Super Gut: A Four-Week Plan to Reprogram Your Microbiome, Restore Health, and Lose Weight

by William Davis, MD (author of Wheat Belly), 2022

Danette’s Aunt recommended this book; it helped her lose 30 pounds and feel so much better all around. His premise is that modern life has wreaked havoc on our microbiome and that destruction and proliferation of bad bacteria up the digestive tract, SIBO and SIFO – Small Intestinal Bacterial Overgrowth and Small Intestinal Fungal Overgrowth – are causing us to have many, many problems that we look to pharmaceuticals to cure, when really, simply restoring a health gut biome would fix us. His 4-week plan involves first killing the bad bacteria that is in the small intestine, mainly through natural antibiotics like clove oil or oregano oil – a few drops in olive oil twice a day – and his Super Gut Yogurt, which is these 3 species of probiotics: Lactobacillus reuteri DSM 17938, ATCC PTA 6475 (from everidis.com); Lactobacillus gasseri BNR17 from mercolamarket.com called “Biothin Probiotic” with 10 billion CFUs per capsule, and Bacillus coagulans GBI-30,6086 available as the Digestive Advantage product from Schiff, available at Walmart.

It is very hard to test for SIBO and SIFO. SIBO testing involves a breath analyzer. But the symptoms of SIBO are like irritable bowel syndrome, bowel urgency, bloating, fibromyalgia, restless leg syndrome, fatty liver, diverticular disease, various food intolerances, gallstones, autoimmune and neurodegenerative conditions, and type 2 diabetes. Also, rosacea. “Unhealthy bacteria and fungi have been recovered from arteries, breasts, prostate glands, even the human brain, representing an invasion of microbes whose health effects are only beginning to be appreciated.” (page 11).

This invasion starts at birth with a C-section and then not breast-feeding. Babies born via C-section do not get the microbiome from their mothers that comes from the birth canal. Then, formula-fed babies do not get the good microbiome from their mother’s milk. He has recipes for a yogurt that a mother can eat that will pass along the good probiotics to the baby through breast-feeding. He talks about how Nestle encouraged mothers in Africa to formula-feed their babies, rather than breast feed. So these poor women did not breast-feed, instead paying for formula, and then diluting it so it went further, resulting in malnourished babies. Formula feeding was encouraged in the U.S. too – doctors and hospitals were paid to hand out formula. All of these babies did not get the good bacteria that sets them up for a healthy life: Lactobacillus and Bifidobacterium.

So many factors involved in the destruction of our gut: Glyphosate and other herbicides and pesticides destroy good gut biome. Antibiotics destroy good bacteria. Ozone pollution destroys them. NSAIDs destroy good gut biome. Prescription drugs that reduce stomach acid destroy them.

Page 12: “The recent discovery that people who die of Alzheimer’s dementia have brain tissue riddled with fungi, an observation that we shall discuss further, is especially concerning.”

My main takeaways:

1. Eat yogurt everyday. Have I found a good one? Chobani, non-fat plain Greek yogurt, has 6 strains: S. Thermophilus, L. Bulgaricus, L. Acidophilus, Bifidus, L. Casei, and L. Rhamnosus. He says commercial yogurts do not have enough probiotics; that they are not fermented long enough. He recommends 30 to 36 hours and commercial yogurts are only processed for 4 hours, not enough time for the bacteria to multiply. A $33 yogurt maker is MV Power, from Amazon. Also, Suteck, available at Walmart. The L. Rhamnosus in Chobani is the type of probiotic the researcher, Dr. Lisa Brenner, is using to treat PTSD and traumatic brain injury in veterans. (Article in CPR News, November 9, 2025: Can a probiotic help veterans with traumatic brain injury and PTSD?) She is using the specific strain, L. Rhamnosus, in her research with the veterans. This same article recommended an excellent website with a Probiotic Chart – usprobioticguide.com – that lists different strains and what they are good for. Bio-K+ Advanced Bowel Support or Bio-K+ Pro are probiotics in pill form that might be helpful for Wayne. They both have 50 billion of L. acidophilus CL1285, L. casei LBC80R, and L. rhamnosus CLR2.
2. Eat organic foods. The pesticides and herbicides really damage our microbiome.
3. Avoid emulsifiers; Polysorbate 80 especially. Only Daisy sour cream and cottage cheese have no emulsifiers. And Great Value’s heavy whipping cream has polysorbate 80 so only use Horizon Organic Heavy Cream. I had no idea about this! I guess emulsifiers make holes in your gut mucus and allow bacteria to penetrate and enter your bloodstream. The emulsifiers to avoid are polysorbate 80 and carboxymethyl cellulose. They “degrade the mucus lining but also provoke unhealthy changes in bowel flora species and increase intestinal permeability that leads to increased appetite, weight gain, and inflammation and sets us up for autoimmune conditions. We do not yet know how far and wide this applies to other less-potent emulsifiers such as carrageenan, propylene glycol, and lecithin.” Look for ice creams, salad dressings, heavy cream, half and half, non-dairy milks without the added thickeners, gums, mixing agents. “Banish emulsifying agents. Especially avoid polysorbate 80 and carboxymethylcellulose but also carrageenan, sodium stearoyl lactylate, and lecithin.” Page 177.
4. Switch from unsweetened almond milk to Kefir for my morning cereal. I found a Kefir called Lifeway Kefir, cultured low-fat milk. It has 12 live and active probiotic cultures: B. breve, B. lactis, B. longum, L. acidophilus, L. casei, L. cremoris, L. lactis, L. plantarum, L. reuteri, L. rhamnosus, S. diacetylactis, S. florentinus, 25-30 billion CFU at time of manufacture.
5. Think about switching All Bran Buds to something else – organic, high fiber. All Bran Buds have 17g of fiber; soluble 5, insoluble 12.
6. “Avoid all foods sweetened with aspartame, sucralose or saccharine. These include sugar-free sodas, ice creams, frozen yogurts, chewing gum, and other processed foods containing these ingredients.”
7. Always eat foods with “prebiotic fibers:” These are garlic, fermented foods such as Kombucha, kimchi, kefir, yogurt, home-fermented veggies, traditional sauerkraut, fermented pickles. “Prebiotics are nutritional constituents of plants that microbes themselves consume and process. Prebiotics include various fibers such as inulin, the galactooligosaccharides in lentils and kidney beans, and sugars such as lactose in dairy products.” (Page 148).
8. Stick to these noncaloric or minimally caloric sweeteners: Stevia, Allulose, Monk fruit, Inulin, Erythritol, Xylitol. “Note that we avoid most sugar alcohols, such as maltitol, lactitol, and sorbitol, because they behave much like conventional sugar and can cause loose stools even with consumption of modest quantities.” (page 191)
9. Switch to Extra-Virgin Olive Oil for all my oil needs, even sauteing. Do not use “light” olive oil any longer. It doesn’t have the good stuff.
10. Try Yakult, which is L. casei Shirota, and he says is good for deep sleep.

His list of things to do to promote a healthy gut: Avoid sugars, Avoid synthetic noncaloric sweeteners, Banish processed foods that contain emulsifying agents, Choose organic (even meats), Filter drinking water (chlorine and fluoride have adverse effects on the mucus lining of the intestines), Avoid or minimize wheat and grains (“…the gliadin protein of wheat and related proteins of other grains increase intestinal permeability so that undigested food components, microbes, and toxic breakdown products can sleep into the bloodstream.”, Go light on alcohol, Get off NSAIDs and stomach acid-suppressing drugs.

He says the science of probiotics in pill form is in its infancy. Only select probiotics that specify the strain. “Clinical studies demonstrate that Lactobacillus rhamnosus GG (ie., the GG strain), for example, hastens recovery from diarrhea after a course of antibiotics, but other L. rhamnosus strains do not.” (page 144).

These are the strains he considers most important:

1. Bifidobacterium infantis ATCC 15697, M-63, and ECV001
2. Lactobacillus reuteri DSM 17938, ATCC PTA 6475, and NCIMB 30242
3. Lactobacillus gasseri – multiple strains including BNR17 and CP2305.
4. Lactobacillus rhamnosus GG and HN001
5. Lactobacillus plantarum 299v and P-F
6. Faecalibacterium prausnitzii A2-165 and L2-6. “This species is responsible for as much as 25 percent of all intestinal production of butyrate, which yields health benefits for the human host.” (page 145)
7. Bifidobacterium longum BB536
8. Akkermansia muciniphila ATCC BAA-835
9. Bacillus coagulans GBI-30,6086 and MTCC 5856. “The presence of this microbe supports the proliferation of other healthy strains, including F. prausnitzii. These strains are not included in most commercial probiotics.” (page 146)

He says we need the following: Vitamin D, Omega-3 Fatty Acids, Iodine, Magnesium, Curcumin.

This is what he says about Curcumin: “Unlike the previous four nutrients, there is no intrinsic human need for curcumin–nobody has a curcumin deficiency.

“Instead, we supplement with this compound derived from the spice turmeric to help undo many adverse effects on the microbiome, intestinal mucus, and the intestinal barrier–curcumin is one of a few compounds that favorably addresses all three factors in intestinal health…

“To minimize die-off effects, we start with a modest dose of 300 milligrams twice per day, and increase to 600 milligrams twice per day after several days. Recall that we avoid products with added ingredients such as piperine or bioperine that enhance absorption because we want the curcumin not to be absorbed and to stay within the GI tract.”

Here is a summary of the 4 week program.

Week 1, prepare the soil by eliminating things that disrupted the bowel flora in the first place:

1. Avoid sugars and sugar-containing foods.
2. Avoid aspartame, acesulfame, neotame, advantame, sucralose, and saccharine.
3. Avoid emulsifying agents such as polysorbate 80 and carboxymethylcellulose.
4. Choose organic.
5. “Avoid all wheat and grains and be prepared for the opioid withdrawal process that accompanies this dietary change.”
6. Avoid stomach acid-blocking, anti-inflammatory, antibiotic, and statin cholesterol drugs. Check with doctor first.
7. Replace essential nutrients: Vitamin D, omega-3 fatty acids from fish oil, iodine, and magnesium.
8. Drink his Clove Green Tea: 2 cups water, 1 tablespoon whole cloves, 1 teabag green tea (organic such as Trader Joe’s or Newman’s Own), 1 teaspoon FOS (fructooligosaccharides) powder, 2 tsp allulose (optional), 1 cinnamon stick (optional). Boil water and cloves for 10 minutes, add the teabag for the last 2 minutes, discard the teabag, add FOS, optional allulose, and optional cinnamon stick and drink throughout the day.
9. “Begin a four-week course of curcumin, 300-600 milligrams twice per day to rebuild the intestinal barrier and address dysbiosis.”

Week 2-reseed your garden:

1. Begin high-potency, multi species probiotic or make his Super Gut Yogurt. Here are the probiotics he recommends: Synbiotic 365 from unitednaturals.com, Vital Flora from vitalplanet.com,
2. Include at least one fermented food every day.
3. Start your own home fermentation.

Week 3-Add water and fertilizer:

1. “Start with small quantities of prebiotic fiber-rich foods, such as 1 teaspoon of inulin or acacia fiber in coffee or yogurt, half a green unripe banana, or half a raw white potato coarsely chopped and blended into a smoothie or shake, or 1 to 2 tablespoons of a cooked legume. Most people tolerate up to 10 grams of prebiotic fibers during their first few days of week 3.”
2. “Build up to 20 grams or more of prebiotic fibers per day from a variety of sources to help cultivate bacterial species diversity.”
3. If this causes excessive gas, bloating, diarrhea, stop them and continue with Super Gut yogurt for 4 weeks. If prebiotics cause persistent distress, it’s a “sign of a severely disrupted microbiome or SIBO.”

Foods rich in prebiotic fibers: legumes, green bananas, raw white potatoes, avocados, blackberries, raspberries, pomegranates, apples, Chia seeds and flaxseed, almonds, walnuts, pecans, hazelnuts, and pistachios, mushrooms, Shirataki noodles, asparagus, jicama, turnips, parsnips, onions, garlic and shallots, carrots, leeks, dandelion greens, radishes, cabbage, Brussels sprouts.

Super fertilizers include clove oil, root vegetables, capsaicin from hot peppers.

Week 4: Grow your super gut microbe garden

1. “L. reuteri for skin smoothing and reduced wrinkle depth, restoration of youthful muscle and strength, deeper sleep, increased libido, appetite suppression, accelerated healing, increased empathy, reduced social anxiety, preservation of bone density
2. “L. reuteri and L. casei for deeper and longer sleep, reduced stress, and enhanced immune function
3. “B. coagulans for reduced inflammation and arthritis pain
4. “L. helveticus and L. gasseri for weight loss and reduced waist size
5. “L. reuteri and B. coagulans for increased strength and accelerated recovery in athletes
6. “B. infantis for mothers to pass on to their babies at birth and breastfeeding to reduce the number of infant bowel movements, reduce colic, and improve sleep and long-term health
7. “L. reuteri, L. gasseri, and B. coagulans found in the Super Gut SIBO Yogurt for eradication of SIBO”

further notes from the book:

Page 32, “Glyphosate, the active ingredient in Roundup herbicide, in particular, is a guilty suspect: it has been shown to effectively eradicate probiotic species like lactobacillus while being ineffective against pathogenic Escherichia coli, Shigella, and all their co-conspirators in the SIBO community, thus enriching populations of unhealthy bacterial overgrowth in the intestinal microbiome.”

Page 39: “We swim in an ocean of factors that disrupt bowel flora. Some changes are self-imposed. Smoking cigarettes or simply indulging in too much alcohol is disruptive to microbial communities. 11,12 Consumption of refined sugar triggers rapid changes in the intestinal bacterial species present, causing loss of healthy species and yielding symptoms of irritable bowel syndrome within days of increased sugar intake. 13 The noncaloric artificial sweeteners aspartame, saccharine, and sucralose are no safer, having been shown to trigger changes in bacterial species that exaggerate insulin resistance and lead to type 2 diabetes and obesity.14 In addition to stomach acid-blocking and anti-inflammatory drugs, preliminary evidence suggests that unhealthy changes in bowel flora composition develop with widely prescribed statin cholesterol-reducing drugs, which cause shifts in bowel flora species to a compositional pattern that resembles the one seen in obesity and diabetes.15″

Page 51: “Have too few Akkermansia and you won’t enjoy this microbe’s stimulated mucus production or its substantial metabolic benefits, such as reduced blood sugar and reduced blood pressure. Have too many, as develops when you fail to consume plentiful prebiotic fiber, and Akkermansia proliferates out of control and consumes the mucus lining. We prevent this last potentially dangerous effect simply by including plenty of prebiotic fibers in our diet.”

He highly recommends adding extra virgin olive oil into your everyday diet. “The oleic acid of olive oil is a great stimulator of Akkermansia proliferation. Making a habit of including some extra-virgin olive oil in your day, by cooking with it, dipping in it (with the Herbed Focaccia Bread recipe, page 252, for example), or simply drizzling it over the top of a dish is a tasty way to stimulate Akkermansia and thereby intestinal mucus health, provided you continue a habit of ingesting prebiotic fibers.” pg 52

“Another interesting class of plant polyphenols that yields intestinal mucus benefits is the catechins of green tea. They cross-link mucus proteins, which makes the mucus lining thicker, less semiliquid, and more like a gel, and thereby more protective including against infectious microbes and endotoxemia.” Pg 54

“But the emulsifiers found in foods such as ice cream, salad dressings, and peanut butter are proving to be major culprits in damaged mucus health…”

“Dr. Benoit Chassaing at the Institute for Biomedical Sciences at Georgia State University in Atlanta is a pioneer in exploring this effect. Chassaing and colleagues have demonstrated that synthetic agents such as polysorbate 80 and carboxymethylcellulose, despite having received the blessing of the FDA as safe food additives, exert potent disruptive effects on the mucus barrier. Transient dissolution of the mucus barrier allows bacteria to contact the intestinal lining and then invade the superficial layer of intestinal cells, which causes inflammation. Emulsifiers also provoke changes in microbial species in the GI tract, increasing populations of Enterobacteriaceae, the organisms of bacterial overgrowth and SIBO. Gut changes introduced by emulsifiers also lead to increased appetite, weight gain, and worsened insulin resistance, prediabetes, and type 2 diabetes.” (pgs. 55-56)

“This phenomenon of endotoxemia, substantiated by Dr. Patrice Cani and French colleagues in 2007, provides the crucial missing link that explains how microbes living in the GI tract can cause, for instance, the skin rash of rosacea, the thyroid inflammation of Hashimoto’s thyroiditis, or the muscle and joint pain of fibromyalgia, effects far outside the GI tract itself. 1 The dominant toxin transported through the blood is lipopolysaccharide (LPS), a component of the cell walls of Enterobacteriaceae, the main species of fecal bacterial overgrowth and SIBO. In other words, the trillions of microbes in the Enterobacteriaceae family living and dying in the GI tract can exert effects on every other organ and tissue of the body when they die and release the components that make up their cells, namely, LPS, into the bloodstream.” (pg 65)

On pages 68 -70, he explains common ailments that might indicate SIBO: Food intolerances (if eating legumes, root vegetables, onions, or any food that contains prebiotic fibers causes excessive gas, bloating, diarrhea, or emotional effects…”These reactions signal the presence of bacteria high up in the GI tract…see most food intolerances for what they really are: SIBO.2-5″; Fat malabsorption; Persistent or recurrent skin rashes like eczema, rosacea, or psoriasis; Prediabetes or Type 2 diabetes, fatty liver, autoimmune condition, fibromyalgia, irritable bowel syndrome, restless leg syndrome, chronic constipation, Parkinsonism or Alzheimer’s dementia; Stomach acid-suppressing drugs and anti-inflammatory drugs; lack of stomach acid; hypothyroidism; history of abdominal surgery.

Page 99, “Investigations conducted by Dr. Ruth Alonso and colleagues at the Autonomous University of Madrid have revealed that the brains of young people who die in car accidents or other traumatic incidences contain no fungi. The brains of elderly people without evidence of dementia reveal a moderate quantity of fungi. The brains of people with dementia reveal dense populations of fungi that fill every part of the brain. Examine the blood and cerebrospinal fluid (which bathes the brain) of people with dementia, and you will encounter high levels of fungal proteins and DNA. Inject a small quantity of fungi into the bloodstream of a mouse and it will develop all the hallmarks of dementia in the brain. 16-19”

“Let’s continue to connect the fungal dots. Research into Alzheimer’s dementia has focused on the beta-amyloid plaque that accumulates in the brains of people with this condition. Pharmaceutical companies have therefore developed drugs that block formation of beta-amyloid plaque. But, when these drugs are administered to human subjects, beta-amyloid plaque is reduced but progression of dementia is accelerated, with faster deterioration of memory and other mental faculties than if they had not taken the drug. It has therefore become clear that blocking beta-amyloid plaque accumulation is not the solution to Alzheimer’s.”

continued on Page 100: “If we reinterpret these phenomena, we can surmise that beta-amyloid plaque is more likely a response and not the cause of dementia, a realization that has dashed decades of work and caused the beta-amyloid plaque theory of dementia to be discarded. Recent research by a team in Boston at Massachusetts General Hospital and Boston University uncovered the fact that beta-amyloid plaque has potent antifungal properties–could the accumulation of beta-amyloid plaque be the body’s response to fungal infection in the brain? Is the solution to dementia to address (earlier in life, preferably) sources of fungal infestation?20″

Pages 101-103 talk about Curcumin: It’s an “antifungal champion.” “Because it is minimally absorbed, about 99 percent of any amount ingested remains within the GI tract to exert antifungal effects before it is then passed out into the toilet. Ironically, intensive efforts have been devoted to increasing absorption of curcumin by adding ingredients such as piperine (an alkaloid found in black pepper) and bioperine (an extract of black pepper) or creating nanoparticle or liposomal forms of curcumin. But, for our antifungal purposes, we actually do not want absorption and want curcumin to stay within the GI tract….The many people who have experienced relief from inflammatory conditions such as knee arthritis and skin rashes are therefore likely inadvertently treating SIBO and SIFO, the probable causes of their inflammatory condition, even when they take forms of curcumin that are minimally or not absorbed.

“Because it possesses antibacterial and antifungal properties, curcumin is not an agent you want to take for extended periods but only during the period when you are working to reduce fungal numbers–fungal eradication is not the goal; a rebalancing of fungal and bacterial populations is the goal.”

“Of the oils, cinnamon oil possesses the most potent antifungal effect while clove oil is rich in a compound called eugenol that increases the thickness of the protective intestinal mucus barrier, an effect that helps intestinal healing proceed. The essential oils can be useful in small quantities, for example, 1 to 6 drops (approximately 33-200 micrograms) diluted in one tablespoon of olive, avocado, fish, or another health oil (oils only, not water).” pages 104-105

“Of all the measures we take to restore a healthy microbiome, reducing fungal numbers may be the toughest step of all.” page 106

Page 126: “Long term, you can stack the odds in your favor of not experiencing recurrence of fungal overgrowth by including these foods in your diet. All have been shown to exert antifungal effects:

Cloves, Oregano, Thyme, Cinnamon, Cumin, Rosemary, Coriander, Peppermint”

page 162: “Extra-virgin olive oil (but not “light” olive oil) also contains polyphenols such as hydroxytyrosol that contribute to creating a healthier environment for bowel flora. …

“…Don’t worry: you cannot overdo consumption of olive oil.”

Noted recipes are Super Gut Yogurt, Herbed Focaccia Bread, Rosemary Turnips, One-minute Strawberry Ice Cream.

Shopping List – Acacia fiber, almond flour or meal, butter, chili pepper sauce, cloves (whole), coconut milk (canned), coconut oil, extra-virgin olive oil, Fructooligosaccharide (FOS) powder, garlic cloves, green tea, ground golden flaxseed, ground psyllium seed, half and half, herbs and spices –fresh and/or dried basil, oregano, rosemary, nutmeg, cinnamon, coriander seeds, cayenne or other hot peppers, turmeric, cumin, curry powder, garam masala, thyme, ginger; Inulin powder, sweeteners: Stevia, Allulose, Erythritol, Xylitol, Inulin, Monk fruit.

Page 299: Lactobacillus casei Shirota, available as Yakult, is good for immunity, mental clarity, and deep sleep. “This strain, which helps increase immunity against viral illnesses, increases mental clarity, and provides deep sleep for some people (especially in combination with L. reuteri), is available as a commercial drinkable product called Yakult. We ferment Yakult to increase the number of bacteria and to make a yogurt that no longer contains the skim milk or sugar in the original source product.”

Lactobacillus rhamnosus GG is great for antifungal effects and curing diarrhea after a course of antibiotics. It’s available as the Culturelle product, with 20 billion CFUs per capsule, at major retailers such as Walmart, Target.

Page 301 – Non-absorbed Curcumin: NOW Curcumin Softgels, Jarrow Formula Curcumin 95, Life Extension Curcumin Elite Turmeric Extract, Solaray Curcumin.

Appendix C is all about eradicating H. Pylori.

He does mention that the science is very new – likened it to Model-T automobiles.