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Gut Healing

Protocols and strategies for repairing gut dysfunction and restoring digestive health.

📖 The Story​

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Michael had reached his breaking point. Years of digestive issues—bloating, food intolerances that kept multiplying, brain fog, and fatigue that never lifted. He'd tried probiotics, changed his diet a dozen times, and spent thousands on supplements that didn't help.

A functional medicine practitioner finally gave him clarity. "Your gut needs healing, not just management. You've got intestinal permeability, some bacterial overgrowth, and your gut isn't producing enough enzymes. We need to address these systematically, not just throw supplements at symptoms."

The protocol wasn't glamorous: remove inflammatory foods, address the overgrowth, support digestion, repair the gut lining, and finally reintroduce foods carefully. It took six months, not six days.

Slowly, Michael's food intolerances decreased. He could eat things that had triggered him for years. The bloating resolved. His energy returned. His brain cleared.

"Why didn't I do this years ago?" he wondered.

The lesson: Gut healing is a process, not a quick fix. Systematic protocols work when random interventions don't.

🚶 The Journey​

The Gut Healing Framework

The 5R Protocol:

PhaseFocusDuration
RemoveEliminate triggers, treat overgrowth2-4 weeks
ReplaceSupport digestionOngoing
RepairHeal gut lining4-12 weeks
ReinoculateRestore microbiome4-8 weeks
RebalanceLifestyle, maintenanceOngoing

Note: These phases often overlap; this isn't always strictly sequential.

🧠 The Science​

Understanding Gut Dysfunction

Common Gut Issues Requiring Healing​

Intestinal Permeability ("Leaky Gut"):

  • Tight junctions between cells loosen
  • Allows unwanted molecules to pass into bloodstream
  • Triggers immune reactions and inflammation
  • Associated with food intolerances, autoimmunity, systemic symptoms

Causes:

  • Chronic stress
  • Poor diet (processed foods, low fiber)
  • Medications (NSAIDs, antibiotics)
  • Infections
  • Alcohol excess
  • Chronic inflammation

SIBO (Small Intestinal Bacterial Overgrowth):

  • Bacteria in wrong location (should be minimal in small intestine)
  • Fermentation happens too early in GI tract
  • Causes bloating, often severe
  • Can cause nutrient malabsorption

Dysbiosis:

  • Imbalanced microbiome
  • Can mean too few beneficial, too many opportunistic
  • Or simply low diversity
  • Contributes to many symptoms

Low Digestive Capacity:

  • Insufficient stomach acid (hypochlorhydria)
  • Insufficient enzymes
  • Insufficient bile
  • Food not properly broken down

The Healing Process​

Gut Lining Turnover:

  • Gut cells regenerate every 3-5 days
  • BUT underlying issues take longer to resolve
  • Microbiome changes take weeks
  • Immune recalibration takes months
  • Full healing: 3-12 months typically

What Needs to Happen:

  1. Remove the source of damage
  2. Provide building blocks for repair
  3. Support the process (not interfere)
  4. Restore healthy ecology
  5. Maintain long-term
## 👀 Signs & Signals

Signs Gut Healing May Be Needed​

SymptomWhat It May Indicate
Multiple food intolerancesIntestinal permeability
Bloating after most mealsSIBO, low digestive capacity
Constipation or diarrheaDysbiosis, motility issues
Brain fogGut-brain axis dysfunction
FatigueMalabsorption, inflammation
Skin issuesGut-skin axis, permeability
Joint painSystemic inflammation
Autoimmune symptomsPermeability, immune dysregulation

Signs of Healing Progress​

SignalWhat It Means
Reduced bloatingFermentation normalizing
Tolerating more foodsPermeability improving
Better bowel movementsFunction restoring
Improved energyAbsorption improving
Clearer thinkingInflammation reducing
Better moodGut-brain axis healing

Warning Signs (Seek Care)​

  • Blood in stool
  • Severe, sudden abdominal pain
  • Unintentional weight loss
  • Symptoms worsening significantly
  • Signs of malnutrition

🎯 Practical Application​

The 5R Protocol in Detail

Remove Triggers​

Inflammatory Foods (Common Triggers):

CategoryCommon IssuesWhy
GlutenZonulin release, immune reactionsPermeability, inflammation
DairyLactose, casein issuesInflammation for some
SugarFeeds problematic bacteriaDysbiosis
AlcoholDirect gut damagePermeability
Processed foodsVarious mechanismsInflammation
Personal triggersIndividual reactionsIdentified through elimination

Elimination Diet Approach:

  • Remove common triggers for 2-4 weeks
  • Note symptom changes
  • Reintroduce one at a time
  • Identify personal triggers
  • See Food Sensitivities

Treating Overgrowth (If Present):

ConditionTreatment Approach
SIBOAntimicrobials (herbal or pharmaceutical)
Candida overgrowthAntifungals, low-sugar protocol
ParasitesAntiparasitics as indicated
H. pyloriTriple therapy or herbal protocol

Common Herbal Antimicrobials:

  • Oregano oil
  • Berberine
  • Allicin (garlic extract)
  • Neem
  • Caprylic acid (candida)

Important: Work with practitioner for antimicrobial protocols

Reducing Stressors:

## 📸 What It Looks Like

Sample 12-Week Protocol​

Weeks 1-4: Remove + Replace

WeekFocusActions
1Elimination beginsRemove gluten, dairy, sugar, alcohol, processed foods
2Add digestive supportEnzymes with meals, ACV before meals
2-4Antimicrobials if neededHerbal protocol with practitioner guidance
1-4ContinueElimination diet, track symptoms

Weeks 5-8: Repair

WeekFocusActions
5Begin repair nutrientsL-glutamine 5g, zinc carnosine
6Increase repairL-glutamine 10g, bone broth daily
7-8Continue repairAdd collagen, DGL if needed
5-8Continue eliminationMaintain restricted diet

Weeks 9-12: Reinoculate + Reintroduce

WeekFocusActions
9Begin probioticsMulti-strain or spore-based
10Add prebioticsStart very slowly
11Add fermented foodsSmall amounts
12Begin reintroductionOne food at a time

Week 13+: Maintenance

  • Continue prebiotics/probiotics
  • Reintroduce foods systematically
  • Identify permanent vs temporary restrictions
  • Establish long-term habits

Sample Daily Protocol (Repair Phase)​

Morning:

  • L-glutamine (5g) on empty stomach
  • ACV in water before breakfast
  • Breakfast with digestive enzymes
  • Elimination-compliant foods

Midday:

  • Lunch with digestive enzymes
  • Bone broth (1 cup)
  • Allowed foods

Afternoon:

  • L-glutamine (5g) if taking divided doses
  • Snack if needed

Evening:

  • Dinner with digestive enzymes
  • Zinc carnosine
  • Allowed foods
  • Stress management practice

Before Bed:

  • DGL or aloe if indicated
  • Adequate sleep
## 🚀 Getting Started

Before Starting​

  • Assess your symptoms (what are you treating?)
  • Consider testing (SIBO, stool test) if uncertain
  • Find practitioner if issues are complex
  • Plan for 3-6 month commitment
  • Stock kitchen with allowed foods

Week 1 Actions​

  • Begin elimination diet
  • Start symptom tracking
  • Add digestive enzyme with meals
  • Begin stress management practice
  • Clear kitchen of trigger foods

Weeks 2-4 Actions​

  • Continue elimination
  • Add antimicrobials if indicated (with guidance)
  • Order gut healing supplements
  • Note symptom changes
  • Prepare for repair phase

Month 2+ Actions​

  • Begin repair nutrients (glutamine, zinc carnosine)
  • Add bone broth or collagen
  • Continue elimination
  • Prepare for reinoculation
## 🔧 Troubleshooting

Common Gut Healing Challenges​

"Die-off" Symptoms (Herxheimer):

  • Temporary worsening when killing pathogens
  • Headache, fatigue, flu-like symptoms
  • Usually 3-7 days
  • Support with binders (charcoal, bentonite)
  • Go slower if severe

"Nothing is working"

  • Have you addressed SIBO? (Often missed)
  • Are you truly compliant with elimination?
  • Is stress undermining healing?
  • May need different approach or more time
  • Consider practitioner guidance

"I can't tolerate supplements"

  • Start with one thing at a time
  • Use lowest doses
  • May need to address stomach acid first
  • May indicate more work needed before supplements

"I'm getting worse"

  • Stop antimicrobials and reassess
  • May be wrong diagnosis
  • May be die-off (see above)
  • Seek guidance

"Symptoms returned after feeling better"

  • May have reintroduced trigger too soon
  • May need longer healing time
  • May indicate incomplete treatment
  • May be stress-related

"I can't afford this"

  • Elimination diet is free
  • Bone broth can be homemade cheaply
  • L-glutamine is relatively inexpensive
  • Prioritize what you can do
  • Skip non-essential supplements
## 🤖 For Mo

AI Coach Guidance​

Assessment:

  1. "What gut symptoms are you experiencing?"
  2. "How long have you had these issues?"
  3. "Have you done any testing?"
  4. "What have you already tried?"
  5. "Are you working with a practitioner?"

Key Coaching Points:

  • Gut healing is a process (3-6+ months)
  • 5R framework provides structure
  • Removal phase is foundation
  • Repair takes time—be patient
  • Lifestyle matters throughout

When to Refer:

  • Suspected SIBO (needs testing/treatment)
  • Complex cases
  • Autoimmune involvement
  • Not responding to basics
  • Need antimicrobial guidance

Example Scenarios:

  1. "I want to heal my gut":

    • Assess symptoms
    • Has testing been done?
    • Start with elimination diet
    • Build systematic approach
    • Set realistic timeline

  2. "I have lots of food intolerances":

    • May indicate intestinal permeability
    • Elimination + repair protocol
    • Goal: expand diet, not restrict forever
    • Patience—healing enables tolerance

  3. "I was diagnosed with SIBO":

    • Antimicrobial treatment indicated
    • Work with practitioner
    • Address underlying cause
    • Repair after treatment
    • Prevent recurrence
## ❓ Common Questions

Q: How long does gut healing take? A: Typically 3-6 months for significant improvement. The gut lining turns over in days, but resolving underlying issues, rebuilding the microbiome, and restoring immune tolerance takes months. Some people need longer.

Q: Do I need a practitioner? A: For simple cases, you can do elimination + basic repair yourself. For SIBO, complex cases, or suspected serious issues, practitioner guidance is recommended. Testing and antimicrobial protocols are best guided.

Q: Will I have to avoid foods forever? A: Not necessarily. Many restrictions are temporary—once the gut heals, foods can often be reintroduced. Some people have true allergies or intolerances that are permanent, but many food sensitivities resolve with healing.

Q: Can I just take supplements without the diet changes? A: Supplements support healing but can't replace removing what's causing damage. An elimination diet is usually essential. You can't out-supplement a bad diet or unaddressed stressors.

Q: What if I can't afford testing? A: Start with elimination diet (free), symptom tracking, and basic gut support. Many people improve significantly without testing. Test if you're stuck or have complex symptoms.

## ✅ Quick Reference

5R Protocol Summary​

PhaseDurationKey Actions
Remove2-4 weeksElimination diet, antimicrobials if needed
ReplaceOngoingEnzymes, HCl, bile support
Repair4-12 weeksL-glutamine, zinc carnosine, collagen
Reinoculate4-8 weeksProbiotics, prebiotics, fermented foods
RebalanceOngoingStress, sleep, long-term habits

Key Supplements​

SupplementPurposeDose
L-GlutamineGut cell fuel, barrier5-15g/day
Zinc carnosineLining repair75-150mg/day
Digestive enzymesDigestion supportWith meals
ProbioticsMicrobiome restorationStrain-specific
Bone broth/collagenBuilding blocks1-2 cups/10-20g daily

💡 Key Takeaways​

Essential Insights
  1. Gut healing is a process—3-6+ months typically required
  2. 5R framework provides structure—Remove, Replace, Repair, Reinoculate, Rebalance
  3. Removal is foundation—can't heal while still damaging
  4. L-glutamine is cornerstone—primary fuel for gut cells
  5. Stress management is essential—stress undermines healing
  6. Food sensitivities often resolve—with proper healing
  7. Work with practitioner for complex cases—SIBO, antimicrobials, not responding
## 📚 Sources
  • Institute for Functional Medicine 5R Protocol Tier B
  • L-Glutamine gut healing research Tier A
  • Zinc carnosine gastric mucosa studies Tier A
  • SIBO treatment guidelines Tier A
  • Fasano - Intestinal permeability research Tier A

🔗 Connections​