The 5R Protocol has become the gold standard in functional medicine for addressing gastrointestinal dysfunction. This systematic approach addresses gut health from multiple angles, creating lasting improvements where symptomatic treatments fail.
Whether you're dealing with IBS, SIBO, leaky gut, or chronic digestive complaints, the 5R framework provides a roadmap for healing. Let's break down each phase.
1. REMOVE: Eliminate the Triggers
The first phase involves removing stressors that damage the gut ecosystem. You can't heal a gut while continuing to assault it. This includes:
- Pathogenic organisms — bacteria, yeast overgrowth (like Candida), and parasites identified through comprehensive stool testing
- Inflammatory foods — common triggers identified through elimination diets (gluten, dairy, soy, corn, eggs)
- Gut-irritating medications — NSAIDs, proton pump inhibitors, antibiotics (when medically appropriate to discontinue)
- Chronic stressors — stress literally shuts down digestive function via the gut-brain axis
Testing may reveal specific pathogens requiring targeted intervention with antimicrobial herbs or, in some cases, prescription medications. Even without positive tests, a modified elimination diet removes common inflammatory triggers and gives the gut a chance to calm down.
Duration: Typically 2-4 weeks for the removal phase, though pathogen eradication may take longer.
2. REPLACE: Restore Digestive Capacity
Many patients have compromised digestive capacity—they're not breaking down food properly. This phase replaces what's missing:
- Digestive enzymes — for better breakdown of proteins, fats, and carbohydrates
- Hydrochloric acid (HCl) — often low in stressed individuals and those over 50; essential for protein digestion and mineral absorption
- Bile acids — if gallbladder function is compromised or the gallbladder has been removed
Signs you may need digestive support include bloating after meals, feeling full quickly, seeing undigested food in stool, or having floating/greasy stools.
Supporting the mechanical aspects of digestion ensures nutrients from food actually reach the cells that need them. You can eat the perfect diet, but if you're not digesting it, you're not absorbing it.
3. REINOCULATE: Restore Beneficial Flora
This phase reestablishes healthy gut flora—the trillions of beneficial bacteria that support digestion, immunity, and even mental health:
- Targeted probiotics — strain-specific for your condition (Lactobacillus for small intestine, Bifidobacterium for large intestine, Saccharomyces boulardii for antibiotic recovery)
- Prebiotic foods — fiber that feeds beneficial bacteria (onions, garlic, asparagus, Jerusalem artichoke, green bananas)
- Fermented foods — when tolerated: sauerkraut, kimchi, kefir, yogurt, kombucha
The goal is establishing a diverse, resilient microbiome that supports immune function, produces beneficial metabolites (like short-chain fatty acids), and keeps pathogens in check through competitive exclusion.
Important: Some patients with SIBO or histamine intolerance may react negatively to probiotics initially. Timing matters—reinoculation often works better after the Remove phase has addressed overgrowth.
4. REPAIR: Heal the Gut Lining
The intestinal lining—just one cell thick—often requires targeted support after damage from inflammation, infections, or food sensitivities:
- L-glutamine — the primary fuel source for intestinal cells (enterocytes), typically 5-10g daily
- Zinc carnosine — supports mucosal integrity and has anti-inflammatory properties
- Deglycyrrhizinated licorice (DGL) — soothes and protects the gut lining
- Aloe vera — promotes healing and reduces inflammation
- Collagen peptides — provides amino acid building blocks for tissue repair
- Omega-3 fatty acids — reduce inflammation and support membrane integrity
This phase can take weeks to months depending on the severity of damage. "Leaky gut" (intestinal permeability) doesn't heal overnight—but it does heal with consistent support.
5. REBALANCE: Lifestyle for Long-Term Success
The final phase addresses lifestyle factors that maintain gut health long-term. Without this, improvements are often temporary:
- Stress management — chronic stress directly impairs gut function via cortisol and the vagus nerve
- Sleep optimization — the gut repairs during sleep; poor sleep = poor gut health
- Regular movement — exercise promotes healthy motility and microbiome diversity
- Mindful eating practices — eating slowly, chewing thoroughly, eating in a relaxed state
This phase is about building sustainable habits that support the gut for life, not just during a healing protocol.
Clinical Pearls for Practitioners
The 5Rs aren't always strictly sequential. Complex cases may require working on multiple phases simultaneously. Some key considerations:
- Some patients need extended time in Remove before other phases will be effective
- Testing guides treatment—comprehensive stool analysis, food sensitivity panels, and organic acid tests provide valuable data
- Patient adherence is crucial—the protocol requires significant lifestyle changes; develop your motivational interviewing skills
- Healing isn't linear—expect some ups and downs along the way
The 5R Protocol exemplifies functional medicine's systematic, root-cause approach. When properly implemented, it transforms gut health—and by extension, whole-body health. Because as Hippocrates said over 2,000 years ago: "All disease begins in the gut."
