Microbial diversity

Using fermented foods well

Sauerkraut, kefir, kimchi: what the studies show and how to include them.

How solid is the research? Trust score 3 of 5:Promising

A well-designed randomised trial shows more diversity and fewer inflammatory markers. It is small, and its predefined primary goal was not met.

Healthy state

Fermentation means that microorganisms grow in a controlled way in a food and transform its components. Lactic acid bacteria turn milk sugar into lactic acid and so make yoghurt or kefir from milk, and sauerkraut or kimchi from cabbage. Yeasts and acetic acid bacteria take over in kombucha or water kefir. The acid lowers the pH, keeps spoilage organisms and pathogens at bay and preserves the food; the technique is much older than the knowledge of microbes. An expert panel defined fermentation in exactly this way in 2021: deliberate growth of microbes and their enzyme work on a food.

What ends up in the jar or cup depends strongly on the product. Depending on how it is made, yoghurt and kefir from milk contain millions to billions of live microbes per gram, kefir also contains yeasts. Added to this are lactic acid and other organic acids, small protein fragments and, because the microbes have already broken down part of the milk sugar, often better tolerance in people with lactose problems. In vegetables, fibre and plant compounds are retained but partly reworked by the microbes. Sourdough bread, wine and beer are also fermented, but baking, filtering or pasteurising usually leaves them without live cultures.

On the way through the body only part of the microbes survive. Thinning begins with chewing and saliva, stomach acid at a pH of around 1 to 3 kills many more, and bile and pancreatic juice in the small intestine kill still more. Milk and fat buffer the acid and help some microbes get through, which is why yoghurt and kefir do well. Those who eat them usually do not settle them permanently, though: they are guests passing through who disappear from the stool again after you stop. Their value lies in what they do along the way, namely supplying acids and other substances, coming into contact with the mucosa and immune cells, and nudging the microbial community.

The best study on this comes from Stanford. 36 healthy adults ate either more and more fermented foods or more and more fibre for ten weeks. In the fermented group, Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity” diversity rose with the amount and several inflammation markers in the blood fell. The fibre group did not show this pattern. This is an exciting hint, not proof: the group was small, and the primary goal set in advance, a difference in diversity, was not reached statistically. Larger studies must show whether it holds. In everyday life, taste and variety are also simple arguments for fermented foods.

live culturesGutguests passing through
Unpasteurised fermented foods bring live cultures. Most only pass through but act along the way.

Disrupted state: causes and effects

The first misunderstanding is the label. “Fermented” or “lacto-fermented” on a shelf does not have to mean anything alive. Canned sauerkraut, pickles in vinegar, yoghurt heated after ripening and many ready-made sauces kept their flavour but not their cultures. “ Probiotics Live microorganisms that are meant to provide a benefit in sufficient amounts. The effect depends on the individual strain. ” is also a stricter term: it requires a precisely named strain in sufficient amount with a proven benefit. A jar of sauerkraut contains a colourful mixture that differs from batch to batch, which makes it something different, neither better nor worse.

The second topic is biogenic amines. During ripening, some microbes convert amino acids into Histamine A messenger substance of the body that is also found in aged and fermented foods. Too much can cause headache, flushing or diarrhoea. More in the chapter “Histamine intolerance: much searched, little proven”, tyramine and similar substances. There is particularly much in long-aged cheese, salami, sauerkraut, wine and beer, and in tinned fish. People whose breakdown in the gut, mainly by the enzyme DAO (diamine oxidase) An enzyme in the gut wall that breaks down histamine from food before it reaches the blood. More in the chapter “DAO: the enzyme that intercepts histamine from food”, is weak can react with headache, flushing, palpitations, a runny nose or diarrhoea. Tyramine plays a role elsewhere too: anyone taking certain older antidepressants (so-called MAO inhibitors) can get dangerous blood pressure spikes from tyramine-rich food. That belongs in a conversation with a doctor.

Third point: fermentation continues in the gut, and a sensitive gut can feel that. People who already bloat a lot often tolerate large amounts of kefir, kombucha or kimchi badly, because fermentation products and gases arrive along with the microbes. In Small intestinal bacterial overgrowth (SIBO) Too many bacteria in the small intestine, where normally few live. Bloating and diarrhoea are typical; it is usually diagnosed with a breath test. More in the chapter “When the small intestine is too densely colonised”, some affected people report that fermented foods make symptoms worse because they keep fermenting in the small intestine; this is not proven, it is a plausible observation. Spicy kimchi can bother reflux, and sauerkraut, kimchi and miso are often very salty, which matters with high blood pressure. Depending on the type, kombucha contains a lot of sugar plus some alcohol and acid.

Fourth, safety. Industrially made products are usually well controlled. With home-made ones, hygiene decides: with too little salt, too much air or a contaminated vessel, mould or film yeast can grow, and some moulds produce toxins you cannot smell. Raw and fresh-milk products can contain Listeria in pregnancy and with a weakened immune system. With a severely weakened defence, for example during chemotherapy, live cultures themselves are an issue because in rare cases they can enter the bloodstream. For most people fermented foods are well tolerated, but it is worth knowing your own starting point.

pasteurisedGutno live cultures
Heated or pasteurised, the cultures are dead. The taste remains, the live bacteria do not.

What often helps

Lifestyle

Diet, exercise, sleep, social contact and dealing with stress.

  • Several small servings a day In the Stanford study, participants gradually ate up to six servings a day, such as yoghurt, kefir, kombucha and kimchi. Diversity increased and several inflammatory markers went down. A serving can be a spoonful of sauerkraut as a side or a small glass of kefir; the point is regularity, not large amounts. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [1]
  • Chilled section instead of cans Look for “unpasteurised” or “with live cultures”. What stands on the shelf at room temperature and was heated after ripening usually contains nothing alive any more. You also protect the cultures at home before heating: add sauerkraut cold to a warm meal, do not cook it along. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.
  • Increase slowly Start with small amounts and raise them over weeks. If you bloat a lot or react to histamine, be careful and try one product at a time so that you can link a reaction to its cause. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.
  • Combine with fibre The study examined fermented foods on top of everyday eating with plenty of vegetables, legumes and whole grains; it did not pit them against fibre. Live microbes arrive best with food for them: sauerkraut on a plate of vegetables or kefir with your oats makes more sense than a glass of kefir alone. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [1]
  • Watch salt and sugar Salt-pickled vegetables and miso quickly put a lot of sodium on the plate, kombucha and fruit yoghurt a lot of sugar. If you have high blood pressure or want to cut sugar, choose unsweetened plain products and small servings. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.

Natural supplements

Supplements do not replace a medical check-up. Discuss dosage and interactions with your doctor or pharmacist.

  • Probiotics are no substitute Probiotics contain a few selected strains, fermented foods a broad mixture. The study results cannot be transferred. Guidelines recommend probiotics only for certain strains and uses, not across the board. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [2]
  • If capsules, then targeted Fermented foods vary from batch to batch, capsules are consistent. If you try capsules, choose by strain and intended use, and decide after four to eight weeks whether it does anything. More in the chapters on probiotics and Saccharomyces boulardii. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [2]

Medical treatments

Information, not a treatment recommendation. Decide together with a doctor. Approval and availability differ from country to country.

  • Ask first if your immune system is weakened If you take immunosuppressants or receive chemotherapy, discuss live cultures with your doctor first. The same applies to raw-milk products in pregnancy. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [3]
  • Clarify reactions to histamine and tyramine If headache, flushing or diarrhoea regularly follow cheese, sauerkraut, wine or salami, a food diary with a doctor or dietitian helps more than guessing. If you take MAO inhibitors, get advice on tyramine-rich food. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [4]

In the mood for something completely different? Another one, at random

How we rate the evidence
Trust score 5 of 5:Established
Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies.
Trust score 4 of 5:Well supported
Several randomised studies in humans with largely consistent results.
Trust score 3 of 5:Promising
Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies.
Trust score 2 of 5:Plausible
Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms.
Trust score 1 of 5:Experimental
Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.

Sources

  1. Wastyk et al. 2021: Fermented foods increase diversity and lower inflammatory markers (Cell)
  2. Su et al. 2020: AGA guideline on probiotics in gastrointestinal disorders (Gastroenterology)
  3. Caffrey et al. 2025: Identifying and safely consuming fermented foods, review (Advances in Nutrition)
  4. Review 2025: Evidence for dietary management of histamine intolerance (International Journal of Molecular Sciences)
  5. Marco et al. 2021: ISAPP consensus on fermented foods, definition, safety and benefits (Nature Reviews Gastroenterology & Hepatology)
  6. Hertzler and Clancy 2003: kefir improves lactose digestion and tolerance in 15 adults
  7. Review 2018: toxins in fermented foods and how to prevent them

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