When Do Fermented Foods Outperform Probiotic Supplements? - Dr. Kara Fitzgerald (2024)

Taking a probiotic supplement certainly is convenient for both practitioner and patient; and yes, we use probiotic supplements very regularly in our therapeutic plans for patients. But fermented foods also have their own compelling advantages. Don’t forget about these long-used superfoods!

The term probiotic applies to a microorganism that confers a clinically-evidenced health benefit. Probiotics exist both in food and supplement form; in food form, the culturing of beneficial microorganisms requires fermentation that is not subsequently followed by heating or canning that would inactivate the live organisms. Fermented foods that aren’t ‘live’ still have many of the benefits we’re about to cover, but they don’t add probiotics.

Here are five benefits you can get from fermented foods that you can’t get from a probiotic supplement:

1. A Head Start with Digestion

Bacteria and yeast increase the digestibility of food both because they directly consume food components and release their broken down metabolites, and because digestive enzymes can also be released into the food from microbes after they die, further aiding the process of breaking down food, even before it enters your mouth.

Several difficult-to-digest compounds in food, such as lactose and oligosaccharides, can be broken down by fermentation. Lactose-intolerant individuals can therefore often tolerate cultured dairy products (which contain lactose), and IBS patients can sometimes better-tolerate fermented grains (which contain oligosaccharides). Protein, the building block for practically all functions of the human body, can be partially predigested by fermentation, aiding in its absorption. Fats can be freed into non-esterified fatty acids, which improves digestibility.

This is an especially important consideration when digestive function is developing, as in infancy, or compromised due to aging, stress, and illness. A deficiency in digestive function can create a vicious cycle where nutrient absorption is reduced, nutrient status becomes compromised, and the body is even less able to produce digestive enzymes and repair damaged tissue.

Incidentally, a recently-published double-blind, randomized, placebo-controlled trial (considered ‘gold standard’ research by many) of over 400 infants found the most-reduced incidence of colic and improved stool consistency in babies fed a fermented formula with prebiotics. Other emerging data suggest that fermented formula given to pre-term infants is associated with reduced levels of fecal calprotectin (a marker for gastrointestinal inflammation).

In addition, breaking down protein components in food can be important for an individual whose immune system is overactive and prone to developing food sensitivities or even allergies. Those immune reactions occur primarily towards proteins rather than other macronutrients when they aren’t properly digested and in the context of increased gut permeability and other immune stressors.

One example of reduced allergenicity is in fermented milk proteins. Certain lactic acid bacteria can degrade casein and whey, which are the most allergenic proteins in milk, rendering the fermented milk product less allergenic*. The fact that the milk product is also consumed with immunomodulating microbes may also help reduce reactivity.

*note that fermented dairy products are NOT suitable for someone with a true dairy allergy.

2. More Nutritious Food with Fewer Anti-Nutrients

Fermented foods are more nutrient dense than their unfermented counterparts. Not only that, but those nutrients can become more bioavailable (easier to absorb) with fermentation because anti-nutrient levels are reduced.

Take kefir, for example, which is a type of cultured milk with low levels of lactose (since it is broken down by fermentation), high levels of beneficial bacteria and yeasts, and… added nutrients. During fermentation, the broad spectrum of microbes that are found in kefir starters produce additional vitamins including B1, B2, B6, B12, folate and biotin. These B vitamins are essential for myriad metabolic functions, including cellular energy pathways and methylation. Find out how to support healthy methylation and epigenetics here including by supporting a healthy microbiome.

Improvements in nutrition content can be found in other research on cultured foods: Natto, a traditional Japanese fermented preparation of soy beans contains three times the quantity of vitamins B1 and B2 than the original soy bean, and five times the quantity of vitamin B12. Fermenting fruit and herbal smoothies with Lactobacillus plantarum and other species enhances vitamin C and beneficial phytonutrient levels. Cultured olives contain can contain double the levels of polyphenols compared with non-fermented samples, including increased hydroxytyrosol, tyrosol, luteolin and quercetin.

Fermentation reduces anti-nutrients such as phytic acid by up to 40%. Phytic acid is compound found in many grains, legumes, and seeds. Since it can bind essential minerals, such as iron, it reduces their availability for absorption. Breaking down phytic acid by fermentation therefore increases the bioavailability of minerals and helps maintain healthier levels in the body.

3. Fewer Food Pathogens and Toxins

The addition of protective cultures during fermentation naturally limits the growth of harmful microbes in foods. This effect is related to several factors, including competition for available nutrients, as well as organic acids and bacteriocins produced during the fermentation process. This is why fermentation has traditionally been used to preserve foods from spoilage long before refrigeration.

As an added bonus, fermentation reduces the absorption of potentially-harmful mycotoxins (mold toxins such as aflatoxin B1 and ochratoxin A) that are sometimes found in grain products, likely by partially degrading them to less harmful byproducts.

4. Diversity of Species in Live Fermented Foods

Probiotic foods contain a wide diversity of microorganisms—many more species than are found commercial supplements and including specific therapeutic strains that are sought after in probiotic supplements. When grown on a petri dish, bacteria from probiotic pills colonize in tidy white circles, but dishes plated with fermented foods bloom in “colorful, disorderly splotches.” This according to a Boston University lecturer who put this question to the test in her own lab.

Commercially-available fermented foods have also been evaluated by Researchers at the Maryland University of Integrative Health. This is a select list of foods that they researched. A longer list can be found below as an Appendix to this article, or edited as a PDF available to download here.

In particular, note some of the crossover of species between fermented foods and therapeutic probiotic supplements. A common serving size for yogurt is 225 g. So if there are100 million CFUs per gram, this equates to 22.5 billion CFUs per average serving.

Selected Commercially Available Cultured Foods in the United States (Source):

Do Microbes in Fermented Food Survive Digestion?

It’s an important question! There are studies and academic texts that demonstrate (or argue) that many probiotic microbes in foods can survive digestion in the harsh gastric environment and when they come into contact with digestive enzymes and bile salts secreted by the liver and gallbladder. Lactobacilli and bifidobacterial species appear to be especially resistant to damage, with adaptive strategies including upregulation of ATPase transport proteins that remove excess hydrogen ions from the bacterial cell, amino acid decarboxylation (the carboxylic terminals of these protein components are acidic), and reduced fluidity and proton permeability of fatty acid membranes.

The availability of carbohydrate substrate may enhance this adaptability, suggesting that food ingestion alongside beneficial microbe species can enhance their survival. Food also acts as a buffering agent against the acidity of the stomach.

5. Signaling Molecules That Regulate Human Metabolism

As cultured bacteria or yeast consume carbohydrate or protein for their own energy production, they also create byproducts. Of those, the metabolically-active byproducts which we call bioactives, have marked effects on human health that are recognized in scientific literature. Because of the length of time of fermentation, these bioactives are produced in much greater quantities than can be achieved with simple probiotic supplementation alongside meals.

Conjugated linoleic acid, or CLA, is a compound produced from linoleic essential fatty acids. Certain strains of bacteria (those that possess linoleate isomerase—many lactic acid species) produce CLA from linoleic acid, including those used for natural fermentation of pickles. These naturally fermented pickles (not those brined in vinegar) have greater amounts of this supernutrient than their fresh counterparts. Consumption of CLA has been associated with weight loss, heart health, and blood sugar regulation.

GABA (gamma-aminobutyric acid) acts as a calming neurotransmitter in the body and can be produced endogenously from glutamic acid via the enzyme glutamate decarboxylase. However, several Lactobacillus strains also produce GABA and it is therefore present in many fermented foods.

Other examples of microbial bioactives include genistein and daidzein produced by fermenting soy products with bacteria and yeast. Fermenting soy milk increases the concentration of these bioactives up to 50% of total isoflavone concentration (from 8% in nonfermented soy milk). Daidzein can be further metabolized, by bacterial action only, to a potent bioactive called s-equol, best known for its estrogen receptor modulating and antioxidant activity. S-equol has been shown to reduce hot flashes and muscle stiffness associated with menopause. Fermented soy milk has been shown to contain up to 10% s-equol, when cultured with Bifidobacteria strains B. pseudolongum, B. longum and B. animalis.

More bioactives that have been found in fermented foods include compounds that may be able to reduce blood pressure (natural ACE inhibitors), reduce cholesterol, break down blood clots, modulate the immune response, reduce inflammatory cascades, and reduce cholesterol.

How to Choose Fermented Foods

The art of fermentation has been practiced and passed down for thousands of years. Globally, the options for fermented foods are practically endless. Grains, meats, dairy, vegetables, juices, teas, and legumes all have fermentable properties. Where you live may dictate what fermented foods are available to you. In some parts of the world, fermented foods make up a considerable portion of the diet, in others, they are almost rare. In the United States, unless you are making your own fermented foods, it can take a little effort to find quality fermented foods. Here are a few tips for finding clean fermented foods:

• Just because a food is fermented does not mean that it is automatically healthy. When choosing fermented foods, it is important to remember the foundations of healthy eating. Choose clean, sustainable, organic and whole-foods whenever possible. Watch out for added ingredients such as sugar, dyes, and other additives.
• Choose raw fermented foods whenever possible. Pasteurization will kill beneficial microbes. Although, even if a food is pasteurized, it may still have many benefits of digestibility, nutrient content, and bioactive content associated with fermentation.
• Look for fermented vegetables that are described as lacto fermented in the refrigerated section of your grocery store. These are vegetables that rely on traditional bacterial fermentation methods instead of doing pseudo-fermentation with vinegar.
• Choose organic, unsweetened fermented dairy and non-dairy yogurts and kefirs, or, for increased digestibility and fermented benefit, explore fermenting your own.
• Get inspired by recipes including our own Turmeric-Pickled Daikon, as one tasty example that we can vouch for.

Historically, dozens of nutrient-rich foods have been traditionally fermented, including vegetables, dairy products, meats, grains, teas, and legumes. This immense food group offers an astounding variety of flavors and nutritional benefits.

Eating Fermented Foods for Beginners

Fermented foods have a unique flavor, texture, and aroma. If you don’t come from a background where fermented foods are a staple, you may feel overwhelmed by these new flavors and textures. Here are some good introductory fermented food ideas that may help you explore these amazing foods:

• Lacto Fermented Pickles – Very similar to vinegar-brined pickles with a little extra zing.
• Raw milk cheese – Fermented raw cheese contains the anti-inflammatory bioactive alkaline phosphatase speculated by some to be foundational in the low incidence of cardiovascular disease in France.
• Raw Apple Cider Vinegar – A delicious addition to dressings and marinades. Also, can be made into as a digestive tonic. Mix 1 tablespoon of raw apple cider vinegar with 8 oz of water and drink before a meal.
• Miso – A fermented legume and grain paste that can be easily added to soups. Miso has a very mild flavor and very friendly to the new fermented food eater. You can seek out chickpea- or adzuki bean-based miso preparations if you’re avoiding soy.
• Lacto-fermented Sauerkraut – tangy with a little bit of crisp. Excellent with a sausage and a little bit of mustard.
• Curtido – El Salvadorian fermented cabbage mixture with a little bit of oregano and jalapeno. Traditionally eaten with pupusas but also tastes great on spiced meats such as in tacos or with chorizo.
• Fermented Sauces – There are many fermented sauces and condiments out there including chlli sauces, nama shoyu soy sauce, mustards, and horseradish. Explore your natural foods store to see what is available.
• Fermented Ginger – my favorite by far! Top a stir fry or eat with nori rolls.
• Umeboshi Plum – Very tart paste that is wonderful in a nori and rice roll.

Maintaining Balance: When Fermented Foods May Not Be So Beneficial

Having a healthy balance of bacteria, yeast, and even some parasites is essential for optimal health and wellness. When the balance is thrown off, even friendly bacteria can become a problem. Most bacteria in fermented foods are lactic acid producing bacteria. Lactic acid producing bacteria can be a problem if you have an overgrowth of these bacteria in your digestive system. People who have SIBO or who follow a low FODMAP diet may also find that fermented foods can stimulate the bacterial overgrowth in their small intestine, causing discomfort. Fermented foods may need to be reduced or avoided in these situations until some digestive healing has occurred. Individuals who have an immune response to yeast may benefit from removing fermented foods until they can balance their immune response and work on repairing any leaky gut as well or yeast overgrowth. Fermented foods tend to be high in tyramines, which may cause headaches in sensitive individuals. Fermented foods also contain natural histamines, which may accumulate in the body and cause reactions in individuals who are highly intolerant to histamine.

Contributions to this article: Julia Lammers MS CNS contributed to this article. Julia holds a master’s degree in Human Nutrition from the University of Bridgeport, CT, and is certified through the Board for Certification of Nutrition Specialists. She is a nutrition enthusiast and lover of good food, especially when shared with friends. She believes nutrition is foundational for building our best selves and that good nutrition can be exciting, flavorful, and satisfying. Julia was a resident in our Functional Nutrition Residency Program from September 2017 to August 2018, which provides supervised experience hours in a multidisciplinary setting for those seeking CNS certification. Julia’s work with us continues even after her residency has concluded.

Appendix: Common Fermented Foods Commercially Available in the United States (Adapted From Source)