Protocol·Digestion·Beginner·Reviewed June 9, 2026
Microbiome Restoration Protocol.
A foundational stack that supplies beneficial bacteria alongside the prebiotic fibers and fermentation substrates they need to recolonize and thrive in the gut. The goal is to rebuild microbial diversity, support the intestinal barrier, and improve overall digestive comfort.
The microbiome restoration protocol in brief.
A quick summary. The full stack, with dose and timing for each supplement, is below.
The Microbiome Restoration Protocol is a beginner stack of 5 supplements aimed at digestion: Probiotics, Inulin, Sodium Butyrate, L-Glutamine, and Zinc Carnosine. 2 are core and the rest are optional add-ons, at roughly $35-60/mo. Each supplement below lists its dose, timing, role, and the evidence behind it.
What is in the microbiome restoration protocol.
Dose, timing, role, and evidence tier for each supplement. Core items carry the protocol; optional ones are situational. Open any name for the full profile.
| Supplement | Dose | Timing | Role | Evidence |
|---|---|---|---|---|
| Probiotics | 10-20 billion CFU daily | With or just before a meal, consistently each day | Core | Moderate |
| Inulin | 5-10 g daily, started low and increased gradually | With a meal; split doses if tolerance is an issue | Core | Moderate |
| Sodium Butyrate | 300-600 mg daily | With food | Optional | Emerging |
| L-Glutamine | 5 g daily | On an empty stomach, morning or between meals | Optional | Emerging |
| Zinc Carnosine | 75 mg daily (providing about 16 mg zinc) | With or without food, often split twice daily | Optional | Emerging |
Delivers live beneficial strains (such as Lactobacillus and Bifidobacterium species) that transiently colonize the gut, compete with less favorable bacteria, and can ease bloating and irregularity while diversity is being rebuilt.
A prebiotic fructan that is fermented by colonic bacteria, selectively feeding Bifidobacteria and supporting short-chain fatty acid production that nourishes the gut lining.
Supplies the primary short-chain fatty acid that colonocytes use as fuel, supporting the integrity of the intestinal barrier and helping reduce low-grade gut inflammation as the microbiome recovers.
The preferred energy substrate for rapidly dividing intestinal epithelial cells; supplementation supports mucosal repair and tight-junction integrity, which complements microbiome rebuilding.
A zinc-carnosine complex that adheres to the mucosa and supports gastric and intestinal lining repair, helping protect the barrier environment in which a healthy microbiome can re-establish.
How the pieces combine.
The mechanistic rationale for stacking these together rather than taking them in isolation.
- Inulin acts as the prebiotic fuel for the live strains in Probiotics, forming a synbiotic pairing that improves the odds that beneficial bacteria establish and produce short-chain fatty acids.
- Sodium Butyrate provides directly the same short-chain fatty acid end-product that fiber fermentation generates, reinforcing colonocyte fuel supply and barrier support while the fermentation capacity of the microbiome recovers.
- L-Glutamine and Zinc Carnosine work on the host side to repair and stabilize the gut lining, giving the rebuilt microbial community a healthier surface to colonize.
Cost and commitment.
A rough monthly cost and how involved the protocol is to run.
The evidence behind it.
Overview citations for this protocol. Each supplement's own profile carries its full source list.
- Sanders ME, et al. Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nature Reviews Gastroenterology & Hepatology. 2019.
- Valdes AM, et al. Role of the gut microbiota in nutrition and health. BMJ. 2018.
Common questions.
Quick answers drawn from the stack above.
What is in the Microbiome Restoration Protocol?
The Microbiome Restoration Protocol combines 5 supplements for digestion: Probiotics, Inulin, Sodium Butyrate, L-Glutamine, and Zinc Carnosine. 2 are core; the rest are optional.
How much does the Microbiome Restoration Protocol cost?
NutriStack estimates the Microbiome Restoration Protocol at about $35-60/mo, depending on the forms and brands you choose and whether you run the optional add-ons.
Is the Microbiome Restoration Protocol backed by evidence?
Each supplement in the protocol carries its own evidence tier (0 rated strong here) and links to PubMed-cited sources. NutriStack does not rank or score brands and takes no manufacturer payments; this is an informational reference, not medical advice.
Build it in the app
Run the microbiome restoration protocol in NutriStack.
Add the stack to NutriStack to track timing, screen it for interactions, and see a Stack Score that updates as you tune it.