Health Protocol
A comprehensive six-month protocol for rebuilding a compromised gut microbiome — drawing from centuries of traditional healing practices, grounded in contemporary microbiology.
Start here
Before going into the restoration protocol, it helps to understand the problem clearly — what has likely gone wrong, why it persists, and what the path back looks like.
The gut has been understood as a seat of life, intelligence, and vitality by virtually every healing tradition in human history. It houses over 100 trillion microorganisms — more than ten times the number of cells in the human body — and contains roughly 500 million neurons, more than the spinal cord, earning it the name "the second brain." This enteric nervous system communicates directly with the mind, the immune system, and virtually every organ. When this community is disrupted, harmful bacteria and yeasts overgrow while beneficial strains collapse. The result is chronic diarrhea, irregular motility, inflammation, and a gut lining that becomes increasingly permeable. Six months of on-and-off symptoms suggests a deeply destabilised ecosystem, not a simple passing infection.
Short courses of treatment — a round of medication, a week of probiotics — rarely fix dysbiosis of this duration because they don't address the underlying ecology. The harmful species recolonise faster than the beneficial ones, which take weeks to establish firmly. Without the right food environment (prebiotics, fermented foods, diverse plants) and without addressing stressors that keep the gut in a reactive state, the cycle repeats.
Recovery requires three things working together: soothing the inflamed gut lining so it can begin to heal, inoculating with beneficial bacteria through fermented foods and targeted supplements, and feeding those bacteria with the plant diversity and prebiotics they need to establish permanent colonies. This takes months, not weeks. Traditional cultures all around the world understood this well and developed practices that work, which western, historically reductive science is only just beginning to realize, as it is just now beginning to acknowledge complexity and emergent properties in certain areas.
The protocol
Recovery requires three things working together, in sequence: soothing the inflamed gut lining, inoculating it with beneficial bacteria, and feeding those bacteria until they establish permanent colonies. Each phase builds on the last. See the What to Eat section for exactly what to eat during each phase.
Weeks 1–3
Stop the damage. Create the conditions for healing to begin.
The gut lining is inflamed and permeable. Before anything else can work, you need to calm the immune response, stop the fluid loss, and give the gut near-complete digestive rest. This is not the time for probiotics or fibre — both can worsen symptoms at this stage. The priority is soothing the lining, restoring electrolytes, and using targeted interventions for acute flares. Think of this phase as stopping the bleeding before you treat the wound.
Weeks of diarrhea deplete sodium, potassium, and magnesium dangerously. Simple oral rehydration solution: 1 litre water, 6 tsp sugar, ½ tsp salt — sip throughout the day. Coconut water is the traditional Caribbean and tropical-medicine alternative — naturally rich in electrolytes and far better tolerated than plain water. Consider magnesium glycinate at night.
1–2 capsules at the onset of an acute episode adsorbs toxins and slows motility. Used in traditional medicine worldwide including West African medicinal charcoal practices. Do not take within 2 hours of medications. Limit to 2–3 days per episode — not a daily remedy.
Weeks 3–8
Begin introducing beneficial bacteria — very slowly.
Once symptoms have stabilised, rebuilding can begin. This phase is about progressive inoculation — introducing beneficial microbes through fermented foods and targeted supplements while the gut lining is calm enough to host them. Start with 1 tablespoon of yogurt per day and increase only every 3–4 days if tolerating it. Going too fast causes bloating and setbacks. Herbal support (slippery elm, soursop leaf, ginger) continues throughout.
This is a yeast, not a bacterium — antibiotics cannot kill it. It has the strongest clinical evidence of any probiotic for diarrhea recovery. Begin this immediately, even before introducing fermented foods. Add Lactobacillus rhamnosus GG and Bifidobacterium longum alongside it. See the Probiotic Strains section for full detail.
Months 2–4
Nourish the bacteria that are establishing. Expand diversity aggressively.
Beneficial bacteria need food to survive and multiply — specifically prebiotics: resistant starch, plant fibre, and polyphenols. This phase introduces those foods deliberately and expands plant variety toward the research-backed target of 30+ different plant species per week. Each plant feeds a different bacterial community. Fermented vegetables are introduced now. The microbiome begins to genuinely rebuild its complexity and resilience during this phase — this is where the long-term work happens.
Months 4–6+
Transition from treatment to lifestyle.
By this point a functioning microbiome should be maintainable through food and habit alone. Supplement dependence reduces. The goal is to embed what worked — daily fermented foods, plant diversity, stress management, sleep, regular mealtimes — as permanent practice rather than temporary protocol. Traditional cultures maintained gut health across lifetimes through exactly these habits. This phase has no end date.
Nutrition
This is your practical eating reference. Each phase builds on the last — don't jump ahead. The pattern is: bland and binding early, then fermented and probiotic, then diverse and prebiotic, then normal life with good permanent habits.
Weeks 1–3
Zero irritation. Maximum digestive rest. Easy calories only.
White rice, rice porridge (congee), rice water, plain boiled or baked chicken, plain steamed or baked fish, bone broth (sip constantly), ripe banana, boiled or baked plantain, applesauce, plain scrambled or poached eggs, arrowroot porridge, boiled yam, boiled cassava, boiled sweet potato, boiled breadfruit, pumpkin soup (blended smooth), plain oatmeal (well-cooked), saltine crackers, plain toast, coconut water.
Rice water, weak ginger tea, cinnamon tea, coconut water, bone broth, plain water. Sip constantly throughout the day — dehydration is the immediate danger. Avoid juice, coffee, and alcohol entirely.
Season with salt only. No pepper, garlic, onion, or any spice yet. Avoid everything not on the eat list: raw vegetables, fibre, dairy, beans, spicy food, fried food, coffee, alcohol, artificial sweeteners, and processed food.
Weeks 3–8
Everything from Phase 1, plus the following — introduced one at a time, every 3–4 days.
Begin with 1 tablespoon of plain whole-milk yogurt per day. After 1–2 weeks of tolerating that, add kefir (start with 2 tbsp). Do not rush this. Too much too soon causes bloating and sets you back. These are your primary probiotic delivery system — more effective than most supplements.
Steamed carrots, zucchini, callaloo (cooked well), steamed okra (its natural mucilage soothes the gut lining — a staple of West African and Caribbean gut medicine), pumpkin, butternut squash. Cook everything thoroughly — no raw vegetables yet.
Avocado (gentle fat, easy fibre), coconut milk in soups and porridges (anti-inflammatory, easy to digest), red lentils cooked until completely collapsed with no visible skins (the most digestible legume — small portions only), soft-baked sweet potato with skin (introduces resistant starch).
Salt, fresh ginger, mild thyme, cinnamon. Still avoiding: raw onion and garlic, spicy food, fried food, coffee, alcohol, beans (except red lentils), raw vegetables.
Months 2–4
Everything from Phase 2, plus the following. Aim for 30+ different plant foods per week — keep a list.
Sauerkraut, kimchi, lacto-fermented pickles (make them, but if you must buy them make sure they say "live cultures" on the label — vinegar-pickled don't count). Start with 1 tsp/day and increase slowly over weeks. These are more potent than yogurt and dramatically increase microbial diversity.
Black-eyed peas, kidney beans, chickpeas, gungo peas (pigeon peas), lentils. Soak overnight, discard soaking water, cook thoroughly. Introduce one variety at a time. These become one of your most important prebiotic foods.
Sweet peppers, green beans, beets, eggplant, broccoli and cauliflower (cooked), spinach, kale (cooked), breadfruit (roasted or boiled — high in resistant starch when slightly underripe), moringa leaves (exceptional nutrient density and gut anti-inflammatory properties — add to soups or use as powder), sea moss (traditional Caribbean gut-soothing food — soak, blend into gel, add to drinks or porridge).
Aged cheeses (cheddar, gouda, parmesan — probiotic and easy to digest), miso (add to soups after cooking, never boil it), tempeh, whole grains (brown rice, oats, cornmeal porridge), raw vegetables — only once symptoms have been stable for several weeks.
Cooked garlic and onion, turmeric, allspice, thyme, a small amount of scotch bonnet if tolerated. Treat your spice rack as medicine — ginger, turmeric, garlic, and thyme every day, not occasionally.
Months 4–6+
Eat normally — with these non-negotiable daily practices.
2–3 servings of fermented food every day. Diverse plants as the foundation of every meal. Bone broth regularly — weekly at minimum. Continue using ginger, turmeric, garlic, and thyme as daily cooking ingredients. Minimize ultra-processed food, artificial sweeteners, and alcohol permanently — these are the main ongoing threats to a rebuilt microbiome.
Eat at regular times (the gut has its own circadian rhythm), in a calm and seated state, chewing thoroughly. Smaller meals more often are kinder to a compromised gut than large meals. Warm food and drinks are preferred over cold during recovery. Avoid drinking large quantities of liquid with meals — it dilutes digestive enzymes.
Alcohol (even small amounts disrupt gut flora significantly), artificial sweeteners (sorbitol, sucralose, saccharin, aspartame — strong negative effect on gut bacteria), emulsifiers (polysorbate 80, carrageenan — common in processed foods, read labels), and ultra-processed food generally. These are not "reduce" items — they actively work against everything else in this protocol.
Herbal medicine
These remedies appear across multiple traditional systems independently — which suggests genuine efficacy. Most are now supported by research. Ordered roughly by priority for gut recovery.
Native American · FDA-recognised demulcent
The inner bark contains mucilage that coats and soothes the entire digestive tract, forming a protective gel film. Mix 1 tsp powder in warm water or broth; drink before meals. Particularly good in weeks 1–3. Also available as capsules. Particularly good for the raw, burning feeling of inflamed intestines.
North African · Middle Eastern · widely adopted in Caribbean herbalism
Also rich in mucilage. Cold infusion is best — steep 1 tbsp of root in cold water for 4–8 hours, strain and sip through the day. Heat breaks down the mucilage, so don't boil it. Excellent for IBS-type symptoms and intestinal irritation. Safe for long-term use.
Ayurveda · TCM · Caribbean & African tradition
Modern research confirms it reduces gut inflammation, eases spasm, and has antimicrobial properties against harmful bacteria without significantly harming beneficial ones. Simmer 3–4 slices of fresh ginger in water for 10 min; drink as tea before meals. Add liberally to broth and cooked foods.
Mediterranean traditional medicine
Used for centuries specifically for diarrhea. Contains tannins with an astringent, binding effect, plus fibre that absorbs water in the gut. Mix 1–2 tsp into warm water or banana. Has a pleasant chocolate-adjacent taste. Well-suited to the early stabilisation phase; safe for daily use.
Ayurveda · South and Southeast Asian tradition
Curcumin has potent anti-inflammatory and gut-barrier-supporting properties — shown in research to upregulate tight junction proteins (molecular seals between gut cells). Best absorbed with black pepper and fat. "Golden milk" — turmeric, black pepper, ginger, honey in warm milk — is both traditional and genuinely effective. Use in phase 2+, not during acute diarrhea.
Caribbean · West African · Latin American tradition
Soursop leaves have been used throughout the Caribbean and West Africa for generations specifically for digestive complaints — diarrhea, gut inflammation, and stomach cramps. Steep 3–5 dried leaves in boiling water for 10 minutes. Drink 1–2 cups daily. Has anti-inflammatory and mild antimicrobial properties confirmed in research. A foundational gut remedy across the Afro-Caribbean diaspora.
Jamaican & Caribbean folk medicine · West African roots
One of the most widely used plants in Jamaican bush medicine. Cerasee (Momordica charantia) is traditionally brewed as a "bush tea" for stomach ailments, diarrhea, and intestinal cleansing. Steep a handful of the vine and leaves in boiling water for 10 minutes. Strongly bitter — considered in Caribbean tradition to be a sign of potency. Use 2–3 times per week; very potent, not for daily long-term use.
Widely used across African diaspora, Caribbean & beyond
Chamomile (manzanilla in Latin American tradition) is deeply embedded in Caribbean household medicine for gut spasm and inflammation. Contains apigenin — anti-spasmodic and anti-inflammatory. Safe for long-term use. Drink as tea 2–3 times daily. Particularly helpful when stress is a driving factor in gut symptoms, which it frequently is.
Ayurveda (isabgol) · South Asian tradition
A soluble fibre that absorbs water and normalises stool consistency — works for both diarrhea and constipation depending on hydration. Start with ½ tsp in a full glass of water; must be taken with plenty of fluid or it worsens things. Introduce in phase 2 only, once the acute phase has resolved.
TCM · Ayurveda · West African tradition
Used across ancient medical traditions including West African herbalism. DGL (deglycyrrhizinated licorice) soothes the stomach and intestinal lining without blood-pressure effects. Chew 1–2 DGL tablets before meals. Excellent for gut lining repair in phase 1–2.
Caribbean · Central American · West African tradition
Petiveria alliacea is widely used in Caribbean and Central American traditional medicine for digestive issues, gut inflammation, and as a general tonic. Has documented antimicrobial properties against gut pathogens. Brew as a tea from dried leaves. Use sparingly and not during the inoculation phase — its antimicrobial strength can disrupt beneficial bacteria being established.
Home fermentation
A single tablespoon of properly fermented food can contain 100+ billion CFU of diverse strains — most commercial probiotic capsules contain less than 1% of that. Home fermentation lets you boost the effectiveness and cultivate specific strains at a fraction of the cost.
Universal · The "amplifier" method
Uses a commercial probiotic capsule to seed a batch of yogurt, dramatically amplifying the bacterial count and introducing specific strains not usually in store-bought yogurt. Re-culturable 5–7 times before needing new capsules.
Global tradition · Sauerkraut / kimchi method
Relies on naturally occurring Lactobacillus on vegetable surfaces — the oldest fermentation method in the world. Salt creates selective pressure that allows beneficial bacteria to dominate. Start with just 1 tsp per day — the bacterial count is very high.
Central Asia / worldwide · Dairy-free
A SCOBY (symbiotic culture of bacteria and yeast) producing a mildly fizzy, lightly sweet drink. Excellent for those sensitive to dairy. Rich in diverse Lactobacillus and beneficial yeast strains. The grains are reusable indefinitely.
Pre-Columbian Mexico · still made throughout Latin America
Made from pineapple peel and core (which you'd normally discard) — both carry wild yeasts and bacteria. Mildly sweet, slightly fizzy, extremely gentle on the gut. A pre-Columbian fermented beverage still made throughout Mexico.
Japan · East Asian tradition
Fermented soybean paste containing Aspergillus oryzae, diverse Lactobacillus, and beneficial enzymes. A staple of Japanese longevity culture. The critical rule: never boil miso — heat above 70°C destroys the beneficial organisms.
Eastern Europe · Slavic tradition
One of the oldest fermented drinks in Eastern Europe, described in Russian chronicles from the 9th century. Rich in diverse bacterial strains, B vitamins, and easily digestible sugars. Beet kvass also supports liver function.
Microbiology
Not all probiotics are equal. These specific strains have the strongest clinical evidence for diarrhea and dysbiosis recovery. Look for these names on supplement labels.
The gut-brain axis
Virtually every traditional system of medicine — Ayurveda, TCM, Caribbean and African healing traditions — placed enormous emphasis on the connection between emotional state and digestion. Modern neuroscience confirms it: the gut has its own nervous system (the enteric nervous system) and communicates constantly with the brain via the vagus nerve. Chronic stress is not just a background condition — it actively degrades microbiome diversity, increases gut permeability, and accelerates gut motility.
Digestion begins in the mouth. Thorough chewing (Ayurveda recommends around 30 chews per bite) predigests food mechanically and signals the digestive cascade below. Eating while distracted or stressed suppresses digestive enzyme secretion.
The gut has its own circadian clock. Eating at consistent times synchronises this clock with the body's master rhythm — improving gut motility, enzyme output, and microbial composition. Irregular meal timing is associated with dysbiosis.
The vagus nerve directly regulates gut function. Practices that increase vagal tone — slow deep breathing (4 counts in, 6 counts out), cold water on the face, gargling, humming — can measurably reduce gut hypermotility within minutes.
The gut microbiome has its own circadian rhythm and actively repairs the gut lining during sleep. Poor sleep quality is independently associated with gut dysbiosis. Aim for 7–9 hours; gut healing happens primarily in the overnight fast.
Moderate aerobic exercise (walking 30 minutes daily) consistently increases gut microbial diversity in studies. It also reduces the stress hormones that drive gut inflammation. Avoid intense exercise during the acute phase — it can worsen leaky gut.
A 12-hour overnight fast (e.g. finish eating by 8pm, breakfast after 8am) activates the migrating motor complex — the gut's self-cleaning mechanism, which is disrupted when we snack continuously. Traditional cultures fasted naturally by not having food available at night.
Acute relief
Even mid-recovery, acute episodes happen. These are the time-tested remedies — from Caribbean kitchens, West African herbalism, and South Asian tradition — to reach for immediately. The goal is to calm the gut fast, stop fluid loss, and not undo the rebuilding work you've done.
The single most universal acute diarrhea remedy across Africa, the Caribbean, Asia, and Latin America. Boil 1 cup of white rice in 6 cups of water for 20–30 minutes. Strain out the rice and drink the cloudy, starchy liquid warm throughout the day. The soluble starch coats and soothes the gut lining, slows motility, and provides gentle calories without irritating the gut. In Jamaica and across the Caribbean, this is the first thing a grandmother reaches for. Drink freely — it's also rehydrating.
Green (unripe) bananas are a cornerstone of Caribbean folk medicine for diarrhea — particularly in Jamaica, Trinidad, and Barbados. They are rich in pectin and resistant starch that bind the stool and slow gut transit. Boil 2 green bananas (skin on) until very soft, mash the flesh with a pinch of salt and a small amount of broth or coconut water. Eat warm. Far gentler and more effective than ripe banana alone, which is sweeter and less binding.
Used throughout the Caribbean and Pacific as rehydration for generations before oral rehydration salts were invented. Fresh coconut water contains the near-ideal electrolyte balance for gut rehydration — potassium, sodium, magnesium, and natural sugars. Drink 1–2 glasses during a flare. In emergencies, uncontaminated young coconut water has historically been used intravenously in field medicine. If fresh coconuts aren't available, choose 100% coconut water with no added sugar.
Across the Caribbean and West Africa, soursop leaf tea is brewed specifically during acute gut episodes — diarrhea, cramping, gut spasm. Steep 4–6 dried soursop leaves in boiling water for 12–15 minutes (longer and stronger than the maintenance brew). Drink 1 cup, wait an hour, assess. The anti-spasmodic and anti-inflammatory compounds work relatively quickly. A trusted Jamaican remedy often described as "cooling the belly."
Take 1–2 capsules (500–1000mg) at the onset of an acute episode, with a large glass of water. Adsorbs toxins, pathogens, and irritants in the gut and slows motility. Used in traditional medicine worldwide — in West Africa, medicinal charcoal from specific burned plants has been used for gut complaints for centuries. Do not take within 2 hours of medications or supplements — it adsorbs those too. Limit to 2–3 days maximum per episode.
A classic Caribbean combination — particularly prominent in Grenadian and Trinidadian folk medicine, two cultures with deep herbal traditions. Nutmeg has documented anti-motility and anti-spasmodic properties; ginger reduces gut inflammation and spasm. Simmer 4 slices of fresh ginger with a small grating of whole nutmeg in 2 cups of water for 15 minutes. Add honey. Drink 1 cup slowly. Nutmeg is potent — a small grating only, not a spoonful.
During a severe flare, give the gut complete digestive rest. Consume only bone broth (and water, coconut water, rice water) for 24–48 hours. Bone broth provides gelatin, collagen, glycine, and minerals that actively repair the gut lining while requiring almost no digestive effort. This is the gut equivalent of splinting a sprain — it doesn't heal instantly, but it stops further damage and creates the conditions for repair. A practice found across West African, Caribbean, and Asian culinary medicine.
Roasted or dried plantain flour made into a porridge is a traditional gut remedy across West Africa, Nigeria, Ghana, and the Caribbean diaspora. Unripe plantain is exceptionally high in resistant starch and pectin — more so than green banana — which forms a gel in the gut that slows transit and feeds beneficial bacteria. Dry-roast slices of unripe plantain, grind into flour, cook into a thin porridge with water and a pinch of salt. Eat warm and plain. Increasingly studied in clinical settings for IBS and diarrhea.
Flare-ups during the rebuilding process are normal — they don't mean the protocol has failed. The pattern you're looking for over time is: flares becoming less frequent, less severe, and shorter in duration. Track this. A food-symptom diary is invaluable here. If a flare lasts more than 3 days, involves fever or blood, or is significantly more severe than usual, contact your doctor.