Fermented foods and gut health: what yogurt, kefir, kimchi and kombucha have been shown to do

Kombucha has a shelf in most supermarkets now, kimchi has moved from specialist grocers to the chilled aisle, and kefir sits beside the milk. The labels promise live cultures and good bacteria, and the implied claim is that these foods improve the gut and, through it, general health.

Humans have eaten fermented foods for thousands of years, mostly because fermentation keeps food from spoiling. Serious study of what they do in the body is much more recent, and it is uneven. One small, careful trial at Stanford produced a striking result in 36 adults. Yogurt has decades of population data behind it. For most other fermented foods, the science has not caught up with the marketing.

What counts as a fermented food?

The word is used loosely, so an expert panel met in 2019 to pin it down. Their definition, published in Nature Reviews Gastroenterology & Hepatology, covers “foods made through desired microbial growth and enzymatic conversions of food components”. Bacteria, yeasts or molds are allowed to grow on purpose, and they change the food as they do.

That takes in yogurt, kefir, cheese, sauerkraut, kimchi, miso, tempeh, sourdough bread, kombucha and also beer and wine. It does not mean all of these deliver live microbes to the gut. Baking kills the organisms in sourdough, and many shop-bought products are heat-treated after fermentation. The panel also separated fermented foods from probiotics, which are specific microbes tested for a specific benefit.

What happened when people ate more fermented foods?

The most cited experiment was run by Justin and Erica Sonnenburg, microbiologists at Stanford, with the nutrition researcher Christopher Gardner. According to the university, 36 healthy adults were randomly assigned to a 10-week diet that included either fermented or high-fiber foods. The fermented group ate yogurt, kefir, fermented cottage cheese, kimchi and other fermented vegetables, and drank vegetable brine and kombucha. Blood and stool samples were collected before, during and after.

The two diets behaved very differently, and not in the way the team predicted. In the paper’s summary, the high-fermented-food diet steadily increased microbiota diversity and decreased inflammatory markers. Diversity means the number of different microbial species living in the gut. Gardner notes in the release that low diversity has been linked to obesity and diabetes. Larger servings brought stronger effects.

The inflammation result was just as distinct. The levels of 19 inflammatory proteins measured in blood samples also decreased, among them interleukin 6, a signaling molecule that rises in chronic inflammatory conditions. “This is a stunning finding,” Justin Sonnenburg said in the university’s release. “It provides one of the first examples of how a simple change in diet can reproducibly remodel the microbiota across a cohort of healthy adults.”

Fiber, the better-known gut food, did not match it. None of these 19 inflammatory proteins decreased in participants assigned to a high-fiber diet, and their microbial diversity stayed flat. Erica Sonnenburg offered a likely reason: “The data suggest that increased fiber intake alone over a short time period is insufficient to increase microbiota diversity.” Ten weeks may be too short for a depleted gut to rebuild the microbes that digest fiber.

The paper itself, published in the journal Cell, is more guarded than the release. It describes a 17-week study with 18 people in each arm, and it reports that the cytokine response score (primary outcome) was unchanged. That score, a measure of immune reactivity, was the result the trial was designed around, and the release does not mention it. Its closing line is hedged: fermented foods “may be valuable” against low microbial diversity and inflammation.

Do fermented-food eaters have different gut microbes outside a trial?

Slightly. Researchers at the University of California San Diego analyzed stool samples and diet records from thousands of volunteers in a citizen-science project. They found that fermented food consumers have subtle differences in their gut microbiota structure compared with people who rarely ate such foods.

The difference really was subtle. In everyday diets, where fermented foods are a small part of what people eat, the microbial signature is faint. The Stanford result came from a diet deliberately loaded with them.

Which fermented foods have evidence for health outcomes?

Yogurt, mainly. Harvard researchers followed more than 190,000 health professionals for up to three decades and tracked who developed type 2 diabetes. Total dairy made no difference. But yogurt intake was consistently and inversely associated with diabetes risk across all three groups, with each daily serving linked to a rate about 17% lower. When the team added 11 other studies, the figure held. The authors’ conclusion draws the contrast: other dairy foods and consumption of total dairy are not appreciably associated with incidence of the disease.

A systematic review of fermented milk products reached a wider but softer conclusion. Of the papers screened, 108 studies were included in the final review, and most reported favorable results for digestion, weight or heart health. Its firmest finding was a narrow one. A causal relationship exists between lactose digestion and tolerance and yogurt consumption, meaning that people who struggle to digest milk sugar tolerate it better in yogurt, because the bacteria have already broken much of it down.

For kimchi, sauerkraut, kombucha and miso there is nothing comparable. Small trials and laboratory studies exist, and population data are confounded by everything else in the diets of people who eat them.

How might fermented foods affect the gut?

Reviewers at Ireland’s Teagasc food research center have laid out three routes. Fermentation creates new compounds, such as short protein fragments with biological activity. It destroys others: compounds that block mineral absorption, and lactose, are removed from the food substrate by the microbes. And the microbes themselves, alive or dead, may interact with the gut lining and its resident bacteria.

Much of that evidence comes from cell cultures and animals. The reviewers are explicit about the gap. In their words, it is important that any such perceived benefits are underpinned by rigorous scientific research.

What do dietary guidelines say about fermented foods?

Very little so far. Dairy appears in most national guidelines, but the fermented milk review noted that there have been few specific recommendations for yogurt and cultured dairy products. The expert panel that wrote the definition discussed efforts to have fermented foods treated as a category of their own in national advice, which shows they are not treated that way yet.

Small trials and healthy volunteers: the gaps in fermented food research

The Stanford trial is the strongest experiment and it has clear limits. Eighteen people ate the fermented diet. All were healthy. The measurements were of microbes and blood proteins, and nobody knows whether lowering those proteins in a healthy person prevents any disease. There was no group that simply carried on eating normally.

Products also differ. Two jars labeled kimchi can contain different microbes in different numbers, and a pasteurized product may contain no live ones. Results from one food do not transfer automatically to another.

How fermented foods fit into the diet of someone with a digestive condition or a weakened immune system depends on their health, which their own doctor assesses.

Outside of yogurt, nobody yet knows whether changing the gut’s microbes with fermented food improves health.