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

by William Davis

This means that twenty-some feet—greater than the length of your car—of small bowel between the duodenum and cecum cannot be visualized. This has proven to be a perennial problem in pinpointing, for instance, a source of bleeding from the small bowel, which could be a leaking two-millimeter blood vessel twelve feet down from the duodenum, twelve feet up from the cecum, and completely inaccessible to a scope.

Relearning the lessons of life and health is every bit as worthwhile and necessary, perhaps more so, in the world of the microbiome.

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.

Many of us began life without the advantages of a healthy microbiome, engage in unhealthy diets that worsen the situation, then are exposed to numerous factors in modern life that further favor overgrowth of unhealthy bacterial species at the expense of protective species.

A shift in oral flora to species that ferment sugars from grains acidifies the oral cavity, leading to tooth decay.

The primary food source for bacteria in the human GI tract is a specific form of fiber called “prebiotic fiber.” Humans lack the digestive enzymes to break down prebiotic fibers, but bacteria can metabolize them and convert them to compounds that, in turn, nourish human intestinal cells. Bacterial “digestion” is therefore crucial to human health.

Prebiotic fibers are the primary food source for many species of intestinal bacteria, which convert them into metabolites crucial for human health.

Probiotic bacteria such as Lactobacillus and Bifidobacterium species are on your side. They stimulate mucus production, yielding a thicker, more protective lining, and produce metabolites (e.g., butyrate, propionate) from prebiotic fibers that nourish the intestinal lining.3

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, here, 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.

Include healthy foods such as prebiotic fiber–containing garlic and onions, polyphenol-rich vegetables and fruits, oleic acid from olive oil—all of which cause Akkermansia to bloom—and this species can be maintained at around 5 percent of total bowel flora, happily munching on the nutrients you provide and staying away from your mucus.

For people who are missing Akkermansia, a probiotic containing this species may be among the strategies to consider.

prebiotic fibers, polyphenols in fruits and vegetables, oleic acid richest in olive oil. You cannot overdo these nutrients, and abundant intakes will not lead to Akkermansia overproliferation. It’s only when you are deprived of these nutrients that Akkermansia is forced to become a mucus consumer.

Gut changes introduced by emulsifiers also lead to increased appetite, weight gain, and worsened insulin resistance, prediabetes, and type 2 diabetes.

being vigilant in your choices of peanut butter, ice cream, and other fat-containing products, or even better, return to eating foods that don’t require labels, like eggs and avocados.

perhaps you feel fine but are not aware that diet soda, ice cream, and ibuprofen can trigger unhealthy changes in your microbiome.

SIBO is an invasion of your small intestine: unhealthy fecal bacterial species proliferate in the colon, outmuscle beneficial probiotic species, then ascend to take up residence where they don’t belong, in the small intestine.

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.

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.

Avoiding offending food(s) is not a solution, although it can serve to reduce symptoms in the near term; addressing the microbial disaster that created the food intolerances in the first place is more likely to yield meaningful long-term solutions. The majority of food intolerances represent SIBO with increased intestinal permeability that leads to entry of microbial and food by-products into the bloodstream that provoke immune responses, which are mistakenly interpreted as food intolerances.

At-home detection of breath hydrogen is likewise a game-changer for intestinal health. It is a bacterial mapping process used to determine whether bacteria have invaded the upper GI tract.

Fungal species occupying our GI tracts and other nooks and crannies of our bodies live quietly, without causing health problems, until a course of antibiotics, steroids, overconsumption of sugars, excessive alcohol intake, or stomach acid–suppressing drugs—many of the same factors that enable SIBO to develop—allow fungi to proliferate.2,5,6 Any situation in which the intestinal lining becomes inflamed, such as in dysbiosis, SIBO, Crohn’s disease, ulcerative colitis, and probably irritable bowel syndrome, also creates an environment favorable for fungal proliferation.

(CFUs stands for “colony-forming units” and represents the number of living microorganisms in a sample.)

Among the most effective are food-sourced essential oils from cinnamon bark, clove, oregano, and peppermint.

these oils have proven to be more potent antifungal agents than the conventional antifungal drugs amphotericin B and fluconazole. 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.

Because they can also be caustic and burn the sensitive lining of your mouth and GI tract, never take essential oils directly. Dilute very small quantities in an edible oil instead.

Long term, you can stack the odds in your favor of not experiencing a 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

Because “official” dietary guidelines, such as those provided by the USDA and the US Department of Health and Human Services that advocate cutting fat and increasing grain consumption, have been such an unmitigated disaster—to a substantial degree, they are responsible for the modern epidemics of obesity, type 2 diabetes, fatty liver, and autoimmune diseases

eliminating carbohydrates is a really bad idea. Yet there are millions of people who have embraced ketogenic, carnivorous, or other variations of extreme low-carb diets. (When carbohydrate intake is slashed to around 10 grams per meal, metabolism of fat stores causes the release of a by-product called ketones, thus the label “ketogenic diet.”)

Because our microbiome has drifted so far off course, just following a healthy diet and life practices is no longer sufficient to regain control over our disrupted microbial universe.

As we age, we lose the ability to activate vitamin D production in the skin, especially after age forty.

vitamin D deficiency amplifies intestinal inflammation.

We begin by eliminating factors that disrupted bowel flora in the first place: » Avoid sugars and sugar-containing foods. » Avoid the synthetic noncaloric sweeteners aspartame (and related acesulfame, neotame, and advantame), sucralose, and saccharine. » Avoid emulsifying agents such as polysorbate 80 and carboxymethylcellulose. » Choose organic foods whenever possible. » Avoid all wheat and grains and be prepared for the opioid withdrawal process that accompanies this dietary change. » Avoid or minimize drugs, including stomach acid–blocking drugs, anti-inflammatory drugs, antibiotics, and statin cholesterol drugs. Of course, consult your doctor to do this or get a well-informed doctor to help you. » Replace essential nutrients, lacking in modern diets, that impact the microbiome and intestinal barrier: vitamin D, omega-3 fatty acids from fish oil, iodine, and magnesium. » Drink Clove Green Tea, which rebuilds a healthy intestinal mucus barrier. » Begin a four-week course of curcumin, 300–600 milligrams twice per day, to rebuild the intestinal barrier and address dysbiosis.

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 alone is a big step. (See below: Wheat and Grains: The Great Health Disrupters....