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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12 Common Causes of Bloating and Their Solutions

Adapted from episode 45 of The Perfect Stool podcast.

Most people experience bloating at some point in their lives, maybe even frequently, but when is it normal, and when is it a sign of a more serious root cause?

To start, let’s define bloating. Bloating is when gas builds up in the digestive tract and pushes the stomach outward, causing pain and tenderness. I’m well familiar with bloating as it was one of my primary symptoms of gastrointestinal distress from a young age. For me it usually happened after big meals out where I’d get what I now call a food baby, and I did look about 6 months pregnant. But it became more and more frequent for me as I got older, and not just after big meals, to the point where I was not just bloated after every meal but even often woke up bloated.

If you’re unsure if you’re bloated, most people describe it as feeling as if you’re full, like you’ve just had a huge meal, or have a tight feeling in your stomach and abdomen. You might also find that your stomach is swollen and painful to touch and you also may have gas and/or excessive burping. This can take all the fun out of eating, so here’s twelve common causes and their solutions.

#1: Your Eating and Drinking Habits

Sometimes bloating is caused by something simple and mostly harmless, like eating too much at once, eating too quickly, or even chewing gum. Simple tips like eating and drinking more slowly, chewing gum less frequently, eating smaller meals, and not drinking with a straw could all help if there is no underlying GI issue. Many people also swallow excess air while drinking, so double check your drinking technique, especially if you’re also dealing with frequent burping. Carbonated drinks can also cause bloating because of the extra gas you’re drinking.

#2: You’re Lactose Intolerant

Bloating is a common sign of lactose intolerance, which is incredibly common in adults. If you’ve done a genetic test like Ancestry or 23andme and have access to your raw data, you can find out whether you have the gene for lactase persistence (lactase being the enzyme that digests lactose) by running it through a free tool called Genetic Genie. If you don’t have the lactase persistence gene, lactose intolerance is likely a root cause for you. If you notice bloating after enjoying some cheese, yogurt or ice cream, you’re definitely not alone. Around 75% of the global population is estimated to have some degree of lactose intolerance! Thankfully, lactose and dairy-free foods are widely available, so you may not have to sacrifice the foods you love to avoid dairy. Or you can take a lactose digestant tablet/dairy enzyme pill* or two with meals containing dairy. But be aware that casein intolerance, which is an intolerance to the protein in dairy, is also a thing.

#3: You Might Have a Gluten Sensitivity

Gluten is another common trigger of bloating and other GI issues, both for people with celiac disease as well as people with non-celiac gluten sensitivity. Signs of celiac disease include bloating and gas, abdominal pain, anemia and diarrhea, among others. Some people with gluten sensitivity don’t have celiac disease, but experience similar symptoms. In their case, eliminating gluten can increase their digestive comfort and help avoid bloating and gas. If you do have a positive celiac test, it’s essential to strictly eliminate all sources of gluten to avoid further damage to the intestines, and dairy too for a while as the villi in your small intestine are healing. So I’d recommend getting tested for celiac and if it’s negative, going gluten free for a few weeks then reintroducing gluten to see if your symptoms go away and then return when your reintroduce gluten.  

But ideally, if you suspect a food sensitivity or have never checked for this, I recommend a basic elimination diet where you eliminate the most common problematic foods at the same time, as often your gut needs time to heal if you have one or more food triggers. The foods I’d eliminate are gluten, dairy, soy, corn, highly processed foods with tons of ingredients, processed seed oils, added sugar in any form, artificial sweeteners except Stevia, monk fruit extract*, allulose* or erythritol*; caffeine and alcohol, or as many of those as you can handle for 3-4 weeks and then one by one reintroduce foods a couple times a day for 2 days then wait two more days to check for a reaction before reintroducing another food.

#4: You Eat High Fiber Foods Inconsistently

Even if you don’t have any food intolerances, high fiber foods such as legumes (such as beans, lentils and peanuts) or cruciferous vegetables like cabbage, cauliflower and broccoli can cause uncomfortable bloating and gas. By slowly introducing nutritious and high fiber foods like beans and lentils and then including them regularly in your diet, rather than eating a ton of beans in a very occasional bowl of chili, you’re less likely to experience bloating after eating them.

#5: Poor Enzyme Function

Poor enzyme function can cause bloating with certain foods, even healthy ones like raw fruits and vegetables. If you have issues with these foods or see pieces of undigested food in your stool, a general digestive enzyme* may be helpful to take with meals.

#6: You Have Low Bile Flow

If fatty foods cause you bloating and discomfort and you have light colored stool, low bile flow due to poor gallbladder function may be at work. Bile is produced by the liver and stored in the gallbladder. The gallbladder is then responsible for secreting a bolus of bile to the stomach to aid in digestion. When it is not functioning properly and you eat high-fat foods, you may experience other symptoms such as nausea and gas. Other conditions can cause gallbladder dysfunction, including hypothyroidism and fibromyalgia. Other symptoms of gallbladder dysfunction include headaches, problems losing weight, pain in the feet or right shoulder, hormonal imbalances, yellowing skin, and constipation or diarrhea. Natural healing strategies can help improve gallbladder function, including starting your meals with a bitter food to stimulate bile flow like dandelion leaves, which are free in most of our yards, just be sure they’re pesticide free, other bitter greens, lemon zest or beets. Or you could take Swedish bitters before meals or consider a bitter aperitif before dinner like Campari, Aperol, amari, pastis or ouzo. If you’ve had your gallbladder removed or have been diagnosed with low bile flow, you may want to take Ox Bile supplement* with fatty meals. I’ve linked to good brands of these supplements or you can also look for them in my Fullscript dispensary to compare prices.

#7: You May Be in a Fight or Flight State of Stress While Eating

Bloating may start during a period of high stress, as eating in a sympathetic, or fight or flight state, rather than a parasympathetic, or rest and digest state, will leave food stagnating in your stomach. If you find yourself visibly stressed at meal time, stopping to take 4 or 5, 5-5-7 breaths, which is 5 seconds in, 5 seconds hold and 7 seconds exhale, can help trick your body into a parasympathetic state so that you can digest better. Then using meditation, exercise, yoga, therapy or coaching to manage your stress and working to eliminate the underlying cause is a longer-term solution.

#8: Too Many Sugar-Free Foods

Some sugar alcohols, common in many sugar-free or “diet-friendly” sweets such as light ice cream and sugar-free candy and gum, are also a major cause of bloating for many people. The bacteria living in the large intestine ferment sugar alcohols like xylitol, sorbitol and mannitol quickly and produce large amounts of excess gas. Although sugar-free gum and ice cream may sound appealing, you may be causing bloating and other digestion issues by choosing these foods. Erythritol*, Stevia, monk fruit extract*, and allulose* are safer choices for alternative sweeteners that shouldn’t cause you GI distress, except perhaps nausea for some people with erythritol.

#9: SIBO

If all these solutions have been tried and failed, you may have a gut infection from an overgrowth of dysbiotic bacteria, candida or other fungi. Officially, this may mean a diagnosis of SIBO or small intestine bacterial overgrowth, which is the root cause of most cases of IBS. Some GI doctors will test for SIBO with a hydrogen/methane and the newest addition, hydrogen sulfide breath test, which are taken after eating a low fiber diet for 24 hours, or after an overnight fast. I don’t use them with my clients as they’re not terribly reliable and don’t tell you anything about fungal overgrowths, which most GI docs don’t believe in, parasites, or other potential causes of bloating. Rather, I prefer the GI Map* or the Organic Acids Test, depending on my clients’ other symptoms, history of antibiotic and other medication use and past testing.

If your GI doc diagnoses you with SIBO, you may be prescribed rifaximin or Xifaxin, which is an antibiotic that only impacts your digestive tract, but I think it’s wiser to use herbal antimicrobials because they also reduce fungal overgrowths, and just taking antibiotics will often leave you overgrown in fungi like candida and cause more long-term issues.

The primary short-term diet change recommended for SIBO that is solely bacterial in nature is a low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) diet. This diet involves limiting high-FODMAP foods for a period of time and monitoring for a decrease in symptoms. Some examples of high-FODMAP foods include wheat, milk, onions, garlic, cauliflower, cabbage, artichokes, beans, apples, pears and watermelon but there’s a whole long list you can find by Googling it. Removing these foods will deplete the bacteria in your gut, so it’s important not to do this long term, but rather once your symptoms are gone for a couple weeks, to start reintroducing foods by groups and checking for a reaction to a given group. On a longer-term basis, you may need to limit quantities of these foods if you find yourself with recurrent SIBO. You’ll also need to determine the root cause of your SIBO, which if it isn’t from dysfunction of one of your digestive organs as I’ve already discussed, is likely related to issues with peristalsis, or intestinal motility in the small intestine, leading to stagnation of food, which causes bacteria to overgrow. That can be from vagus nerve dysfunction, which can stem from a stressful event or a brain injury or could be from low serotonin, which can arise from a poor diet, lack of exercise, a lack of exposure to natural light, chronic stress or insufficient protein intake or digestion. 

Taking probiotics may also be helpful with bloating and SIBO, as they can help restore a healthy gut microbiome. However, it can take time for the microbiome to rebalance, so be patient when starting a probiotic and don’t expect immediate results. One with evidence to help with SIBO is Saccaromyces Boulardii*, which is a beneficial yeast. Another home remedy to try for consistent bloating is peppermint oil*, which has been shown to help IBS patients with bloating. You can take one gel cap 15 minutes before meals. It used to be helpful to me but does sometimes lead to a pepperminty stomach sensation and burps.

#10: Candida Overgrowth

Digestive system candida or fungal overgrowth, also known as SIFO, or small intestinal fungal overgrowth, is one of the most common conditions I find in my clients and is best diagnosed using the Organic Acids Test. Candida is a yeast that is present in all healthy people but can grow unchecked when the bacterial balance of the microbiome is off, usually due to antibiotic usage or a high sugar diet. Other symptoms of a candida overgrowth include sugar cravings, brain fog, rashes, a white tongue and vaginal yeast infections in women. Treatment for SIFO is trickier and can take longer than SIBO treatment, as it can take some time to restore the microbiome’s balance and bring the candida levels down, and usually requires removing added sugar and simple carbohydrates for a while, as well as other foods that stimulate candida growth.

#11: You May Have Low Stomach Acid

Low stomach acid levels can also be a cause of bloating. When you have insufficient stomach acid, it makes it hard to digest proteins, so proteins may not be completely broken down into amino acids. Stomach acid is also protective against pathogenic bacteria, so you are more susceptible to overgrowths of bacteria like E Coli, that thrive in a neutral pH environment, and are often at the root of SIBO.

We tend to have decreased stomach acid as we age and when we’re under stress. Taking a small dose of Betaine HCl*, which is just hydrochloric acid or stomach acid, with meals can help not just increase your acid and help with protein digestion and sterilizing your food, but will also help stimulate bile and enzyme flow, so this is a good thing to try if you’re middle aged or older, under stress, or are experiencing these symptoms. Another sign of potentially low stomach acid is GERD or acid reflux, as the pH of the stomach regulates the opening of the lower esophageal sphincter and an insufficiently acidic stomach environment can lead to a sphincter left open for acid to go up, which can cause heartburn, a warmth in your chest or a subtle cough.

#12: H. Pylori

A common bacterial infection that also causes low stomach acid is H. pylori or Helicobacter pylori. It’s a bacteria present in many people’s gut microbiomes that can cause gastric inflammation, GERD, insomnia, nausea, and for some virulent strains, ulcers and stomach cancer. I’ve seen it in many of my clients, even at levels that are not considered abnormal, and when I educate them on how to eliminate it in a safe way using mastic gum (and not triple antibiotic therapy as a GI doctor might prescribe) they always feel better.

Overall, bloating is an unpleasant and avoidable experience that I personally put up with for way too long. It’s not normal to have a food baby after eating unless you just ate an entire 16-inch pizza and it’s definitely not normal to wake up bloated. I can’t tell you how much better I feel and look now that I don’t regularly bloat after eating. So if you find that you have consistent, painful bloating and simple behavior- and diet-based interventions haven’t helped or feel too overwhelming to sort through, please set up a free, 30-minute breakthrough session or a one-hour consultation and we can talk about the best next steps for you to solve your bloating problem!

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