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

by William Davis

All living creatures on this planet have a unique and individual microbiome: spiders and mosquitos, squirrels and chipmunks, trout and turtles. Humans likewise have a microbiome unique to our species but that differs for each individual. But the practices of modern life—shopping in a grocery store and eating food served from a drive-through window rather than killing or foraging your next meal; bathing in a hot shower in place of a dip in a lake or river; taking a course of antibiotics for a sinus infection instead of toughing it out—add up to wreak cataclysmic alterations in the composition and location of the microbes we harbor in and on our bodies.

But it is not uncommon for unhealthy bacterial species to ascend from the colon where they belong into the ileum, jejunum, duodenum (parts of the small intestine), and stomach, a situation labeled “small intestinal bacterial overgrowth,” or SIBO. The disruptions of bacterial populations that cause SIBO often also enable fungal species to similarly proliferate and climb up the length of the GI tract to inhabit places they do not belong, and this condition is called “small intestinal fungal overgrowth” (SIFO). Sadly, it is the rule, rather than the exception, that doctors fail to recognize these situations but “treat” the varied diseases they cause that show on the surface. You can see how someone with unrecognized SIBO, for instance, who suffers from conditions that are not readily reversible such as diverticulitis, Hashimoto’s thyroiditis, or colon cancer, can end up taking a long list of prescription drugs and even undergoing serious medical procedures such as gallbladder or weight loss surgery.

But modern life has eradicated this species from 96 percent of people in the Western world. Today, only 4 percent—fewer than one in twenty people—continue to enjoy the presence of this marvelous species.16,17 Among the many benefits of L. reuteri is its unique capacity to trigger the release of the hormone oxytocin from the human brain, which has been demonstrated through an elegant series of experiments conducted at the Massachusetts Institute of Technology (MIT). Think about that: a microbe living in your GI tract determines an important aspect of your brain’s functioning.18 Oxytocin is the hormone of empathy and connectedness. It is the hormone that surges when you are in love or feel closely connected to another person or pet your dog. Oxytocin helps you see the other side of an argument, cultivates sympathy for the plight of other people, and reduces social anxiety.

But we can go further to ensure that Akkermansia species are vigorously stimulated by including plenty of olive oil in our diet.

Another interesting class of plant polyphenols that yields intestinal mucus benefits is the catechins of green tea.

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.

Although only polysorbate 80 and carboxymethylcellulose have been studied to date, it is likely that most other, perhaps all, food additives with emulsifying properties, such as carrageenan, dextran sulfate, and propylene glycol, among others, have the same detrimental effects.

Which factors can you correct or change now to prepare your garden of bowel flora? • Avoid sugars: Sugars are to bowel flora as breadcrumbs are to birds and ducks: they will take the bait. Consume, say, sugary soft drinks or snacks, and you are delivering bacteria and fungi an invitation to ascend and proliferate. Lots of sugar in your diet is a virtually guaranteed setup for both SIBO and SIFO. • Avoid synthetic noncaloric sweeteners: 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. • Banish processed foods that contain emulsifying agents: We’ve discussed how polysorbate 80 and carboxymethylcellulose not only 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. Until the details are sorted out, we follow a commonsense rule: choose natural whole foods such as avocados, eggs, green vegetables, and others that have no added synthetic ingredients. When buying processed foods, look for brands with the shortest list of ingredients that you can recognize by name. Choose, for instance, salad dressings with olive oil, vinegar, salt, ...

» Begin a four-week course of curcumin, 300–600 milligrams twice per day, to rebuild the intestinal barrier and address dysbiosis.

These are the steps you’ll take to correct microbiome-disrupting factors: • Avoid sugar—in all its forms. We avoid sucrose, dextrose, high-fructose corn syrup, coconut sugar, brown sugar, agave nectar, turbinado sugar, maltose, maltitol, maltodextrin, rice syrup, and the dozens of other code names for various forms of sugar—they’re all sugar and they all cultivate unhealthy bacterial and fungal species even after just a few days of consumption. • Avoid synthetic, noncaloric sweeteners. Avoid aspartame and related acesulfame, neotame, advantame, sucralose, saccharine, and all foods sweetened with them. This means that nearly all “diet” sodas are off the menu. • Banish emulsifying agents. Especially avoid polysorbate 80 and carboxymethylcellulose but also carrageenan, sodium stearoyl lactylate, and lecithin. • Choose organic. Minimize exposure to herbicides, pesticides, antibiotics, and genetically modified foods that also contain glyphosate and the Bt toxin by choosing organically grown and raised foods. • Filter drinking water. Filter tap water to avoid chlorine, chloramine, and fluoride. • Avoid wheat and grains. By eliminating wheat and grain foods from your diet, you avoid the protein gliadin, which increases intestinal permeability and slows intestinal peristalsis (the natural propulsive movement of the GI tract). You are also thereby reducing exposure to the antibiotic effects of the herbicide glyphosate and avoiding a major source of intestinal inflammation. This alo...

Opt for real, single-ingredient foods, preferably those that don’t require a label. Avocados and eggs are safe, as are broccoli, salmon, and a handful of walnuts—no added sugar or synthetic sweeteners, no emulsifiers, no preservatives, no labels or nutritional panels required. When shopping, you will find yourself spending nearly all your time in the produce section, butcher/meat section, and dairy section, rarely needing to venture into the inner aisles, which are packed top to bottom with processed foods.

Wheat and grain elimination can be among the most unsettling, confusing, but powerful strategies that begins the process of rebuilding healthy bowel flora. It means that, though you may be avoiding foods like breads, pizza, pasta, pretzels, and crackers, you will be unrestricted in including foods such as eggs, butter, vegetables, olive oil, beef, fish, poultry, and nuts—there are plenty of whole, unprocessed foods that are safe and healthy.

One of the very important benefits of the Super Gut program is that it reverses insulin resistance. Insulin resistance occurs when the liver, muscles, brain, and other organs respond poorly to insulin, the pancreatic hormone that allows us to metabolize carbohydrates by taking blood sugar out of the blood to use as energy. This lack of response to insulin causes the pancreas to compensate by producing greater amounts of insulin in order to get organs to take up glucose from the blood.

The ideal intake of EPA and DHA is higher than most people think: 3,000–3,600 milligrams per day of EPA + DHA (total)—this is the dose of EPA and DHA, not fish oil. Ideally, divide it into at least two doses, such as 1,500–1,800 milligrams in the morning and another 1,500–1,800 milligrams in the evening or with dinner.

ALTERNATIVE FLOURS AND MEALS Almond flour (from blanched almonds), almond meal (from whole almonds) Walnut or pecan meal—best suited to making piecrusts Coconut flour Ground golden flaxseed Sesame flour Lupin flour Ground psyllium seed

ALTERNATIVE NONCALORIC OR MINIMALLY CALORIC SWEETENERS Stevia Allulose Monk fruit Inulin Erythritol Xylitol

The ideal intake of elemental magnesium is in the range of 450 to 500 milligrams per day for adults, divided into two or three doses. This level of intake contributes to reductions in blood pressure, blood sugar, and heart rhythm disorders, as well as adds to effortless episodes in the bathroom.

Now that we’ve prepared the soil, removing the microbiome equivalent of rocks and other debris, we next begin the process of “reseeding” your garden of bowel flora with healthy bacterial species, including keystone species. » Begin a high-potency, multispecies probiotic from the list provided in Appendix A or make probiotic yogurt from the recipe provided. » Include at least one fermented food, either purchased or homemade, in your diet every day. » Start your own home fermentation efforts. (I’ll show you how to get started fermenting at home.)

You can buy a fermentation kit, but it’s really simple to assemble your own with items you likely already have on hand. The basic ingredients are as follows: • Vegetables: Raw onions, peppers, asparagus, cucumbers, radishes, garlic, carrots, cabbage, green beans, daikon radish, and others—any vegetable can be fermented. Chop the vegetables into bite-sized pieces. Combine vegetables to create unique flavors, for example, asparagus and onions, green beans and garlic. • Herbs and spices: Peppercorns, dill, garlic cloves, coriander seeds, mustard seeds, caraway seeds, rosemary, oregano. Many people also add grape or berry leaves to increase crispiness. • Sea salt or other salt: Use any salt, but not iodized salt (iodine kills microbes). • Water: Use filtered water, spring water, or distilled water, that is, water without chlorine or fluoride. Fermenting vegetables is, like baking or pottery making, an entire world to explore. Basic Fermentation Fill a jar or fermentation vessel with water, then add salt until the water tastes lightly to moderately salty, typically 1½ tablespoons per quart of water. Add the vegetables and your choice of herbs or spices, such as peppercorns, dill, and coriander. Stir to mix the vegetables with the salt water and to release any trapped air bubbles. Submerge the vegetables and cover them with a plate or other clean object to keep them below the surface, then cover the vessel to keep pests out. The system should not be airtight but only loosely cov...

In your third week of this health- and microbiome-rebuilding program, let’s get comfortable with prebiotic fibers. They are the water and fertilizer for your garden of bowel flora, crucial for cultivating microbes and health. For maximum benefit, include a source of prebiotic fiber in every meal, a habit that will make this important strategy effortless over time. In the Super Gut program, we go beyond prebiotic fibers by using other strategies that also enable beneficial species to proliferate. » 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. » Build up to 20 grams or more of prebiotic fibers per day from a variety of sources to help cultivate bacterial species diversity. » If you prove intolerant to the initial level or to the increase in prebiotic fibers (excessive bloating, gas, or diarrhea), consider stopping them while continuing other Super Gut efforts (probiotics, fermented foods) for another four weeks, then try to reintroduce prebiotic fibers. If intolerance persists, move on to the SIBO and SIFO management program in Appendix B because prebiotic fiber intolerance is a reliable sign of a severely disrupted microbiome or SIBO.

FOODS RICH IN PREBIOTIC FIBERS The following foods offer lots of grams of prebiotic fiber to feed our friendly microbes. Legumes: Kidney beans, black beans, white beans, other starchy beans, chickpeas, hummus, lentils, and peas are rich sources of galactooligosaccharide, or GOS, a form of prebiotic fiber. Keep servings small, for example, a quarter to half cup that contains no more than 15 grams of net carbohydrates (total carbohydrates minus fiber) to minimize blood sugar consequences. Hummus and chickpeas provide 8.0 grams of prebiotic fiber per half cup (13.5 grams net carbohydrates). Lentils contain 2.5 grams of prebiotic fiber per half cup (11 grams net carbohydrates). Most beans provide around 3.8 grams of prebiotic fiber per half-cup serving. White beans are the richest source, with twice this quantity (12 grams net carbohydrates per half cup). Green bananas and plantains: And I mean green. Not green-yellow, or a little green at one end, but green. If in doubt, taste it: it should not have any sweetness at all. A medium, seven-inch-long green banana contains 10.9 grams of prebiotic fibers and 0 grams of net carbs in contrast to the high-sugar/high-carb, low-fiber content of a ripe banana. A green banana is tough to peel and virtually inedible, so slice it lengthwise and scoop out the pulp, chop it coarsely, and use in one of the prebiotic smoothie recipes below. Bananas generally stay green for four to five days in the refrigerator, or you can peel, chop, and store ...

Here is the menu of beneficial microbes: » 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 » L. reuteri and L. casei for deeper and longer sleep, reduced stress, and enhanced immune function » B. coagulans for reduced inflammation and arthritis pain » L. helveticus and B. longum for reduced anxiety, improved mood, and reduced depression » L. casei for enhanced mental clarity and focus » L. reuteri and L. gasseri for weight loss and reduced waist size » L. reuteri and B. coagulans for increased strength and accelerated recovery in athletes » 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 » L. reuteri, L. gasseri, and B. coagulans found in the Super Gut SIBO Yogurt for eradication of SIBO

The recipes for all these fermented yogurts and other foods can be found in Super Gut Recipes, including the proper strains and where to source them. Smoother Skin with Reduced Wrinkles, Accelerated Healing L. reuteri yogurt, a half cup per day. Consider mixing in collagen hydrolysates, 10 grams per day, to your yogurt. Deeper Sleep with Extended REM L. reuteri yogurt, a half cup per day. Can be combined with L. casei Shirota for greater effects. If these species are fermented separately, consume a half cup per day of each yogurt. If fermented together, consume half to one cup per day. If fermented together, ferment at 104°F–106°F. Consider tracking your sleep with an actigraphic device such as an Apple Watch, Whoop, Oura Ring, or FitBit, and specifically track duration of sleep, deep sleep, and REM. Reduced Inflammation and Arthritis Pain Bacillus coagulans yogurt, a half cup per day. Consider adding Clove Green Tea for its mucus barrier–strengthening effects that reduce endotoxemia. Reduced Stress L. casei yogurt, a half cup per day. The effect is increased by combining with L. reuteri yogurt. If fermented separately, consume a half cup per day of each yogurt. If fermented together, ferment at 104°F–106°F and consume half to one cup per day. Also consider L. infantis for added benefit. Both species blunt the abnormal rise in morning cortisol that defines many stressful situations. (Prolonged stress that has reduced adrenal gland release of cortisol may not respond to thi...

The recipes provided here fall into four categories: 1. Yogurt recipes: These recipes yield large numbers of specific species and strains of bacteria and thereby substantial health benefits. 2. Beverage and smoothie recipes: A smoothie is an easy way to get a wallop of prebiotic fibers as a tasty snack or meal replacement. 3. Side dishes, main dishes, and condiments: Various dishes that make use of ingredients that aid your efforts to reprogram your intestinal microbiome, such as spices in a delicious tea that increase the thickness and protective capabilities of your intestinal mucus lining and rosemary in baking for its ability to discourage overgrowth of Staphylococcus aureus and Candida albicans. 4. Desserts: Dishes that illustrate how you can make your sugar- and grain-free life delicious and fun when entertaining friends or enjoying holidays and keep the children and grandchildren happy.

AVOCADO LIME DRESSING: 2 medium avocados, pitted, skin removed ½ cup extra-virgin olive oil ¼ cup white wine vinegar ¼ cup fresh cilantro, coarsely chopped 1 clove garlic, minced, or 1 teaspoon dried garlic powder Juice of one small lime ½ teaspoon salt Sweetener equivalent to 1 tablespoon sugar ¾ cup water In a blender or food processor, combine the avocado, oil, vinegar, cilantro, garlic, lime juice, salt, sweetener, and water. Blend or process until uniformly mixed. Use immediately or store in an airtight container in the refrigerator.

SALMON WITH AVOCADO LIME SAUCE Dress up your salmon with this unique sauce that offers the antibacterial and antifungal properties of ginger, and cilantro and coriander (the leaf and seed from the same plant), and the prebiotic fiber of avocado plus the Akkermansia-cultivating effect of the oleic acid in olive oil. Makes 2 servings 1 avocado, pulp removed 3 tablespoons extra-virgin olive oil 2 tablespoons lime juice (fresh or bottled) 2 tablespoons onion, minced ¼ cup fresh cilantro, chopped 1 teaspoon freshly ground ginger, or ½ teaspoon dried ginger ½ teaspoon ground coriander 3 tablespoons white wine vinegar ½ teaspoon salt 2 tablespoons extra-virgin olive oil or butter 2 8-ounce salmon filets In a blender, combine the pulp of one avocado with 3 tablespoons of olive oil and lime juice, onion, cilantro, ginger, coriander, vinegar, and salt and blend until smooth. Set aside. Season both sides of the salmon with salt and pepper to taste. In a large skillet, heat 2 tablespoons of oil over medium-high heat. Place salmon filets, skin side up, in the oil and cook for 4–5 minutes. Flip the salmon and cook for an additional 4–5 minutes. Serve the salmon topped with the avocado lime sauce.

ONE-MINUTE STRAWBERRY ICE CREAM Here is a way to make your own ice cream that involves almost no effort. Note that, for this time-saving shortcut to work, the strawberries (or other berries or fruit) must be frozen. This is how you can enjoy a bowl of ice cream sans the intestinal mucus- and microbiome-disrupting effects of synthetic emulsifying agents. Makes 2 cups 8 ounces heavy whipping cream or canned coconut milk 1 cup frozen strawberries or other berries or fruit 1 green, unripe banana, scooped out of the peel and coarsely chopped Sweetener equivalent to 1 tablespoon sugar ½ teaspoon vanilla extract In a blender, combine whipping cream, berries, banana, sweetener, and vanilla. Blend until the mixture is smooth.