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Could this super yogurt solve your gut issues?

Reading time: 15 minutes

A depleted gut microbiome is behind a host of modern degenerative diseases, but Dr William Davis, author of Super Gut, has a creamy solution. Cate Montana reports

The average human living an average lifespan on planet Earth consumes approximately 60 tons, or 120,000 pounds, of food over the course of their lifetime.1 We hope most of that tonnage is efficiently digested and utilized as it passes through the gastrointestinal tract, where a group of over 100 trillion microorganisms live.

These bacteria, known as our gut microbiota, go about their jobs of using said food to harvest energy and maintain gut lining integrity. As they do so, they busily protect their human host from pathogens and regulate the body’s overall health and immune function.

At least that’s what the vast collection of bacteria, archaea (single-cell microorganisms) and eukarya (microorganisms that have a membrane-bound nucleus) that colonize the average 25-foot length of our small and large intestines is supposed to be doing. Unfortunately, due to the overwhelming assault of processed foods, chemicals, antibiotics, pharmaceuticals, synthetic additives, herbicides, pollutants, stress and much more, efficiency is about the last thing most people can expect from their gut.

In 2021, a global study found that about 40 percent of the world population suffers from at least one digestive disorder, such as diverticulitis, chronic constipation, diarrhea, indigestion, irritable bowel syndrome (IBS), celiac disease or Crohn’s disease, and dysbiosis (unbalanced bacterial growth in the intestinal tract). Among the diseases found, constipation and indigestion were the most prevalent.2

Of that number, a large majority suffer from small intestinal bacterial overgrowth (SIBO), a proliferation of unhealthy fecal bacteria in the colon that travel up into the small intestine, where they don’t belong. These invaders trigger abdominal pain, nausea, diarrhea or constipation, bloating and unintentional weight loss.

According to traditional medical sources, such as the Mayo Clinic in the US, the form of dysbiosis we call SIBO results from “structural problems and some diseases” as well as from complications of abdominal surgery. Antibiotics are the usual treatment. Sometimes surgery is recommended as well.

But there are other voices with other ideas, loud voices in the medical world. One is cardiologist Dr William Davis ( The renowned author of the best-selling Wheat Belly book series believes SIBO and other gut-related health issues due to dysbiosis that is in part caused by antibiotics.

“The administration of antibiotics has wreaked havoc on people’s microbial balance over the last century,” he says in his latest book Super Gut: A Four-Week Plan to Reprogram Your Microbiome, Restore Health, and Lose Weight (Hachette Go, 2022). “A combination of factors associated with modern life—from modern processed foods to stomach acid–blocking drugs—has created a gut that is almost no longer human; it’s something I call a ‘Frankenbelly.’

“Real health horrors result from a Frankenbelly: from irritable bowel syndrome and constipation to ulcerative colitis and Crohn’s disease, from polycystic ovary syndrome and colon cancer to depression and despair, from social isolation to thoughts of suicide. These are all effects of this thing we, as a society and as individuals, have created via disruptions in the microbiome.”

Disturbing ramifications

Disturbances and imbalances in bacterial populations weaken the integrity of the intestines themselves, decreasing the healthy mucosal lining that protects the epithelial layers and allowing bacterial waste and other microorganisms into the bloodstream. From there the waste and microbes can enter all the organs of the body.

Not surprisingly, studies show that gut dysbiosis is associated with an increased risk of atherosclerosis, heart attack, blood clots and stroke.3 It’s known to contribute to liver toxemia4 and pancreatic cancer.5

Gut dysbiosis triggers immune system disorders and causes inflammatory diseases,6 directly contributing to type 2 diabetes, rheumatoid arthritis, asthma, obesity and conditions such as endometriosis. It’s known to play a role in the development of depression and its progression.7 It also often enables fungal species to climb up into the small intestines, creating small intestinal fungal overgrowth (SIFO), which often occurs alongside SIBO.

“Uncorrected SIBO can permit an autoimmune condition like rheumatoid arthritis or lupus to emerge, increase risk for coronary artery disease, allow insulin resistance to persist or worsen, increase blood sugar, raise blood pressure, contribute to fatty liver, or lead to diverticular disease and even colon cancer,” says Davis. “Uncorrected SIBO may even expose you to increased risk for neurodegenerative diseases.”

According to Davis, the medical community is poorly equipped to handle the proliferating health problems resulting from an unbalanced, deficient microbiome, never mind to understand their underlying source. Most doctors never make the gut connection and end up treating whatever disease shows up on the surface—addressing the symptoms rather than the actual problem.

“Rather than address the proliferation of unhealthy bacterial and fungal species responsible for generating dark emotions, anxiety and suicidal impulses, doctors prescribe antidepressant and antianxiety medications to block their effects,” Davis explains. “Rather than chart the location of errant microbes that underlie conditions like hypertension and atrial fibrillation, they prescribe medications that push blood pressure down and suppress abnormal heart rhythms.

“Rather than decipher the microbial disruptions that cause weight gain and type 2 diabetes, they resort to gastric bypass and medications that forcibly regulate blood sugar. All these conventional but misguided efforts also come, of course, with a considerable price tag and long lists of side effects.”

Another common recommendation by doctors is the elimination of foods known to trigger gut issues in many people, such as dairy. People with inflammatory bowel diseases such as IBS, ulcerative colitis and Crohn’s disease are often advised to avoid eating foods fermented by microbes, such as fruit, sugars, sorbitol, legumes and dairy products, all of which contain FODMAPs.

This acronym stands for fermentable oligosaccharides, disaccharides, monosaccharides and polyols, which are types of carbohydrates and sugar alcohols that unfriendly microbes rely on. Severely restricting them can reduce the excessive gas, bloating, abdominal pain and diarrhea they trigger. However, aside from missing out on a lot of delicious eats, Davis says, there is a major downside to the food-elimination approach to health.

“By avoiding FODMAPs in your diet, you’re essentially starving bacteria—good and bad—of their preferred foods. Starving microbes changes the composition of the microbiome as some species die out. For instance, it reduces important beneficial species such as Bifidobacterium longum (which plays a major role in regulating mood) and Faecalibacterium prausnitzii (the most vigorous producer of a fatty acid that heals and nourishes the intestinal lining).

“Whereas reducing the number of SIBO-related species is good, reducing or sometimes even eliminating beneficial species is detrimental,” Davis says. “And, if you lose species, you cannot grow them back. Like taking aspirin for a headache, avoiding FODMAPs is only a symptom-limiting strategy and does not address the root cause, and it may even make your microbiome situation worse in the long term.”

Everyone is affected

It’s pretty much a given that virtually everyone living a modern life is experiencing some degree of gut dysbiosis, whether they’re symptomatic or not. Who hasn’t taken antibiotics at some point in their life? Walked barefoot on a lawn treated with Roundup? Eaten ice cream that contains polysorbate 80? Put aspartame in their tea or coffee? Or taken a couple of ibuprofen for a headache?

All of these seemingly simple, everyday things contribute to the dysregulation of our microbiome. And they all add up.

But here’s the good news. According to Davis, the solution to this enormously complex problem is as simple as eating a half-cup of yogurt every day for a month.

Not store-bought yogurt filled with emulsifiers that kill off beneficial gut microbes and loaded with sugar and artificial sweeteners that may trigger abnormal synthesis of short-chain fatty acids, messing up the health of the intestines and their microbial residents.8 Rather, you need a DIY, bacteria-rich, probiotic yogurt you can make in your kitchen in 36 hours.

“Thankfully, many of the health struggles that can be blamed on a disrupted microbiome can be reversed simply by shifting toward a healthier diet, addressing common nutrient deficiencies, and restoring healthier bacterial species to the GI tract after we’ve beaten back undesirable microbes,” writes Davis.

“The sorts of benefits we can reap from restoring the healthy human microbiome will go farther than just relief from, say, being overweight or having acid reflux. The strategies I’ll share with you can also yield smoother skin, accelerated healing and increased feelings of empathy for other people—benefits that you likely had no idea originated with the microbial universe within.”

Causes of gut dysbiosis

An imbalanced microbiome can result from a wide range of factors in today’s world, and the ones listed below are some of the most common. Some are more avoidable than others, so it’s up to each of us to take control of what we can.

Antibiotics. Broad-spectrum antibiotics kill a wide range of bacterial species, which encourages fungal growth and SIFO. They also promote the proliferation of harmful bacteria in the body. Large amounts of antibiotics are absorbed from non-organic commercial meats and farm-raised fish.

Artificial sweeteners. Aspartame, saccharine and sucralose trigger changes in bacterial species that exaggerate insulin resistance and lead to type 2 diabetes and obesity.

Automobile exhaust. When it’s exposed to sunlight, exhaust alters bowel flora composition.9

Baby formula. Breastfed infants have greater populations of probiotic Lactobacillus and Bifidobacterium species, whereas Enterococcus and Enterobacter species—which typically inhabit the colon and characterize bacterial overgrowth—dominate in formula-fed children.

C-section. The 32 percent of children delivered by C-section begin life with a different (and weaker) microbiome than vaginally delivered children.

Emulsifiers. Polysorbate 80 and carboxymethylcellulose, found in foods such as peanut butter, ice cream and salad dressings, disrupt intestinal mucus health. This causes endotoxemia, a systemic increase in plasma lipopolysaccharide (LPS) levels leading to inflammatory diseases. Carrageenan, dextran sulfate, maltodextrin and propylene glycol are also to be avoided.

Herbicides and pesticides. Glyphosate, the active ingredient in Roundup, eliminates probiotic species like Lactobacillus and Bifidobacterium while allowing pathogenic species to flourish. The pesticide chlorpyrifos disrupts the intestinal mucus barrier and allows higher levels of toxic lipopolysaccharide (LPS) into the bloodstream, increasing the potential for insulin resistance, type 2 diabetes and obesity.

Low-carb diets. Ketogenic, paleo, carnivore and Atkins diets all drastically reduce prebiotic fibers, polyphenols and other nutrients gut microbes need, starving them out of existence.

NSAIDs. Nonsteroidal anti-inflammatory drugs, such as ibuprofen and naproxen, diminish the mucus lining and microbiome composition.

Statins. These commonly prescribed cholesterol-reducing drugs appear to have a complex relationship with the gut microbiome. Studies show that statins influence the microbiome10 and that gut bacteria influence the effectiveness of statins,11 which may explain why they don’t work for many people.

Stomach acid–blocking drugs. Medications such as proton pump inhibitors reduce stomach acid, enabling unhealthy microbes to descend from the esophagus and ascend from the colon, colonizing the entire GI tract.

Sugar. Refined sugar causes loss of healthy bacteria. Overconsumption of sugars opens the door to increased fungal species that ascend the GI tract and wreak havoc.

How to spot SIBO

You may have SIBO if you notice these symptoms:

  • Allergies
  • Alzheimer’s disease
  • Anxiety and negative emotions
  • Autoimmune diseases
  • Bowel urgency
  • Constipation
  • Depression
  • Dementia
  • Diabetes
  • Fibromyalgia
  • Food intolerances
  • Gallstones
  • Heart disease
  • IBS
  • Obesity
  • Restless leg syndrome
  • Skin rashes
  • Social isolation
  • Seizure disorders

There are three ways to test for SIBO. First, an endoscopic exam can help to confirm whether SIBO is present. However, according to Davis, it’s a flawed method because it’s invasive, the results are subject to contamination and it identifies only severe cases of SIBO in which bacteria have ascended high up in the GI tract.

Another option is a laboratory breath analysis. It measures H2 gas in the breath after you consume a sugar or prebiotic fiber.

Finally, an at-home AIRE breath test requires you to blow into the AIRE device after consuming a sugar or prebiotic fiber, and breath H2 gas levels will register on your smartphone. The device is available at FoodMarble (

Davis recommends either the herbal antibiotic route (see below) or the yogurt route (see below) for healing gut dysbiosis and SIBO.

Bacterial strains to reintroduce

The following strains can improve your gut health to resolve SIBO or help you maintain it after you recover. You need purchase each desired bacterial strain only once to obtain a single capsule that you can ferment into yogurt or other food. After that, you can start future batches using a starter from your first fermentation.

We’ve included websites where you can find each of these strains below. You can also find most of them on Amazon. For more details about how to choose high-quality probiotics, see ‘Supplements in the Spotlight.’

Bacillus coagulans GBI-30, 6086. These coagulans strains reduce abdominal pain, diarrhea, constipation and inflammation. The Digestive Advantage Daily Probiotic from Schiff is a good source.,

Bifidobacterium longum BB536. May provide relief from compulsive behaviors.,

Lactobacillus casei Shirota. Increases immunity against viral illnesses, increases mental clarity and provides deep sleep for some people (especially in combination with L. reuteri). Most widely available in Yakult, a fermented milk drink.,

Lactobacillus gasseri BNR17. Helps the body process, store and eliminate sugars. Reduces abdominal fat. Increases overall strength.

Lactobacillus helveticus R0052 and Bifidobacterium longum R0175. This combination of species lifts mood and reduces anxiety.,

Lactobacillus plantarum 299v. Reduces bloating, abdominal discomfort and bowel frequency in people with IBS. Antibacterial and mucus-stimulating effects.,,

Lactobacillus reuteri DSM 17938, ATCC PTA 6476 and SD 5865. The L. reuteri strains have a unique capacity to trigger the release of the hormone oxytocin, the hormone of empathy and connectedness, from the human brain.

“People consuming L. reuteri–rich yogurt are reporting additional effects such as deeper sleep with vivid dreams, reduced appetite, greater optimism and less social anxiety,” says Davis. “Many experience a flood of empathy and desire for human connection.” BioGaia Gastrus tablets (widely available online) are a readily available form.,,

Lactobacillus rhamnosus GG. The GG strain is superior to other strains of L. rhamnosus for recovery from diarrhea after a course of antibiotics or for antifungal effects. It’s commercially marketed as Culturelle.,,

Oxalobacter formigenes. These bacterial species can consume toxic oxalates, naturally occurring compounds in foods such as nuts, spinach, beets and chocolate, that can deposit crystals in joints and tissues, triggering pain and inflammation. They don’t seem to be available in supplement form yet, but you may be able to get them by consuming fermented foods like kefir and kimchi.

Herbal antibiotic SIBO protocol

To try the herbal antibiotic method, choose one of the following:

Metagenics CandiBactin-AR, one or two capsules twice daily, and CandiBactin-BR, two capsules twice daily.,

Biotics Research FC-Cidal, one capsule twice daily, and Dysbiocide, two capsules twice daily.

Follow your chosen regimen for 14 days or until an H2 breath test yields low values (less than 4 on an AIRE device).

Additional suggestions

  • Disrupt biofilms using N-acetyl cysteine (NAC), 600–1,200 mg twice daily with your herbal antibiotic.
  • Eat Super Gut SIBO Yogurt every day for 30 days.
  • Try antifungals for SIFO.

Super Gut SIBO Yogurt

Rather than fermenting three different species separately, ferment all three strains together to generate an anti-SIBO mix of probiotic species. This process limits the resulting microbial counts of L. gasseri, which preliminary experience suggests is quite potent, so that we do not induce an excessive die-off reaction too quickly.

To start this ferment, you can use the raw probiotic products, 1–2 tablespoons of yogurt made with each individual species (curds and/or whey; see ‘Bacterial strains to reintroduce’, above, for more details about the probiotic species) or a couple of tablespoons you saved from a prior batch of this mixed yogurt. Create single-strain yogurt if you want the stronger effects from that one kind of bacterial strain.

For prebiotic fiber, inulin powder and raw potato starch, such as from Bob’s Red Mill, work best. Choose a high-fat, high-calorie liquid, such as half-and-half (equal parts milk and heavy cream) or whole milk, to ferment. Fat is nutritious, and calories don’t matter.


10 BioGaia Gastrus tablets, crushed (total 2 billion CFUs), or 2 Tbsp L. reuteri yogurt

1 capsule L. gasseri (10 billion CFUs) or 2 Tbsp L. gasseri yogurt

1 capsule B. coagulans (2 billion CFUs) or 2 Tbsp B. coagulans yogurt

2 Tbsp prebiotic fiber

1 quart organic half-and-half (half milk, half heavy cream) or other liquid, divided

Fruit, sweetener or other flavorings (optional)


  1. In a medium-sized bowl, combine the starting probiotics, fiber and 2 tablespoons of half-and-half. Make a slurry to ensure the prebiotic fiber does not clump. Stir until well mixed.
  2. Stir in the remaining half-and-half. Cover lightly (e.g., with plastic wrap), place in your fermenting device and ferment at 106°F (41°C) for 36 hours.
  3. Remove from fermenting device and add fresh fruit and sweetener if desired. Chia seeds are a great addition as well. Eat immediately or chill if you prefer it cold.

To make future batches, use 2 tablespoons of curds or whey from a prior batch. You can re-inoculate later batches using additional capsules if desired, but it’s not necessary. Bacteria grow naturally!

Following this recipe, single-strain yogurts contain over 200 billion CFUs per half-cup serving, and mixed-strain yogurts contain 60–80 billion CFUs of each strain per serving.

Added boost

Take nonabsorbable curcumin along with either the herbal antibiotic or the yogurt protocol. A nonabsorbable form is free of ingredients like piperine that increase absorption. Whether you choose the herbal antibiotic regimen or the yogurt, add curcumin for its antifungal and intestinal-barrier-strengthening effects: 300 mg twice daily building up to 600 mg twice daily over several days—take for 14 days. To learn more, search for “curcumin” in Dr Davis’s blog at

Yogurt makers

Many yogurt makers use a preset temperature range of 108–114°F (42–45°C), which will kill some of the needed microbes, like L. reuteri. Shop for a yogurt maker that has a programmable temperature range of 68–131°F (20–55°C) and a 48 hour-long fermentation setting (see below).

Alternative to dairy yogurt

Coconut milk yogurt is a nutritious choice for those who are sensitive to dairy. Choose a coconut milk that’s free of additives (guar gum is okay). The sugar in this recipe will be consumed by the microbes, so there won’t be any left when you eat it.


13.5 oz coconut milk

¾ tsp guar gum

2 Tbsp sugar

1 Tbsp raw potato starch

10 BioGaia Gastrus tablets, thoroughly crushed to powder


  1. Heat coconut milk over medium heat to 180°F (82°C) or until just below a boil; remove from heat and let cool 5 minutes.
  2. Add guar gum, sugar and potato starch and blend for a minimum of 1 minute or until mixture thickens to consistency of heavy cream.
  3. Cool mixture to 100°F (38°C) or room temperature, then mix in the Gastrus powder.
  4. Ferment at 100°F (38°C) in a fermenting device for 48 hours. Remove from the device and eat immediately or chill if you prefer.

Commercial prebiotic fibers

These fibers are ideal for feeding helpful bacteria strains and are available through nutrition retailers like Vitacost ( and iHerb (,, from Amazon, and in health food stores.

  • Inulin (from Jerusalem artichokes)
  • Acacia fiber
  • Glucomannan
  • Galactooligosaccharide powder
  • Garden of Life Organic Fiber
  • Swanson Ultra Inulin
  • NOW Certified Organic Inulin Prebiotic Pure Powder
  • NOW Certified Organic Acacia Fiber
  • Jarrow Formulas Prebiotic Inulin–FOS
  • Cutting Edge Cultures Prebio Plus
  • Micro Ingredients Organic Inulin Powder
  • Hyperbiotics Organic Prebiotic Fiber Blend

Mucus-building clove tea

Davis says people with gut issues almost always have a compromised intestinal mucus barrier. Restoring the health and thickness of the mucosal lining of the intestines is super important for gut healing. This tea does the following:

  • The eugenol oil from the cloves encourages proliferation of Clostridia species, which helps increase the thickness of the intestinal mucus lining.
  • The green tea catechins (antioxidants) convert mucus from semiliquid to semisolid gel, increasing the mucus’s protective capacity.
  • The fructooligosaccharide (FOS) prebiotic causes the bacteria Akkermansia to proliferate, increasing mucus production.

Use whole cloves rather than ground and choose an organic green tea high in catechin (matcha teas, for example). Sweeten with allulose, which has prebiotic fiber properties, or another gut-friendly sweetener (see below).


2 cups water

1 Tbsp whole cloves

1 tea bag green tea

1 tsp sweetener

1 cinnamon stick for flavor (optional)


  1. Combine water and cloves and bring to a boil.
  2. Reduce heat and simmer for 10 minutes.
  3. Add tea bag the last 1–2 minutes of simmering. Discard tea bag.
  4. Stir in sweetener. Sip throughout the day.

Safe sweeteners that don’t wreck your gut


After SIBO is gone

To prevent recurrence

  • Keep eating yogurt. Experiment with different strains to produce particular desired effects, like enhanced mood, decreased inflammation or greater strength.
  • Continue eating prebiotic fibers.
  • Take a multispecies probiotic supplement regularly.
  • Consume fermented drinks like kombucha and kefir, fermented vegetables like sauerkraut and kimchi, and fermented meats like salami.

Super Gut SIFO protocol without addressing SIBO

  • Curcumin regimen (see ‘Added boost,’ above).
  • One or two food-sourced essential oils (oregano, cinnamon or cloves). Start with 1–2 drops in 1 tablespoon olive, avocado or melted coconut oil twice daily; build up gradually to 5–6 drops per tablespoon of oil twice daily for a minimum of four weeks or until signs of fungal overgrowth have diminished.

Recommended probiotics post-SIBO

Why doesn’t taking probiotics regularly eliminate gut dysbiosis and SIBO? “We cannot rely on conventional probiotic formulations to eradicate SIBO because they have only limited effects and do not typically reverse SIBO,” says Davis.

“High H2 breath readings, food intolerances and fibromyalgia, for instance, usually persist despite regular consumption of probiotics. This should come as no surprise because conventional probiotics are prepared without attention to choosing species and strains that have specific SIBO-eradicating effects.”

After completing the SIBO protocol (either yogurt or herbal antibiotics), be sure to maintain probiotics in your diet. The following are recommended:

United Naturals Synbiotic 365 contains 20 billion CFUs of L. rhamnosus GG, L. reuteri UALre-16 (NCIMB 30242), L. gasseri BNR17, Saccharomyces boulardii and other strains.,

Klaire Labs Ther-Biotic Synbiotic contains 50 billion CFUs of seven strains, including L. rhamnosus GG and L. reuteri UALre-16 (NCIMB 30242). You can make yogurt with this product.

Vital Planet Vital Flora offers a variety of reliable and diverse probiotic blends to choose from containing 60–100 different strains.

BiotiQuest Sugar Shift contains eight strains, including L. plantarum TBC LP-36, L. reuteri PCR07 and Leuconostoc mesenteroides TBC LM-37, that helps reduce blood sugar levels.

Jarrow Formulas Jarro-Dophilus EPS Digestive Probiotics contains eight strains, including L. rhamnosus R0011, L. helveticus R0052 and B. longum BB536, that studies have shown can improve gut and immune health.

Temperature-control yogurt makers

If you’re looking for a yogurt maker to make your own probiotic yogurt, here are two good options. Both have glass containers to make the yogurt in rather than plastic.

If you can’t get hold of a yogurt maker, you can also try using a sous vide machine if it allows for the right time and temperature ranges.

Probiotic Yogurt Maker, $59.99

Featuring adjustable temperature control from 68–131°F (20–55°C) and up to 48 hours of runtime, this yogurt maker comes with eight 6-oz glass jars and BPA-free plastic lids. It’s available in the UK via Amazon, but Ultimate’s website states that it should only be used with a standard North American power outlet.

Pure Plus Yogurt Maker, $109.95/£88.95
US:; UK:

This pretty pastel-green yogurt maker uses water-bath technology to maintain accurate and even temperatures, which can be set to 78–122°F (25–50°C). It comes with a 2-L (2.1-qt.) borosilicate glass container with a silicone sleeve and lid and has a 36-hour digital timer. Also check out the Pure model that comes with four ceramic jars.

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