Targeted Microbial Therapy: Eight Powerful Foods That Heal from the Inside Out

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My interest in fermented foods and their medicinal powers began nearly twenty years ago when my mother, a Weston A. Price Foundation member, suggested that I try the GAPS diet to address the severe joint pain that I was experiencing. The GAPS diet features fermented foods as staples, along with other healing foods like meat stock and animal fats.¹ Discovering the power of fermented foods—and what I call “targeted microbial therapy”—changed the course of my life.

Nowadays, the recommendation to eat some fermented foods is becoming more common, backed up by a growing body of research. A 2021 Stanford University study highlighted the benefits of fermented foods rather dra­matically.² A husband-and-wife research team³ at the School of Medicine’s Department of Microbiology and Immunology conducted a clinical trial in which they randomly assigned thirty-six healthy adults to one of two ten-week dietary interventions; one group ate a diet high in fermented foods (yogurt, kefir, fermented cottage cheese, fermented vegetables, vegetable brine drinks, kombucha or other non-alcoholic fermented beverages) and one group ate a high-fiber diet (fruits, vegetables, legumes, grains, nuts and seeds).⁴

Many people think that fiber is what builds the microbiome, but as this study showed, that was not the case. Over the course of the ten weeks, it was the participants who ate a diet high in fermented foods who displayed increased microbial diversity, “with stronger effects from larger servings,” as well as decreased levels of nineteen out of nineteen inflammatory mark­ers. These findings were consistent across all participants in the fermented foods group. By contrast, microbial diversity in the high-fiber group remained unchanged, and none of the inflammatory markers decreased. In this article, I will describe eight types of fermented foods and what makes them so powerful.

WHERE TO START? TRY FERMENTED VEGETABLES

Fermented vegetables are one of the easiest fermented foods with which to start. Once you have learned to make simple vegetable ferments, you can ferment any vegetable you like.⁵ When you eat a raw, unfermented vegetable, your body has to work to unlock the nutrients, whereas the nutrients in fermented vegetables are immedi­ately bioavailable and ready to help your body.

Consider the humble cabbage. One cup of raw cabbage contains about twenty-five micro­grams of vitamin C, but fermenting it increases the vitamin C content tenfold, so that one cup of fermented cabbage has two hundred fifty mi­crograms of vitamin C. This is one of the most nutrient-packed, vitamin-C-filled foods that you can eat. Fermentation also turns the vitamin K₁ in cabbage into vitamin K₂, which tells calcium where to go in your body. In addition, all fer­mented foods, including fermented vegetables, are loaded with bioavailable B vitamins.

I recommend fermented vegetables or fer­mented vegetable brine for any gastrointestinal (GI) issue, such as vomiting, diarrhea or gall­bladder issues. A fermented beverage like beet kvass can also help with constipation. If you are “stopped up,” drink eight ounces of beet kvass or the liquid from another fermented vegetable, and it will clear you out. Beet kvass is also very hydrating, promoting electrolyte balance. I have even seen fermented vegetable brine actively stop a pancreatitis attack. A friend went to the hospital, but after they sent her home, she was still experiencing diarrhea and vomiting. I gave her a spoonful of fermented vegetable brine and some kefir, and by the next day, she was up and about. I suggest that everyone keep fermented vegetables in their fridge at all times.

The microbe that makes this so magical is Lactobacillus plantarum (renamed Lacti­plantibacillus plantarum).⁶ It is a “transient” microbe, meaning that it does not proliferate in your body—it just passes through. L. plantarum is a gentle binder that grabs onto bad microbes and escorts them out the back end. Hospitals use L. plantarum in cases of extreme diarrhea, although they may not tell you that they’re using microbial medicine or that you can make your own at home!

Another notable aspect of fermented vegetables is that they are prebiotic as well as probiotic. You are getting fiber, but the fiber is already broken down. This is fantastic for people who have small intestinal bacterial overgrowth (SIBO), a form of dysbiosis involving “increased bacterial colonization of the small intestine with some of the bacteria more characteristic of the colon microbiota.”⁷ Although SIBO is not very well known, it is actually quite common. In practical terms, it shows up as intolerance to things like fruits, vegetables and whole grains, triggering bloating, gas and abdominal discom­fort. In cases of SIBO, the predigestion aspect of fermented vegetables is very helpful because the body doesn’t have to do as much work.

KOMBUCHA

Kombucha is a fermented tea traditionally made by fermenting sugar and black, white, green and/or oolong (Camellia sinensis) tea with a “symbiotic culture of bacteria and yeast” (SCOBY), also referred to as a pellicle, which is composed mostly of bacterial cellulose.⁸ The culture includes acetic acid bacteria, lactic acid bacteria and yeasts such as Saccharomyces cerevisiae. Even a small serving of kombucha may contain anywhere from fifteen to thirty microbe strains as well as colony-forming units (CFUs) up into the tens of billions. Like fer­mented vegetables, kombucha is loaded with bioavailable B vitamins.

Different microbes prefer different environ­ments, so the type of tea used will make a differ­ence in the microbial profile of the kombucha.⁹ Black tea, for example, is higher in tannins, and not all microbes appreciate that. Green tea is more favorable for L. plantarum. You can also change the type of tea you use with different batches to broaden the kombucha’s microbial profile. I will use green tea one time and white tea the next. This makes your SCOBY stronger and more diverse.

The same microbes that create the cellulose pellicle create their own form of glucosamine, which makes kombucha excellent for joint health. Another compound in kombucha is gluc­uronic acid, which binds and removes toxins, thereby supporting liver health and helping with liver detoxification. Thus, consuming kombu­cha can help with skin conditions like eczema, which are often a sign of poor liver function.¹⁰ In addition, thanks to its acetic acid component, kombucha helps with weight loss and blood sugar regulation (comparable to drinking a little apple cider vinegar before a meal). If you are making kombucha and you forget about it for a while, it will actually turn into vinegar, and you can use it just like vinegar in your cooking. Remembering that L. plantarum is a binder that helps to move toxins out of the body, kombucha can also be a great support for those suffering from diarrhea.

In addition to being good for joint, skin and metabolic health, kombucha can be helpful in clearing C. diff (formerly Clostridium difficile, now Clostridioides difficile), a microbe linked to severe “poop” problems. Hospitals’ standard response to C. diff is antibiotics, but they don’t work, so gastroenterologists are now recom­mending fecal transplants for many patients with recurrent C. diff.¹¹ Rather than going that route, drink kombucha instead! A friend cleared C. diff by doing a two-week broth fast, during which she also drank kombucha three times a day. At the end of the two weeks, the C. diff was gone.

Kombucha is very high in polyphenols, which happen to be abundant in tea as well as in deep red fruits and vegetables such as ber­ries, pomegranate and red cabbage. Hibiscus is also high in polyphenols, and I like to use it as a flavoring for my kombucha. Polyphenols interact in important (and bidirectional) ways with gut microbes,¹² including Akkermansia muciniphila, which lives in the mucus lining. Akkermansia eats polyphenols, so keeping your Akkermansia well fed will help your gut lining remain thick and intact. However, if your diet is deficient in polyphenols—whether because you are eating a high-carbohydrate and junk food diet or a low-carb carnivore diet—guess what your Akkermansia does? It’s got to eat, so it eats the mucus lining, contributing to “leaky gut.”¹³ In my view, a short-term carnivore diet may be helpful for some acute issues, but it is wise to add back kombucha or another source of polyphenols as soon as possible.

Kombucha is fantastic for someone who is getting off of alcohol. Often, the desire for alco­hol is driven by microbes such as Candida that have grown accustomed to the carbohydrates in the alcohol; swapping alcohol for kombucha can help kick out the Candida and repopulate the gut microbiome with healthier microbes.

Interestingly, when I started drinking kom­bucha daily, I stopped getting bitten by mos­quitoes. Mosquitoes come after people who are low in B vitamins, so if you get gobbled up by mosquitoes, this is your notice to start drinking kombucha or eat more fermented foods.

Many store-bought kombuchas are now available, but generally they will be a lot less potent than homemade kombucha, for several reasons. First, store-bought kombucha is not fermented for nearly as long as homemade, because companies need it to be shelf-stable— they don’t want bottles exploding in the store. Second, flavored kombuchas are diluted with a lot of juice. This also makes the sugar content of store-bought much higher. When you make kombucha at home, you have a lot more control over how much sugar is left in it. The only store-bought kombucha I trust is the GT’s brand, because I was able to grow my original SCOBY from a GT’s bottle. In a pinch—if someone doesn’t have access to homemade and has diar­rhea or is taking antibiotics—then store-bought is better than nothing, but I would try to get plain rather than flavored. It will make it better for you if you leave a store-bought kombucha on the counter for a day or two to ferment off a little more of the sugar.

KEFIR SODA

Another fermented (probiotic) beverage is kefir soda. I use a culture from Cutting Edge Cultures.¹⁴ What I love about this specific soda culture is that it includes the beneficial yeast Saccharomyces boulardii as well as bifidobac­teria and L. plantarum. S. boulardii binds to pathogenic bacteria and other toxins, preventing them from attaching to the intestinal lining, and has well-documented benefits for gut healing and gut health.¹⁵

Bifidobacteria are of particular interest at the moment because of the intriguing research by Dr. Sabine Hazan demonstrating a decrease in the relative abundance of bifidobacteria six to nine months after receiving a Covid mRNA shot.^16,17 Bifidobacteria are also your “youth microbe.” You get bifidobacteria from birth, but they slowly degrade as you age, so adding them back when you’re older is really good for you. Bifidobacteria also help with food allergies and dairy intolerance in, for example, colicky babies.

Kefir soda is fantastic for children because you can make it quickly, it tastes good and you can flavor it in many ways. It is also very low-maintenance. I make it with a coconut water base and a little maple syrup; then I take a bit of that out, put it in a different bottle, add juice or tea (or whatever flavor I want) and let it ferment for twenty-four hours. In twenty-four hours, you’ve got a busy, active, happy, fermented soda.

NATTO

Natto is an umami-tasting staple in Japan, where they eat it for breakfast. Traditionally fermented from soybeans, it contains Bacillus subtilis bacteria that release spores (what one writer calls “little probiotic babies”) that do well in the large intestine.¹⁸ Natto is rich in vitamin K2 as well as B vitamins, calcium, magnesium, iron, zinc and potassium.

Natto and B. subtilis help to eliminate toxins from the body by creating the equivalent of a surfactant—what amounts to a bubbling cleaning agent—that can neutralize toxins in the gut and prevent biofilm formation.¹⁹ B. subtilis also produces digestive enzymes such as amylase, protease and lipase. (When a naturopath tells you to buy an expensive enzyme supplement, just eat natto instead.) Nattokinase, another one of the enzymes produced by B. subtilis during fermentation, has been found to be a “potent blood-clot dissolving protein,”²⁰ and for that reason, natto­kinase supplements have become a key component of protocols developed to detoxify “spike protein” after Covid vaccination.²¹ For my part, I think someone would derive more benefit from food-source nattokinese—that is, from eating natto—than from taking a random nattokinase supplement that is probably made in China.

Natto is somewhat time-consuming but not difficult to make. The roughly four-day process requires soaking, cooking and inoculating the beans and then letting them ferment for twenty-four hours, but it is not hands-on the whole time. It is also possible to make natto with black beans. However, a helpful feature of natto made with soybeans is that it functions like an estrogenic adaptogen, straightening out your hormone balance—meaning that if you have high estrogen, it will bring it down, and if you have low estrogen, it will bring it up.

MILK KEFIR

Milk kefir is my favorite ferment. I drink a quart every day for breakfast, and I consider it my “multivitamin.” Milk kefir features a high level of microbial diversity—thirty to fifty distinct species of bacteria and yeasts—and CFUs in the hundreds of billions. Even one spoonful a day will provide more probiotic benefits than an entire bottle of store-bought probiotics. Milk kefir has had a powerful impact on my own health—and for my family, neighbors and everyone that I’ve given it to, it has been game-changing.

The beneficial microbes in milk kefir come with a sort of “safety bubble” around them, so that when you drink the kefir, they can travel through the body to the location where they are needed. Milk kefir can rebuild the gut microbiome, and it is also incredibly nutrient-dense, rich in B vitamins, tryptophan, calcium, magnesium, phosphorus, zinc and the fat-soluble vitamins (A, D and K₂). The only thing that isn’t in milk kefir is vitamin C, so when I drink it, I add baobab powder (from the fruit of Africa’s baobab trees), which is very high in vitamin C.

Like kombucha, milk kefir is made with a symbiotic community of bacteria and yeasts, referred to as kefir “grains.” Milk kefir originated in Russia’s Northern Caucasus region, and food historians have ascertained that the traditional process went something like this:

“[M]ilk kefir was made by combining fresh milk and kefir grains inside goatskin bags. During the daytime, the goatskin bags were hung in the sunshine of the doorways, and prodded or pushed by each person who went through the doorway. As the milk kefir was consumed, more fresh milk was added to the goatskin bag, forming a continuous fermentation cycle.”²²

The “grains” eat lactose and break down casein. People who have a dairy intolerance are missing the enzyme needed to digest lactose, but milk kefir takes care of that. My best friend thought she was allergic to dairy, which she couldn’t eat without significant discomfort. After about four months of slowly increasing her intake of milk kefir, her dairy in­tolerance disappeared such that she can once again eat cheese and drink milk. She started with a “shot” of kefir before meals, three times a day, and incrementally worked herself up to four cups a day. I have not worked with anyone with a dairy intolerance who was not able to eventually handle milk kefir, but you have to listen to your body. If your body is telling you, “maybe not,” then you might want to start very slowly or try a different fermented food.

There are many other conditions that can benefit from regularly consuming milk kefir, ranging from issues with blood sugar regulation to constipation²³ and sinusitis. If you have bone density problems, the vitamin K2 in kefir will tell the calcium where it needs to go. It is amazing for skin conditions, including acne, eczema and psoriasis—it has cleared eczema for many of my clients. Research and anecdotal reports also indicate that milk kefir is fantastic for kidney function and can even repair significant amounts of kidney damage,^24,25 so I would highly recom­mend it for anyone who is having renal issues.

Another benefit of the microbes in milk kefir is that they can help strengthen the im­mune system, so kefir is your best friend if you are immunocompromised. When I was a kid, I suffered with asthma and would be hospital­ized every single year with pneumonia. Today, my asthma is gone, and if I get sick, I recover quickly, with none of the respiratory issues that I used to experience. Milk kefir can also take care of sugar cravings. I used to be a serious sugar addict, but when I started drinking milk kefir, it killed the Candida that was making me crave candy and other sweets, and I have no interest in them anymore.

When it comes to making kefir, it is cer­tainly preferable to make it from raw milk if you can, but kefir will “amp up” the nutrients and maximize the potential of any milk you use. If you can’t afford or don’t have access to raw milk, making milk kefir in any form is better than not having milk kefir at all. I have also learned that good microbes will eat the bad stuff during fermentation, so, for example, if you ferment regular store-bought milk, they will eat up the microplastics.

Once you start making milk kefir, all you have to do is strain out the “grains” once a day, give them fresh milk and drink your kefir—it takes me about five minutes a day. Because milk kefir can be rather sour, I do a secondary fermentation. After I strain out the kefir, I put it into a bigger jar, adding another equal part of fresh milk; then I leave it on the counter (with a lid) for another twelve to twenty-four hours. It turns into a thick, creamy, mild milk kefir. When the milk kefir “grains” reproduce, you can either eat them, give them to your friends, put them in smoothies or give them to your animals (dogs, chickens and goats all love them).

If you need to take a milk kefir break, you can temporarily put the “grains” to sleep in the refrigerator. If you strain them out, give them a quart of fresh milk and put them in the fridge, they will go into hibernation. When you want to start up again, strain that milk off and start feeding them again. However, I do not advise leaving them in the fridge for too long. If you are going away for a month, you can freeze them, and they will come back fairly well, although it may take a day or two for them to kick into high gear.

Commercial “milk kefirs” sold in grocery stores are made using far fewer strains—perhaps four to five that are shelf-stable and proliferate easily—and the result does not have nearly the potency of the milk kefir that you make at home. I even left one well-known store-bought brand on the counter for four weeks, and it did not change one bit. That told me that it was not a living food.

THREE YOGURTS

The concept of “targeted microbial therapy” especially comes into play with yogurt. Two single-strain cultured yogurts—made with Lac­tobacillus reuteri and Lactobacillus gasseri, respectively—can do very powerful things both individually and together. Dr. William Davis de­scribes them in his book Super Gut.²⁶ L. reuteri colonizes the upper GI tract (stomach and small intestine), while L. gasseri populates the colon, rectum, urinary tract and female reproductive system. Taken as a team, these two single-strain yogurts form a powerful combo to get rid of SIBO.

Both have bacteriocins (“microbial antibiotics”), which are basically the microbes’ attack dog or protection system to stop other microbes from killing them. L. reuteri has just one bacteriocin, while L. gasseri has five. As an illustration of their power, manufacturers use L. gasseri bacteriocins in fermentation facilities to clean out their vats.

L. reuteri is supposed to be in our gut from birth but is very sensi­tive to antibiotics. In addition to antibiotics from the doctor, we may be exposed to environmental antibiotics, notably glyphosate, which has even been patented as an antibiotic.²⁷ When you eat glyphosate-sprayed grains, you are killing your microbiome. (I recommend eating grain-free at restaurants for that reason.)

I call L. reuteri the “big daddy” of microbes because it helps increase testosterone in both men and women. When testosterone is low, we feel terrible; this is a way to add it back in for more energy and motivation. L. reuteri also increases the “feel-good” hormone oxytocin (consider the implications for happiness if someone takes antibiotics during childhood and wipes out their L. reuteri). For men, L. reuteri can help with infertility, and for women, it will improve libido and sexual health and take care of vaginal dryness. It also increases skin thickness and collagen production.

L. gasseri is great for female issues like urinary tract infections, yeast infections and bacterial vaginosis. A pregnant friend had bacterial vaginosis, which is very hard to get rid of, and she cleared it in a week taking a daily spoonful of  L. gasseri yogurt. It is also good if you have seasonal or food-related histamine issues (such as sneezing, runny nose, headaches or insomnia) because it helps stabilize mast cells. Studies have linked histamine issues to an imbalanced gut microbiome²⁸—due to “bad” bacteria in the gut that secrete histamine—so getting rid of the “bad” microbes and repopulating your gut with L. gasseri can resolve the histamine issues. I recommend starting very slowly, literally “micro dosing” by dipping a spoon into the yogurt and licking it once a day, and then slowly working up. Depending on the severity of the histamine intolerance, it can take a couple of weeks. A little bit of fermented vegetable brine or a little milk kefr can serve the same purpose. I sometimes suggest reducing high-histamine foods during this period to give the body breathing room.

I generally recommend that people make both of these yogurts. Even just one spoonful of each per day, properly cultured, can make a ma­jor difference. You don’t need much because the CFU count is so high. To make them, ferment the starter culture with milk at one hundred degrees for thirty-six hours with a prebiotic such as inulin, FOS (fructo-oligosaccharides) or GOS (galacto-oligosaccharides). (The prebiotic provides food for the microbes after they have finished eating all the lactose.) Thirty-six hours is a very extended fermentation time, but that is how long it takes for the L. reuteri and L. gasseri to proliferate. Importantly, the milk has to be heated or pasteurized because you don’t want any microbial competition—you want the L. reuteri or L. gasseri to be in the hundreds of billions of CFUs for maximum therapeutic potential. Both cultures are available at Cutting Edge Cultures.

A third special yogurt, made with a Cut­ting Edge Cultures starter called Yogurt Plus, includes bifidobacteria (B. longum) as well as L. plantarum, L. reuteri and a couple of other strains. In this case, you’re not trying to culture one specific strain as with the L. reuteri and L. gasseri yogurts. For many people, a history of antibiotics or Covid shots will have wiped out their bifidobacteria, so this is a good way to recolonize the entire GI tract, top to bottom. This yogurt is helpful for anyone with colon issues, including colon cancer. It is also good for metabolic issues and weight management, skin health (acne and eczema) and autoim­mune conditions. Bringing back bifidobacteria can help with colicky babies who can’t tolerate dairy. This is also a good one to consume during pregnancy; if you repopulate your bifidobacteria while pregnant, they will be available to transfer to the baby at birth as nature intended. I make Yogurt Plus with heavy cream and use it as a delicious replacement for sour cream. It is one of the fastest yogurts to make (ready in about ten hours) and gets very thick and creamy.

A SUCCESS STORY

After I healed, the first person I helped was a woman living in another state who I became friends with on social media. She reached out, and eventually I discovered that she was very sick and, in fact, bedridden. Among other condi­tions, she had been diagnosed with ulcerative colitis, Crohn’s disease and gastroparesis. She vomited after every meal and couldn’t eat meat. At her smallest, she weighed eighty-two pounds. When I asked how she had become so sick, she told me that she had had numerous surgeries and antibiotics following a car accident. The anti­biotics had “carpet-bombed” her microbiome.

I told her that if she wanted to heal, she needed to eat fermented foods. For six months, I walked her through how to make them, and today, it is almost unbelievable how much better she is. After six months of drinking milk kefir and kefir soda and eating the L. reuteri and L. gasseri yogurts and cultured vegetables, she is no longer bedridden. She can eat meat again, she has taken herself off of six medications, her collagen has come back and she is able to play with her grandchildren and go on vacations.

This friend also healed her husband, who had horrible eczema all over his body. Initially, we saw no improvement after he started eat­ing the yogurts and fermented vegetables. I speculated that something else was going on and learned that he was taking daily ibuprofen and was eating seed oils when he went out with friends. Three weeks after I told him to stop taking the ibuprofen and stop eating seed oils, his skin was clear.

Both stories demonstrate the fact that fer­mented foods are powerful medicine. For those who want to start eating fermented foods, I suggest listening to your intuition and starting with the one that you feel will help you. I can promise that you will feel better.

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SIDEBARS

VEGETABLE FERMENTATION MADE EASY

Those new to fermentation sometimes find the recipes to be vague or confusing. For example, when a recipe says, “get a cabbage and add two tablespoons of salt” but does not specify the size of the cabbage, what does that mean? Fortunately, you can use a very simple ratio to ferment any vegetable.

Using a scale, weigh the vegetables and any other ingredients. (If it is a vegetable like carrots that does not have a lot of water content and you are adding water, you will need to weigh the water, too.) If you take the weight of the contents and multiply it by .03, that will tell you the amount of salt (by weight) needed for a 3 percent brine. A 3 percent brine makes any ferment safe, ensuring a low enough pH that you will not run the risk of mold. Make sure all weights use the same unit of measurement (such as grams).

RESOURCES AND TIPS

CUTTING EDGE CULTURES: This is an excellent source of starter cultures for fermented dairy and kefir soda (cuttingedgecultures.com).

CULTURED FOOD LIFE: Donna Schwenk’s website includes articles, videos, a podcast, recipes, and a shop selling starter cultures, fermenting accessories and Schwenk’s books (culturedfoodlife.com).

FREEZE-DRIED PROBIOTICS: If you have freeze-dried probiotics, I recommend that you create yogurt from them. The probiotics will be far more effective if turned into food.

BOOKS: Helpful books include Super Gut by Dr. William Davis, Wild Fermentation by Sandor Katz and, of course, Nourishing Traditions by Sally Fallon Morell.

SHIPPING: I have shipped cultures all over the United States, even in the summer, and they are fine without a cold pack or any special shipping treatment.

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REFERENCES

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