Functional Gut Reset
Mark Hyman's Functional Gut Reset is a 5R sequence built to remove irritants and rebuild a damaged, low-diversity gut barrier. It works through five steps: remove trigger foods for 3 to 4 weeks, replace digestive aids, reinoculate with probiotics and fiber, repair the lining, and rebalance stress and sleep, since that barrier damage lets inflammation reach beyond digestion.
Pull out the common gut irritants For 3 to 4 weeks cut gluten, dairy, soy and eggs, plus sugar, alcohol, caffeine and ultra-processed food; you reintroduce them later one at a time
Removes the foods that most often drive a leaky, inflamed gut.
Support digestion A digestive enzyme blend with meals; if you have low stomach acid, betaine HCl can help (work with a clinician first)
Many people under-digest food, which feeds gut problems downstream.
Take a broad-spectrum probiotic A multi-strain probiotic with lactobacillus and bifidobacterium daily; start low and build up if you bloat or have SIBO
Crowds out bad bugs and rebuilds a diverse microbiome.
Eat fermented foods A daily serving of sauerkraut, kimchi, unsweetened kefir or yogurt, miso or natto
Food-based probiotics, the cheapest way to reinoculate.
Feed the good bugs with prebiotic fiber Aim for 25g+ fiber a day; add prebiotic foods (garlic, onion, leek, asparagus, Jerusalem artichoke, dandelion greens, jicama, green banana, flax) and/or a prebiotic fiber supplement (PHGG, acacia or GOS); start low and go slow
Prebiotics feed your probiotics; fiber is the master lever for the microbiome.
L-glutamine for the gut lining L-glutamine powder daily to fuel and repair the cells of the gut lining
Glutamine is the primary fuel for gut-lining cells and supports barrier repair.
Zinc carnosine Zinc-carnosine daily to support the mucosal lining (Hyman uses zinc and zinc-carnosine)
Supports the integrity of the gut barrier.
DGL licorice before meals Deglycyrrhizinated licorice (DGL) before meals to soothe the gut lining
Hyman names DGL as a soothing repair tool for the gut lining.
Bone broth, omega-3 and polyphenols Grass-fed bone broth, an omega-3 (EPA/DHA), and three-quarters of your plate as polyphenol-rich non-starchy vegetables
Amino acids, anti-inflammatory fats and polyphenols rebuild and calm the lining.
Manage stress, sleep and movement Protect sleep, move daily, and keep a stress practice; the gut-brain axis is real
Chronic stress and poor sleep degrade the gut barrier and microbiome.
Add foods back one at a time and test if needed After 3 to 4 weeks, reintroduce removed foods one every 2 to 3 days and watch for symptoms; if problems persist, consider a stool/microbiome test
Pinpoints your specific triggers and personalises the plan.
This protocol works from your actual levels. Testing partner coming soon.
- Gut microbiome test kit
We may earn a referral fee if you book testing through a future partner link; it will never affect which tests are listed here. This is not medical advice or a diagnosis.
A damaged, low-diversity gut barrier (leaky gut) drives inflammation that Hyman links to issues far beyond digestion.
View sources
The Doctor's Farmacy: 3 Steps To Fix Your Gut Health
The Dr. Hyman Show: Do You Need To Take Probiotics?
Hyman: how to heal a leaky gut (the 5R approach)
Not medical advice. This page is for education only and is not a substitute for professional medical care. Consult a qualified clinician before changing your health routine.
Independent curation. YourProtocol is an independent platform. This protocol is based on the publicly available work of Mark Hyman and is not created, reviewed, endorsed by, or affiliated with Mark Hyman or The Doctor's Farmacy.
Is this for you
- Bloating, IBS, reflux or irregular digestion
- People with food sensitivities or inflammation
- Rebuilding the gut after antibiotics
- Anyone who wants a structured gut reset
Cautions
- Supplements here are available through Dr. Hyman's own curated store (drhyman.com), and lab testing through Function Health, which he co-founded; he has a commercial interest in these
- Education based on Hyman's published work and functional-medicine framework, not medical advice; see a clinician for persistent gut symptoms and before using betaine HCl
- The removal phase is short-term (about 3 to 4 weeks) to find triggers, then you reintroduce foods; it is not a permanent restrictive diet, and if you have any history of disordered eating, do this with professional support
- If you have SIBO or feel worse on probiotics or prebiotics, stop and get practitioner guidance, and add fiber and probiotics slowly to avoid bloating
- Supplement forms and doses here are general from his public work; follow label dosing and check interactions
Some links earn us a commission. It never affects our picks or grades. See our affiliate disclosure.