Do fermented foods change the gut microbiome?

What it is

Fermented foods are foods made through microbial fermentation; each typically carries its own population of microorganisms, and those microbes or the compounds they make may interact with the gut microbiome after eating. Fermentation can also produce biogenic amines such as histamine and tyramine.

What the research says

The best-known human trial (Wastyk 2021, Stanford, 18 people per arm) found a high-fermented-food diet steadily increased gut microbiota diversity and lowered inflammatory markers over 17 weeks, but its primary immune outcome (cytokine response score) did not change. A larger 2025 citizen-science trial, so far only a preprint, found no difference in diversity between the fermented-food group and controls. Reviewers note a lack of sufficient clinical trials. Harms include biogenic-amine reactions, and observational data link pickled foods to higher gastric cancer risk in East Asia.

Evidence grade: Limited evidence.

What goes wrong

Some fermented foods can contain biogenic amines (histamine, tyramine, phenylethylamine) above documented toxic doses, associated with migraines, raised blood pressure and tachycardia; sensitivity varies with alcohol and certain medicines. (Source 1)

• Official position, Low certainty.
• Size: narrative review.
• Who: general population.
• How long: not applicable.
• Result: not quantified in abstract.
• Funding: not stated.

Dietary exposure to foods containing high levels of BAs is associated with many adverse health effects, such as migraines, elevated blood pressure, and tachycardia

A meta-analysis of 60 observational studies associated pickled vegetable/food intake with about 50% higher gastric cancer risk, strongest in Korea and China; this is association, not proof of cause, and heterogeneity was high. Not all pickled foods are fermented. (Source 2)

• Meta-analysis, Low certainty.
• Size: 60 studies (50 case-control, 10 prospective)
• Who: mainly East Asian populations.
• How long: not applicable.
• Result: OR 1.52 (95% CI 1.37-1.68) overall; 1.32 (1.10-1.59) in cohort studies; 1.14 (0.96-1.35) outside East Asia.
• Funding: not stated in abstract.

Our results suggest a potential 50% higher risk of gastric cancer associated with intake of pickled vegetables/foods

What the evidence supports

In the Stanford randomized trial, a high-fermented-food diet steadily increased gut microbiota diversity and decreased inflammatory markers in healthy adults. (Source 3)

• Randomized trial, Low certainty.
• Size: 36 randomized (18 per arm)
• Who: healthy adults, California.
• How long: 17 weeks.
• Result: diversity increased and inflammatory markers decreased (exact values not in abstract); secondary outcomes.
• Funding: not stated in the abstract we fetched.

the high-fermented-food diet steadily increased microbiota diversity and decreased inflammatory markers

What the evidence does not support

The Stanford trial's primary outcome, the cytokine response score, did not change; the diversity and inflammation results were not the primary endpoint. (Source 3)

• Randomized trial, Low certainty.
• Size: 36 randomized (18 per arm)
• Who: healthy adults.
• How long: 17 weeks.
• Result: primary outcome unchanged.
• Funding: not stated in the abstract we fetched.

Although cytokine response score (primary outcome) was unchanged

A larger follow-up style trial (147 adults, 8 weeks; preprint, not peer reviewed) found that compared with controls the high-fermented-food group showed no difference in microbial diversity, although it raised some blood immune markers. (Source 4)

• Randomized trial, Low certainty.
• Size: 147 adults.
• Who: healthy Dutch adults, citizen science design.
• How long: 8 weeks plus 21-week follow-up.
• Result: no difference in microbial diversity vs control; CD5, CD6, CD8A, IL-18R1, SIRT2 increased (Q < 0.05)
• Funding: Dutch Digestive Health Fund; several authors affiliated with companies giving project support (Ani Biome, WholeFiber Holding, MyMicroZoo)

Compared to CG, HFF showed no difference in microbial diversity

A 2022 narrative review states that reports have identified a lack of sufficient clinical trials on fermented foods and inconsistency across groups. (Source 5)

• Official position, Low certainty.
• Size: narrative review, not systematic.
• Who: general.
• How long: not applicable.
• Result: not applicable.
• Funding: not stated.

reports have identified a lack of sufficient clinical trials, variation in the different fermented foods being investigated

Where the evidence is mixed

In the same preprint trial, the fermented-food diet increased several blood immune markers, including IL-18R1 (inflammatory signalling), the opposite direction from the Stanford result on inflammation. (Source 4)

• Randomized trial, Low certainty.
• Size: 147 adults.
• Who: healthy adults.
• How long: 8 weeks.
• Result: increases in CD5, CD6, CD8A, IL-18R1 and SIRT2 (Q < 0.05)
• Funding: Dutch Digestive Health Fund; industry-affiliated authors.

The HFF intervention significantly increased blood immune markers including CD5, CD6 and CD8A (T-cell activation), IL-18R1 (inflammatory signaling)

Where the research disagrees

Whether fermented foods reliably raise gut microbiome diversity

• Wastyk et al. 2021 (Stanford), RCT, 36 people, secondary outcome: the high-fermented-food diet steadily increased microbiota diversity and decreased inflammatory markers (Source 3)
• van den Belt et al. 2025 (preprint), RCT, 147 people, preprint: Compared to CG, HFF showed no difference in microbial diversity (Source 4)

A common belief, and what the research shows

The belief: Eating fermented foods is proven to improve health by fixing the gut microbiome.

What the research shows: The key trial was small and its primary outcome was unchanged: "Although cytokine response score (primary outcome) was unchanged". A later larger trial (preprint) found "Compared to CG, HFF showed no difference in microbial diversity".

Questions and answers

What is it?

Fermented foods are made by microbial fermentation, and each typically hosts its own population of microorganisms. Some of those microbes or their products may survive to interact with the gut microbiome. (Source 5)

What does it do in the body?

In one small 17-week trial, a high-fermented-food diet raised gut microbiota diversity and lowered inflammatory markers, but the main immune outcome did not change. A larger preprint trial did not find a diversity difference against controls. (Source 3)

Is it good or bad for you?

The evidence of benefit is limited and comes from few, small trials. Some fermented foods carry biogenic amines that can cause migraines or raised blood pressure in sensitive people, and heavily pickled foods are associated with higher gastric cancer risk in East Asian observational studies. (Source 1)

How do you get more of it?

In the Stanford trial people increased fermented food servings through diet; in the Dutch preprint trial the fermented group added about 6 portions a day including a fermentation-derived liquid supplement. These are what trials gave, not recommendations. (Source 4)

If it is harmful, what reduces it?

Does not apply to fermented foods as a whole. Where a harm exists it relates to biogenic amine content, whose toxicity depends on individual sensitivity, alcohol and certain medicines. (Source 1)

Why might someone be low in it or missing it?

The Stanford authors frame low microbiome diversity and higher inflammation as common in industrialized societies; this is their interpretation, not a tested cause. (Source 3)

Which whole foods contain it or feed it?

Fermented foods themselves (for example yogurt, kefir, kimchi, sauerkraut, kombucha) are the source; which organisms they carry varies by food. The trials we fetched did not publish food-by-food effects in their abstracts. (Source 5)

What happens if you do not have it?

No trial shows harm from not eating fermented foods. Reviewers say more trials are needed to confirm benefits. (Source 5)

How can you test for it, and how reliable is that test?

No validated test for fermented food intake or its microbiome effect exists in the literature we searched; research trials measure diversity by stool sequencing, which is not a clinical test. (Source 5)

We searched: WebSearch for fermented food trials and reviews 2021-2025; MDPI, medRxiv, PubMed abstracts

References

1. Heliyon. A review of biogenic amines in fermented foods: Occurrence and health effects. 2024. PMID 38304783, DOI 10.1016/j.heliyon.2024.e24501. Read the source
2. Cancer Epidemiology, Biomarkers & Prevention. Pickled Food and Risk of Gastric Cancer - a Systematic Review and Meta-analysis of English and Chinese Literature. 2012. DOI 10.1158/1055-9965.EPI-12-0202. Read the source
3. Cell. Gut-microbiota-targeted diets modulate human immune status. 2021. PMID 34256014, DOI 10.1016/j.cell.2021.06.019. Read the source
4. medRxiv. Distinct modulatory effects of high-fiber and fermented-food diets on gut microbiota, immune function, transit time, and sleep quality in a citizen science randomized controlled trial (preprint). 2025. DOI 10.1101/2025.08.05.25332853. Read the source
5. Nutrients (MDPI). Fermented Foods, Health and the Gut Microbiome. 2022. DOI 10.3390/nu14071527. Read the source