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Gut Microbiome Reset Protocol (5R Framework)

health · hard · 8-12 weeks for full protocol, ongoing maintenance

What is Gut Microbiome Reset Protocol (5R Framework)?

A structured functional medicine approach to restore gut microbial balance using the 5R framework: Remove, Replace, Reinoculate, Repair, and Rebalance. Addresses dysbiosis, leaky gut, and chronic digestive issues through systematic gut healing.

Is there evidence for it?

EVIDENCEmoderate

How do you do Gut Microbiome Reset Protocol (5R Framework)?

  1. 1.Remove: Eliminate processed foods, sugar, alcohol, and known food sensitivities for 2-4 weeks. Consider antimicrobial herbs (berberine, oregano oil) if pathogenic overgrowth is suspected.
  2. 2.Replace: Add digestive enzymes with meals and betaine HCl if low stomach acid is identified. Include bile salts if fat digestion is impaired.
  3. 3.Reinoculate: Introduce a multi-strain probiotic (10-50 billion CFU) containing Lactobacillus and Bifidobacterium strains. Add prebiotic fibers (inulin, FOS, acacia fiber) starting at 3-5g/day and increasing to 10-15g/day.
  4. 4.Repair: Support gut lining with L-glutamine (5g 2x/day), zinc carnosine (75mg 2x/day), colostrum, and bone broth. Add omega-3s (2g/day EPA+DHA) to reduce inflammation.
  5. 5.Rebalance: Establish long-term habits including stress management (meditation, breathwork), regular exercise, 7-9 hours sleep, and a diverse plant-rich diet with 30+ different plants per week.

How long does it take?

8-12 weeks for full protocol, ongoing maintenance.

Is it hard to start?

hard.

Source: Rupa Health - Functional Medicine 5R Protocol; PubMed PMC5470704; Nostra Biome Microbiome Solution Guide 2026
gut-health · microbiome · probiotics · prebiotics · functional-medicine · digestion · leaky-gut · 5r-protocol
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