Fermented Foods 101: Probiotics, Bacteria and Gut Health

Adapted from episode 50 of The Perfect Stool podcast and edited for readability.

Fermentation is an ancient tradition used to preserve food without refrigeration and prevent spoilage, which uses microorganisms like bacteria and yeast to break down nutrients into their most digestible form. Some examples of common fermented foods are yogurt, kefir, sauerkraut, kombucha, pickles, miso, tempeh, natto, kim chee, kvass, cured meats, sourdough bread, apple cider vinegar that contains the mother (that cloudy stuff at the bottle of the bottle), and unpasteurized cheeses. Goat’s milk, sheep’s milk and soft cheeses made with A2 milk are especially rich in probiotic bacteria. Consuming fermented foods can help maintain healthy gut bacteria, as they are filled with good microflora called probiotics, primarily lactobaccili, bifidobacteria and one strain of streptococcus called streptococcus thermophilus, which have been shown to improve digestion and absorption of nutrients, and help with a whole host of health issues. 

Despite fermented food’s rise in popularity, many people still only consume probiotics in pill form. There is good evidence to suggest that eating fermented foods has advantages over getting probiotics and nutrients through supplements. First, a huge diversity of species live in fermented foods that you may not find in a supplement. In addition, during the fermentation process, yeast and bacteria interact with carbohydrates, releasing byproducts called bioactives or bioactive compounds. Bioactives are any chemical that have a biological effect on our bodies and include the beneficial bacteria themselves, as well as compounds like plant sterols, carotenoids, polyphenols, oligosaccharides, fatty acids and amino acid derivatives. And because fermented foods ferment for longer and interact with the nutrients in the food as opposed to growing probiotics on one substrate in a factory setting, there’s a higher quantity of bioactives in fermented foods, as compared to most probiotic supplements. Some examples of beneficial bioactive compounds that come from fermented foods are CLA or conjugated linoleic acid (an essential fatty acid otherwise found in meat and dairy from grassfed animals that’s created through fermentation from linoleic acid found in plants), genistein (an isoflavone that’s phytoestrogenic and anticancer due to its anti-angiogenic properties, meaning it inhibits the formation of new blood vessels, which feed tumors) and  gamma-aminobutyric acid or GABA, which is a calming neurotransmitter. Biocatives have numerous health benefits, like reducing cholesterol and helping with immune response. 

Another benefit of probiotic foods is that they’re already partially broken down into nutrients that are easier for your body to assimilate. One concrete example of that is how the probiotic bacteria in yogurt and kefir break down lactose, which many people struggle to digest, during the fermentation process. That’s why many people who are lactose intolerant can still tolerate yogurt. In addition, even if the microbes in probiotic foods don’t survive your stomach acid, they can still release enzymes as they die, which will help you digest your food better, leading to increased nutrient absorption. They can also break down anti-nutrients like phytic acid, which is found in grains, legumes and seeds and binds up minerals such as iron. After fermentation, the minerals become more absorbable. Eight hours of sourdough bread fermentation, for example, almost completely breaks down phytic acid in wheat and rye breads. So even though live bacteria are killed during cooking, nutrients in fermented sourdough bread are still more available because of the fermentation process. 

To make sure you’re getting the maximum benefits from live fermented foods, be sure to choose non-pasteurized or raw fermented foods or foods marked lacto fermented. So for example, the bags of sauerkraut you find in the supermarket are not raw and will have been cooked, killing the bacteria, which doesn’t mean they’re devoid of benefit, but they won’t have the live bacteria. You’ll find much more expensive raw, fermented sauerkraut in the refrigerated section of health food stores and of course you need to eat it cold to keep from killing the beneficial bacteria. Same with typical pickles found in grocery stores versus the more expensive fermented pickles found in the refrigerated section. This of course leads to the question of whether these bacteria actually survive the stomach acid and are delivered to the colon, where most of the fermentation in your own gut takes place. It turns out that lactobacilli and bifidobacteria, the strains most common in fermented foods, are especially resistant to stomach acid and have special strategies to ensure their survival, in particular when they’re traveling on food. This doesn’t mean that they will all arrive intact, but some portion of them will. 

In terms of quantities of probiotics in fermented foods, a serving of typical yogurts, kefirs and fermented beverages like kombucha will have around 10-40 billion CFUs or colony forming units, which is comparable to many commercial probiotics, although when I recommend lacto-bifido probiotics to clients I often shoot for 100 billion CFU per day and one of the most studied probiotics, VSL#3, which is now sold under the name Visbiome*, is 450 billion CFU per packet. There’s a wide range of CFU for other probiotic foods, so here’s an article that gives you the range of possibilities. But for packaged foods, they should list the CFUs on the containers. 

You may be wondering whether you should eat fermented foods if you have SIBO (that is, small intestine bacterial overgrowth), dysbiosis or IBS. I have heard and have personally felt like I’ve experienced bloating and issues from eating fermented foods and probiotics while dealing with bloating from SIBO. That being said, there is one small study supporting probiotics as a treatment for SIBO in which probiotics outperformed standard antibiotics (and by that I don’t mean the $2,000 antibiotic rifaximin or xifaxin which is often prescribed for SIBO). They believe this is because the probiotic bacteria outcompetes the overgrown bacteria but are generally transient and pass through your digestive system rather than colonize it. And I’ll link to that study and all the others I’m mentioning in the show notes and in the transcript which will come out in a week on my blog. 

Another small study showed improvement in diarrhea from bacterial overgrowth with treatment using two strains of lactobacilli, but it did show that ongoing treatment with them would be necessary to maintain the improvements. This is much more practical when considering eating fermented foods versus taking probiotics in the long term. Other reasons that fermented foods may be beneficial in SIBO are due to their anti-inflammatory and immunomodulatory effects, which may help your immune system clear the SIBO, as well as helping to promote a healthy mucous lining in your intestines. If you do feel like you have a bloating response to fermented foods and/or probiotics when you have SIBO, you can either start with very small quantities and build up to see if that helps, or stick to spore-based probiotics (like Megasporebiotic or Proflora 4R – both found in my Fullscript Dispensary*) or S Boulardii probiotics* (which is a beneficial yeast) and hold off on fermented foods until the root cause of the SIBO is addressed. 

Another potential benefit of fermented foods is with candidiasis, which is an overgrowth of the yeast candida, a normal resident in our bodies, which can take place in the mouth, also known as thrush, the digestive tract, the vagina and can also be systemic, especially in people with weakened immune systems. A 2016 review of the research on the benefits of probiotics for candida cited studies which found antifungal effects for lactobacilli and saccaromyces boulardii in vitro, meaning in petri dishes, and for lactobacilli, in vivo, meaning in human studies. In vitro, S. boulardii (whose official name is actually saccharomyces cerevisiae subsp. boulardii) was particularly good at stopping candida albicans from forming filaments called hyphae which make it particularly pathogenic, while lactobacilli were good at inhibiting its growth. Supplementing with selenium also enhanced the antifungal effects of the lactobacilli. In vivo, various strains of lactobacilli were helpful in reducing candida in the oral cavity, urogenital tract and GI tract, by inhibiting biofilm growth by reducing hyphal development. If you’re wondering where to find S. Boulardii in food, I discovered while researching for this podcast that it was actually first found in the fruits mangosteen and lychee and that’s pretty much the only place you’ll find it in food. Typical Americans might not eat those fruit frequently, but funny story, my husband loves mangosteen, which I guess he remembers from living in Malaysia and Panama as a child when his father was in the military. We lived in Australia for a few years when I was doing my doctorate and we took a trip to a small town in northern Queensland called Port Douglas and were hosted by the mayor of Port Douglas who Doug knew from his work. His property was only accessible via boat across crocodile infested waters. And on his property he had a mangosteen tree. Normally mangosteen were pretty expensive and not very good by the time they got to the store, but that evening after dinner, Doug got to eat freely from the tree as many mangosteen as he could have ever desired. But if you don’t eat those fruit much, then you’ll have to look at supplements for S. Boulardii. But anyway, those studies point to the likely usefulness of probiotic foods in preventing candidiasis, which many women likely already knew, as we’re often told to eat yogurt to prevent yeast infections, even by traditional doctors. 

In terms of fermented foods and inflammatory bowel disease or IBD, one peer-reviewed article suggested that the increased prevalence of IBD in western countries and developed Asian countries is due to rapid changes in the environment and diet. In Japan and Korea specifically, traditional fermented foods are consumed less by younger generations due to their strong smells and tastes, along with a reduction in fiber in the diet. The researchers suggest that returning to a more traditional diet should be encouraged to protect public health, create a healthier gut microbiota and decrease rates of IBD.

There are also two studies on mouse models of chemically induced colitis that offer support for fermented foods. In one of the studies, colitis symptoms were alleviated in mice fed a mixture of fermented barley and soybeans by increasing levels of healthy bacteria like lactobacilli and suppressing levels of pro-inflammatory cytokines in colonic tissue. In another study, mice fed a novel yogurt obtained by fermenting two anti-inflammatory bacterial strains, Streptococcus thermophilus CRL807 and Lactobaccilus delbrueckii subsp. bulgaricus CRL864 showed reduced inflammation and developed a healthier immune response compared to controls. 

I wanted to talk more in depth about one fermented food, kefir, a probiotic drink made by fermenting milk, alternative milks or water with kefir grains, because it has many big advocates for its positive health effects, including with gut health issues. Kefir contains more than 50 species of probiotic bacteria and yeasts, and has been found to boost immune function, fight against harmful microbes, help with digestive issues and more. In addition, during the fermentation process, the bacteria from kefir grains produce the B vitamins B1, B2, B6, B12, folate and biotin, some of which I find are commonly deficient in my clients. 

In terms of the evidence supporting kefir for gut health issues, in one study, four groups of mice received different doses of kefir over a four week period while the control group received a placebo. Results demonstrated a significant correlation between the amount of kefir administered and improved the ratio of Firmicutes to Bacteroidetes in the gut microbiome, which is considered a marker of microbiome health, improved athletic performance and decreased fatigue. Other studies have identified additional benefits, like building bone strengthdecreasing proliferation of estrogen-dependent breast cancer cellsdecreasing inflammation and allergies in a mouse model of asthmafighting against foodborne pathogens and supporting skin health

Kefir may also help with gastrointestinal symptoms according to a randomized study of 15 healthy adults with lactose maldigestion, in which participants consumed milk, plain and flavored kefir, along with plain and flavored yogurt. Yogurt and kefir were shown to have a more positive effect on patients’ GI symptoms than milk. Another small study on ten people with chronic constipation matched with healthy controls showed significant improvement in stool frequency and consistency. Another study, however, found no significant improvement in antibiotic-associated diarrhea among 125 children after giving them kefir. 

But more importantly, in a 2019 study on inflammatory bowel disease, 10 Crohn’s disease and 15 ulcerative colitis patients matched with 20 controls received 400 ml/day of kefir over a four week period. After scoring symptoms like stool frequency, consistency and abdominal pain, researchers found that consuming kefir significantly improved patients’ symptoms and helped modulate their gut microbiota.  

And keep in mind that not all kefir products are created equal. Kefir is made from the symbiotic relationship between bacteria and yeast found in kefir grains. Just as pasteurizing and mass producing supplements can reduce the diversity of nutrients available, mass producing kefir can lead to a less effective product resulting from a lack of microbial diversity in the kefir grains. In addition, the type of milk, time, temperature, and different methods of production all contribute to kefir’s effectiveness. So if you decide to make your own kefir, be sure to invest in quality grains. They can originate from different countries too, so if you’d like to learn more about the ones used in the studies mentioned, you can find those in the show notes. 

So in summary, I’m really glad I undertook this podcast topic as I personally haven’t put a lot of emphasis on fermented foods lately, other than making my own sauerkraut, since I stopped eating dairy and making my own yogurt. But now I’m feeling like it would probably be worth my time to figure out how to make kefir with a non-dairy milk or incorporate some good quality, organic kefir info my diet. And I’d encourage those of you with gut health issues to start ramping up your consumption of fermented foods. 

If you’re struggling with constipation or other gut health problems and are ready to get some professional help, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

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