parasitic, fungal) via targeted antimicrobials

Evidence level: strong. The connection between NSAIDs, alcohol, and gut permeability is well-established in mainstream gastroenterology.

Phase 2: Replace (Weeks 1-4, concurrent)

Replace digestive factors that may be insufficient:

• Digestive enzymes: broad-spectrum with meals, especially if bloating occurs within 30 minutes of eating
• Betaine HCl: if low stomach acid suspected (bloating, undigested food in stool, reflux paradoxically). Start with 1 capsule, increase until warmth felt, then back off by 1.
• Bile salts: if fat malabsorption present (pale/floating stools), especially post-gallbladder removal

Evidence level: moderate. Enzyme supplementation has evidence for specific conditions (pancreatic insufficiency). Betaine HCl evidence is largely clinical, not from RCTs.

Phase 3: Reinoculate (Weeks 2-8)

Reintroduce beneficial bacteria through both supplementation and fermented foods:

• Probiotics: multi-strain, 20-50 billion CFU. Lactobacillus and Bifidobacterium species have the most evidence. Saccharomyces boulardii for antibiotic-associated issues.
• Prebiotics: fiber that feeds beneficial bacteria. Start low (GOS, FOS, inulin). If SIBO is present, prebiotics can worsen symptoms initially.
• Fermented foods: sauerkraut, kimchi, kefir, yogurt. Provide both bacteria and postbiotics. Stanford study showed fermented foods increased microbiome diversity more effectively than high-fiber diet.

Evidence level: moderate to strong for specific strains in specific conditions. The general "take a probiotic" advice is weaker than strain-specific evidence.

Phase 4: Repair (Weeks 4-12)

Provide nutrients that directly support gut lining repair:

• L-glutamine: primary fuel source for enterocytes (gut lining cells). 5-10g/day. Best-studied gut repair nutrient.
• Zinc carnosine: stabilizes gut mucosa. 75 mg twice daily. Evidence from H. pylori and NSAID damage studies.
• Collagen / bone broth: provides glycine and proline for connective tissue repair. Evidence is mostly mechanistic, not clinical.
• Butyrate: short-chain fatty acid produced by gut bacteria from fiber. Primary fuel for colonocytes. Can be supplemented directly or produced via resistant starch intake.

Evidence level: L-glutamine and zinc carnosine have moderate clinical evidence. Collagen and bone broth are mechanistically plausible but clinically unproven for gut healing specifically.

Timeline

Minimum commitment: 4 weeks for noticeable improvement. Full protocol: 8-12 weeks. Some individuals with autoimmune-driven gut damage may need 6+ months. The gut lining itself regenerates in days, but restoring microbiome diversity, reducing inflammation, and identifying all triggers takes considerably longer.