About This Article: This article introduces a narrative review that synthesizes existing research. It does not prove that eating fermented foods prevents or treats disease or produces specific health benefits. The studies covered in the review include different levels of evidence—from cell and animal studies to observational and clinical research.

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“Fermented foods are good for you.”

Most people probably believe this. But if you ask someone why they’re good for you, you might be surprised how many struggle to give a clear answer.

A comprehensive review—a scientific paper synthesizing existing research—has now shed light on that “why” from a scientific perspective. Published in 2026 in the international academic journal Folia Microbiologica, it’s a thorough review of medicinal and food fermentation products.

The key concept here is “bioactive compounds.” Let me use this paper as a starting point to carefully trace through how fermented foods are thought to support health.

Fermented Foods Are Made of Microbes and Their Components

Fermented foods are created through the work of microorganisms and the compounds they produce. That said, some commercially available fermented foods don’t contain live bacteria because they’ve been heat-treated during processing. The value of fermented foods comes not just from the presence or absence of live bacteria, but also from the compounds created during fermentation.

The review itself describes fermented foods as “dynamic systems containing microbial communities and bioactive metabolites.” In other words, the value of a fermented food lives not only in the bacteria themselves, but also in the compounds those bacteria create.

31 Bioactive Compounds Related to Fermentation

What drew this review’s attention were the “bioactive compounds”—substances created during the fermentation process. Bioactive compounds are components that have some effect on how our bodies function.

The paper organizes the major bioactive compounds and compound groups involved in fermentation into 31 categories. Let me highlight some representative examples.

First, there are short-chain fatty acids. These are produced when gut bacteria ferment dietary fiber, and they serve as an energy source for the intestinal lining. Second are bioactive peptides—small molecular fragments created when proteins are broken down. Third are polysaccharides. And fourth are compounds formed through changes to polyphenols.

Many of these were either absent or present in only tiny amounts in the original ingredients. Fermentation—a process that unfolds over time—creates entirely new compounds.

Possible Connections to Intestinal Barrier Function, Immunity, and Inflammation

So how do these bioactive compounds work inside our bodies?

The review organizes the connections around several key directions. First, there’s the possibility of maintaining the intestinal barrier—the strength of the gut lining is considered foundational to health. Second, there’s the possibility of modulating immunity, exploring the relationship with a balanced immune state that’s neither overactive nor deficient.

Beyond that, some studies report improvements in markers related to metabolism and shifts that suppress inflammation in the body. Since chronic inflammation is linked to aging and lifestyle diseases, this is a topic many people care about.

In other words, the connection between fermented foods and health can’t be explained by a single compound. Multiple bioactive compounds, with the gut as a starting point, may influence many different parts of the body—and that’s the bigger picture that emerges.

Research on Fermented Foods and Disease Risk

The review also mentions specific foods.

It presents epidemiological and clinical studies examining the consumption of yogurt, kimchi, and kefir (a type of fermented milk) alongside their relationships with colorectal cancer, type 2 diabetes, and cardiovascular disease risk or related markers. Some studies report favorable associations or changes, but the types of food, study subjects, amounts consumed, and research methods are not uniform. These findings don’t prove that such foods prevent disease or that everyone experiences the same benefits.

Fermented foods are not medicine—they’re simply part of everyday meals. This is an important point to consider carefully.

Challenges That Remain

This review doesn’t just speak of promise. It thoughtfully identifies remaining challenges.

One is the difficulty of standardization. Fermented foods vary greatly in their components depending on the microbes involved and the production method. The same “kimchi” doesn’t necessarily contain the same ingredients. That’s why we need better systems to carefully control and measure which compounds are present and in what amounts.

Another is the shortage of long-term clinical trials. We don’t yet have enough research following large numbers of people over extended periods to confirm health effects. To truly understand the power of fermented foods, more rigorous investigation is needed.

A Hint for Your Table

Looking at all this, the picture behind “fermented foods are connected to health” comes into sharper focus.

The connection involves not just the bacteria themselves, but also the diverse bioactive compounds they create over long periods of time. Yet that relationship is still being investigated and verified.

When you incorporate fermented foods, it helps to avoid expecting too much health benefit from any single food and instead focus on overall meal balance. Be mindful of salt in miso and pickles, sugar in yogurt, and potential allergies to dairy and soy products. The foundation is to enjoy fermented foods that work for you in amounts that feel manageable.

In yogurt, miso, natto, and pickles—countless bacteria are at work in each, creating invisible compounds. Let that thought accompany you as you savor these familiar foods.

From Toshi

“Fermented foods are good for you”—we’ve all heard this many times throughout our lives. A bowl of miso soup, a serving of natto, pickles as a side dish. Sometimes yogurt, cheese, or kimchi grace the table. These are such familiar foods, yet when asked “why are fermented foods considered good for health?” I realize that until recently, my own understanding didn’t go much deeper than “because they contain lactic acid bacteria” or “they seem to be good for your gut.”

What I found most interesting about reading this review was the realization that fermented foods’ value isn’t explained solely by live bacteria.

Microorganisms aren’t just passively multiplying in food. They use sugars and proteins from the ingredients to create various compounds. When we eat fermented foods, we’re consuming not just the bacteria themselves, but also the results of the work those bacteria have done over time.

“Live bacteria reaching your gut”—this phrase is simple and easy to understand, and we see it often in product advertisements. But not all fermented foods contain live bacteria. In miso, soy sauce, and foods that are heated during manufacturing or preparation, bacteria may not survive the process. Yet all the compounds created during fermentation don’t simply disappear.

The value of a fermented food can’t be determined by whether the bacteria are alive or dead alone. We need to think about multiple factors together—the compounds created during fermentation, the way ingredients become easier to digest as they break down, and more. This perspective has broadened my view of fermented foods a bit.

The review organizes bioactive compounds and compound groups related to fermentation into 31 categories. Short-chain fatty acids, bioactive peptides, polysaccharides, and transformed polyphenols—just hearing the names can feel overwhelming. But most of these are created as microorganisms break down food ingredients or transform them into other substances.

It doesn’t mean any single fermented food contains all 31 types of compounds. Nor does it mean that everyone who eats them will experience the same changes. Still, the fact that such tiny, invisible bacteria create such a diverse array of substances is truly remarkable.

The color and aroma of miso, the stickiness of natto, the tanginess of yogurt, the complex flavor of kimchi—each one’s character is born not from the raw ingredients alone, but from a combination of microorganisms and time. Unlike the way humans add seasonings to adjust flavors, fermentation slowly transforms the food itself through microbial action. I was struck anew by the realization that the deliciousness of fermented foods comes from the accumulation of invisible transformations.

At the same time, what I think is most important after reading this article is to distinguish between scientific possibility and actual health effects.

The review summarizes the potential connections to intestinal barriers, immunity, metabolism, and inflammation. Studies are cited showing favorable relationships between the consumption of yogurt, kimchi, and kefir and certain disease risks or related markers.

But this is not the same as saying “eat fermented foods and you’ll prevent disease.” In observational research, people who often eat fermented foods might lead healthy lives in other ways too. They may eat more vegetables, or exercise regularly. Health is influenced by many factors—smoking, drinking, sleep, age, and more.

I myself continue to exercise and jog for my health. Running doesn’t mean I can eat whatever I want, nor does eating fermented foods mean I don’t need to exercise. Daily habits—diet, exercise, sleep, rest—don’t function if only one of them is in place.

I think it’s natural to consider fermented foods as one element within a broader lifestyle. Eating a single pack of natto doesn’t dramatically change anything the next day. Eating more yogurt doesn’t automatically make you healthier. Rather than rushing to see special results, incorporating fermented foods into a diet you can sustain without strain is the foundation. That kind of balance feels right for me.

What’s important to keep in mind is not to assume everything with the label “fermented food” is unconditionally healthy just based on the name. Many miso, pickles, and kimchi products are high in salt. Some yogurts and fermented dairy products have lots of added sugar. Cheese can be high in fat and salt depending on the type and amount.

The more we hear that a food is good for us, the more tempted we are to eat more of it. But more isn’t always better. With miso soup, you can emphasize the broth and use less miso. With yogurt, you can check the sugar content. With pickles, you can enjoy them as a small accompaniment to the meal. These ordinary adjustments are easier to sustain over time, I think.

Also, fermented foods vary by type—different raw materials, different bacteria, different production methods. The same miso—whether rice miso, barley miso, or soybean miso—has different flavors. The same yogurt differs between products in the bacteria used, the amount of sugar, and the fat content. You can’t treat everything under the broad umbrella of “fermented food” as the same thing.

That’s why, rather than elevating one food above others, I prefer to appreciate the variety of fermented foods as part of food culture. Yogurt in the morning, miso soup at lunch and dinner, sometimes natto or pickles. You don’t need to eat all of them every single day—you can choose based on what fits your daily menu and how your body feels.

Science gives new explanations to things that have been eaten for centuries. But when something gets dressed up in scientific language, it doesn’t become medicine. Being able to separate what we know from what we don’t yet know—that’s what allows us to confidently use research as a reference for our lives.

Throughout history, humans have harnessed the power of fermentation without ever seeing the microorganisms at work. We’ve passed down safe methods while observing changes in taste, aroma, and shelf life. Modern research is beginning to explain, through language about compounds, genes, and gut environment, what was actually happening in the midst of that long experience.

Ancient wisdom and modern science aren’t in opposition. Science is simply shining new light on food culture that was nurtured through lived experience. I find that relationship fascinating.

Fermented foods are neither a fountain of youth nor a cure-all. Still, the fact that microorganisms, given time, transform food ingredients and create a variety of compounds—there’s plenty of appeal in that alone.

The approach that works for me is this: don’t expect too much from any single food, and stay mindful of salt, sugar, and portion sizes. Keep exercising and jogging, maintain overall meal balance. And within that framework, savor miso, natto, and yogurt with pleasure.

Not “I must eat this because it’s good for me,” but “I eat this because it’s delicious and fits into my life long-term.” The accumulation of those moments feels like it could naturally lead to a healthier life. After reading this review, that’s what I came to feel.

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Toshi / 56 years old, passionate about fermentation, health, and running

※ This article is based on personal experience and publicly available information. It is not intended to diagnose, treat, or prevent any disease. If you have health concerns, please consult a doctor or registered dietitian. See our Disclaimer.