Fermented Foods: The Definitive Guide

You probably know about or have heard about fermented foods. If you haven’t, you somehow missed basically all of human history. There’s evidence that humans have been consuming fermented dairy products, like yogurt, since 10,000 BCE and the evidence for fermented beverages, like mead and wine, wasn’t far behind. (Tamime, 2002)

Our ancestors were utilizing fermentation to preserve their food before refrigeration, but we now know that fermentation doesn’t just extend our access to food for longer time periods, it also has incredible health benefits. Unsurprisingly, those health benefits are the reason that adding fermented foods to our diet is an important part of the Autoimmune Protocol. In this guide we’ll be exploring everything “fermented foods” and making sure you can make informed choices about adding them to your diet.

What is fermentation?

Fermentation is a way for microorganisms to create energy. This natural process occurs when bacteria, mold, or yeast produce enzymes to break down carbohydrates in an oxygen poor environment and turn them into alcohols or acids. (Masterclass staff, 2021) The alcohols or acids preserve the food. The fermentation process also encourages the growth of beneficial probiotics, which are often cited as the number one reason to consume fermented foods. (Coyle, 2020)

What are the benefits of fermented foods?

There’s a pretty long list of health benefits from consuming fermented foods. Here’s just a few of the big ones:

  • Aiding digestion. Fermentation is basically a process of “pre-digesting” food we eat. The microorganisms can break down parts of the foods that are harder for humans to digest, like some forms of sugar and even components of proteins and fats. (Hodges, 2020) A really clear example of this is bacteria that break down casein and whey in dairy, making products like yogurt better tolerated by some who are sensitive to dairy.
  • Increasing nutrients and bioavailability. Fermented foods often have more nutrients after the fermentation process, because a process called biosynthesis allows bacteria to create new nutrients. (Ballantyne, 2020) K2 is an example of a vitamin that can be created in this biosynthesis process during fermentation.
    • Additionally, fermentation helps destroy anti-nutrients making the existing nutrients in the food easier for our bodies to actually take in. Phytic acid, for instance, found in many plant-based foods, binds with some minerals in our digestive tracts, making them difficult to absorb. We don’t produce enzymes to break down phytic acid, but fermentation does that for us, making it easier to absorb minerals like calcium, magnesium, iron, zinc, chromium, and manganese. (Brennan, 2020) This is really valuable for us humans, since we don’t produce minerals ourselves and must take them in via our diets.
  • Regulating the immune system. The probiotics found in fermented foods can help regulate our immune systems and lower inflammation. For example, a lactic acid (not to be confused with lactose) bacteria found in kefir suppresses IgE production. (Hong et al., 2010) IgE is an antibody involved in allergic responses.
    • In a clinical trial conducted at Stanford School of Medicine, healthy adults were randomly assigned to a 10-week diet that included fermented foods like yogurt, kimchi and other fermented vegetables, and kombucha. The diet led to four types of immune cells being less active and levels of 19 inflammatory proteins decreasing in blood samples. Interleukin 6, which is linked to rheumatoid arthritis, among other chronic conditions, was one of the inflammatory proteins that decreased. (Weaver, 2021)
  • Improving gut dysbiosis. Gut dysbiosis generally means “altered state of the gut microbiome, usually associated with disease.” (Mailing, 2021) That altered state means less of the microorganisms with positive effects and more of the microorganisms with negative effects. While there isn’t a lot of evidence that fermented foods permanently colonize our digestive tracts, they are incredibly diverse sources of probiotics that are naturally protected from stomach acid. This means they can reach our intestines and offer a positive impact while passing through our body. (Kresser, 2020) Regularly consuming these foods means having regular exposure to microbial diversity and its benefits. It’s not just adding more diversity that can expose us to positive benefits though. There are also certain strains of probiotics found in fermented foods that can directly decrease populations of less favorable bacteria hanging around in our guts, which helps improve dysbiosis. (Ballantyne, 2020)

Are all fermented foods rich in probiotics?

Nope. As mentioned above, fermentation can occur with bacteria, mold, or yeast, but generally it is the foods that are bacterially fermented that are rich in probiotics. Yeast, from the Saccharomyces family, has probiotic benefits too. Foods that are mold fermented (think cheese), can still be healthy (for those not otherwise sensitive to dairy), but don’t have as much of the same probiotic benefits. (Ballantyne, 2020)

Beyond specifically bacterially fermented foods, there’s also the distinction between foods that have been fermented, but not heated afterwards, and what that means for probiotic benefit. Dr. Kara Fitzgerald’s website offers a clear explanation, “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.” (Hodges, 2020) This all means that fermented foods are richest in probiotics when they are raw and unpasteurized.

Choosing Fermented Foods

Here’s what to look for if you are purchasing fermented foods, rather than making your own:

  • Look for raw and unpasteurized. Pasteurizing is a process of using heat to help preserve a food, but that heat kills the probiotics that are so beneficial in fermented food in the first place. Typically, companies making unpasteurized fermented foods display the fact on their packaging. Look for words like “raw” or “unpasteurized” or sometimes “living.” These foods are also often in the refrigerated section of the grocery store and have very simple ingredient lists that generally include the food, water, and salt.
  • Avoid “extra” ingredients. Look out for fermented foods with things like added sugar, dye, etc. A kombucha ingredient list might say, “water, sugar, tea, culture.” That’s fine, as the sugar is “eaten up” by the yeast and bacteria in the fermentation process. However, if you see sugar or another sweetener at the end of the list, it means it was added. For those of us in the elimination phase of AIP, we might also want to be on the look out for spices and/or nightshades that have been added for flavor. For example, kimchi has added spices and nightshades, some sauerkrauts might have fennel or caraway seed, or pickles might have mustard seed, all of which don’t work during the elimination phase.

Can I make my own fermented foods?

Yes! Of course you can, and at Autoimmune Wellness we’d totally encourage it! Don’t be nervous, it’s surprisingly easy. Here’s a kombucha recipe from Mickey.

We’re not the only ones fermenting in the AIP community though. Check out this recipe for sauerkraut from our friend Nicole at Heal Me Delicious.

How do I get started including fermented food in my diet?

Word to the wise here: Start slow! Any change in our diets will temporarily shake things up digestively and that is especially true with fermented foods, since they are so packed with probiotics. All those new microorganisms are bound to have an impact. Here’s some ways to introduce these foods slowly:

  • Treat ferments like a condiment. Instead of eating a big serving of sauerkraut or drinking a whole bottle of kombucha, for instance, start by adding a tablespoon or two of sauerkraut to your meal or drinking just a ½ cup of kombucha.
  • Work up in quantity and number of servings. Once you are doing well with a condiment size serving, try adding a little more fermented foods and having them at more meals.
  • Try different types of ferments. There is a huge variety of fermented foods, like carrots with ginger or beet kvass. Try experimenting with a new item every week.
  • Be cautious. There are some groups of people who don’t do too well with fermented foods, including those with SIBO, histamine intolerance, yeast sensitivity, and sometimes those with skin conditions like eczema. If that is you, be cautious and check out this Chris Kresser podcast for tips on how to improve your tolerance for these beneficial foods.

What about probiotic supplements?

Probiotic supplements are not necessarily any better than eating fermented foods. Just like fermented foods that don’t appear to actually “re-seed” our GI tracts, probiotics can still have benefits as they pass through. (Mailing, 2021) They may have the benefit of being more “predictable” in terms of the kinds of microorganisms they contain, but less benefit in terms of additional nutrients found in fermented foods. If you’d like to add a probiotic supplement make sure you talk to a provider that can guide you, that you are purchasing supplements that are research validated for safety and efficacy, and that you add them slowly, just like with fermented foods.

There’s your definitive guide to fermented foods! Now tell us, ‘cause we like to do informal research with our community here at Autoimmune Wellness:

  • Have you added fermented foods to your diet?
  • If so, did you notice any positive health benefits?
  • And the thing we really want to know . . . what’s your favorite ferment to eat and/or make?


  1. Ballantyne, D. S. (2020, April 26). The health benefits of fermented foods. The Paleo Mom. Retrieved January 27, 2022, from https://www.thepaleomom.com/the-health-benefits-of-fermented-foods/
  2. Brennan, D. (2020, November 5). 4 foods high in phytic acid and why you should avoid it. WebMD. Retrieved January 27, 2022, from https://www.webmd.com/diet/foods-high-in-phytic-acid
  3. Coyle, D. (2020, August 20). Food fermentation: Benefits, safety, Food List, and more. Healthline. Retrieved January 27, 2022, from https://www.healthline.com/nutrition/fermentation#what-it-is
  4. Hodges, R. (2020, May 6). When do fermented foods outperform probiotic supplements? Kara Fitzgerald ND Naturopathic Doctor. Retrieved January 27, 2022, from https://www.drkarafitzgerald.com/2018/09/26/when-do-cultured-foods-outperform-probiotic-supplements/
  5. Hong, W.-S., Chen, Y.-P., & Chen, M.-J. (2010, September 20). The antiallergic effect of kefir lactobacilli. Institute of Food Technologists. Retrieved January 27, 2022, from https://ift.onlinelibrary.wiley.com/doi/abs/10.1111/j.1750-3841.2010.01787.x
  6. Kresser, M.S., C. (2020, June 23). The 13 benefits of fermented foods and how they improve your health. Chris Kresser. Retrieved January 27, 2022, from https://chriskresser.com/the-13-benefits-of-fermented-foods-and-how-they-improve-your-health/
  7. Mailing, L. (2021, July 23). The ultimate quick-start guide to the gut microbiome. Lucy Mailing, PhD. Retrieved January 27, 2022, from https://www.lucymailing.com/the-ultimate-quick-start-guide-to-the-gut-microbiome/
  8. Tamime, A. Y. (2002). Fermented milks: a historical food with modern applications — a review. Nature. Retrieved January 27, 2022, from https://www.nature.com/articles/1601657.pdf
  9. Weaver, J. (2021, July 12). Fermented-food diet increases microbiome diversity, decreases inflammatory proteins, study finds. News Center. Retrieved January 27, 2022, from https://med.stanford.edu/news/all-news/2021/07/fermented-food-diet-increases-microbiome-diversity-lowers-inflammation
  10. What is fermentation? learn about the 3 different types of fermentation and 6 tips for homemade fermentation – 2022. MasterClass. (2021, September 29). Retrieved January 27, 2022, from https://www.masterclass.com/articles/what-is-fermentation-learn-about-the-3-different-types-of-fermentation-and-6-tips-for-homemade-fermentation

About Angie Alt

Angie Alt is a co-founder here at Autoimmune Wellness. She helps others take charge of their health the same way she took charge of her own after suffering with celiac disease, endometriosis, and lichen sclerosis; one nutritious step at a time. Her special focus is on mixing “data with soul” by looking at the honest heart of the autoimmune journey (which sometimes includes curse words). She is a Certified Health Coach through the Institute for Integrative Nutrition, Nutritional Therapy Consultant through The Nutritional Therapy Association and author of The Alternative Autoimmune Cookbook: Eating for All Phases of the Paleo Autoimmune Protocol and The Autoimmune Wellness Handbook. You can also find her on Instagram.

1 comment

  • Shirley Angela says

    I went slow and am now able to consume fermented foods but my question is about making them. Things that require exposure to air like kombucha or kefir eventually sour in my living environment. I’ve finally come to the conclusion that this is because I have a particularly severe form of lichen planus and this either means that the atmosphere in my house is constantly full of microscopic skin particles or is full of some type of microbe that is involved in severe lichen planus and this overwhelms the microbes in the ferment. I’ve tried a couple of times to setup ongoing brewing of both kombucha and kefir with the same outcome each time. It’s worse in winter when windows need to be shut more. Has anyone else experienced this?

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