Gut barrier and inflammation protocols 6-week protocol 11 food prescriptions

Leaky Gut 6-Week Repair Protocol

Leaky gut, more precisely intestinal hyperpermeability, is the loosening of the tight junctions between intestinal cells. The most direct stool marker is Zonulin, the only known physiological regulator of those tight junctions. Calprotectin, Secretory IgA, and Akkermansia muciniphila add the inflammation, immunity, and barrier-support context. This protocol works at three levels in sequence. Phase 1 removes the most common tight-junction disruptors (alcohol, NSAIDs, gluten, certain lectins, ultra-processed foods) and adds collagen peptides plus L-glutamine to support the cells lining the gut. Phase 2 introduces zinc carnosine and polyphenol-rich foods that specifically raise Akkermansia, the keystone species behind a healthy mucus layer. Phase 3 reintroduces foods systematically while monitoring symptoms, and establishes the long-term diversity targets that keep zonulin in check.

Who this protocol is for

Adults with elevated stool Zonulin, adult-onset food sensitivities, autoimmune flares without a clear trigger, or unexplained skin and joint symptoms suspected to have a gut barrier component.

What to expect, week by week

  1. 1 Week 1 to 2: Symptom changes are subtle at first. Many people report better sleep within the first week, before any digestive change.
  2. 2 Week 3 to 4: Skin clears, joint pain eases, food reactions reduce in intensity (not always frequency).
  3. 3 Week 5 to 6: Energy stabilizes, food reintroduction becomes possible.
  4. 4 Retest Zonulin at 12 weeks. Marker change lags symptom change.

The 6-week food plan

Built from the protocol for Zonulin, the primary marker behind this condition. Phase 1 is partially visible. The full plan with exact quantities unlocks when you upload your stool test PDF.

Phase 1 Weeks 1 & 2 · Remove and Reduce
  • Collagen peptides (grass-fed) See your personalized dose
  • Bone broth See your personalized dose
Phase 2 Weeks 3 & 4 · Seed and Feed Locked
Phase 3 Weeks 5 & 6 · Build and Sustain Locked

Unlock the full personalized version

This is the off-the-shelf protocol for Leaky gut protocol. Upload your stool test PDF and we will build the version that handles your specific marker pattern (most people have 4 to 7 abnormal markers, not just one), with conflicts resolved and a grocery list ready to send to Instacart or Kroger.

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The markers behind this protocol

The primary driver is Zonulin. Click through for what the result means in detail. Supporting markers below often co-occur and inform the full protocol.

Primary driver Elevated Zonulin Supporting marker Low Secretory IgA Supporting marker Elevated Calprotectin Supporting marker Low Akkermansia muciniphila

Common mistakes practitioners see

  • Treating leaky gut as a permanent diagnosis instead of a state. Zonulin responds to inputs.
  • Adding 50 supplements before removing the disruptors (alcohol, NSAIDs, sleep loss).
  • Skipping the reintroduction phase. Permanent food avoidance worsens microbiome diversity over time.
  • Ignoring stress and sleep. Both directly raise Zonulin within hours.

When to escalate

  • Blood or mucus in stool.
  • Severe abdominal pain.
  • Persistent diarrhea with weight loss.
  • New autoimmune diagnosis appearing during the protocol (rule out trigger before continuing).

These signs mean stop the protocol and see a clinician. The protocol is not designed to manage acute or severe disease.

Tests that produce the markers driving this protocol

Diagnostic Solutions Laboratory · Upload supported GI-MAP Genova Diagnostics · Upload supported Genova GI-Effects

Frequently asked questions

Do I need to do the full 6 weeks?
Yes. Symptom changes show up within 2 to 3 weeks for most people, but the underlying microbiome shift takes the full duration. Stopping at week 2 because you feel better is the single most common reason protocols fail.
Can I do this protocol without a stool test?
You can run the off-the-shelf version of this protocol without a test. The trade-off: you lose the personalization that addresses your other markers. Most people on a stool test have 4 to 7 abnormal markers, not just one. The personalized version sequences interventions based on which combinations are present.
What if I have multiple findings on my test?
Almost everyone does. Upload your full PDF instead of running this single-condition protocol. The personalized output handles marker conflicts (for example, fiber that helps one marker can worsen another) and sequences phases in the right order across all of them.
When should I retest?
8 to 12 weeks after starting the protocol is the validated retest window for most stool tests. Earlier than that, the markers have not had time to change. Later than that, you lose the ability to attribute changes to the protocol vs. drift.
Should I work with a practitioner alongside this?
For protocols involving parasites, H. pylori, or significant inflammation (Calprotectin above 120 µg/g), yes. For dysbiosis, low diversity, or low SCFA findings, dietary protocols can be self-directed for most people. The 'when to escalate' section above lists the specific signs that mean stop and see a clinician.

Get the version built for your full report

This protocol assumes a single primary driver. Most stool tests show 4 to 7 abnormal markers. Upload your PDF and get the version that handles all of them, in the right order.

Upload your lab PDF