The health benefits of fermented foods have been acknowledged for centuries and stem from the presence of living microorganisms and the fermentation-associated modifications to the food product’s ingredients.

But how fermented foods shape the composition and activity of the gut microbiota in large populations has been subject to limited study. This is partly explained by the difficulties of in-lab analysis of the intestinal microbiota from stool samples and is currently solved by the advent of genetic tools that allow researchers to characterize the gut microbiome’s composition and function.

A new study of 6,811 subjects from the American Gut Project, led by Rob Knight from the University of California San Diego, explores in depth how fermented foods impact gut microbiota composition and function.

A first one-time snapshot of 6,811 participants showed that those consuming plant-based fermented foods (e.g. kimchi, kombucha and pickled vegetables) at least once a week showed a similarly diverse gut microbiota to that of non-consumers. However, specific microbes were associated with the consumption of fermented plants, highlighting subtle changes in the gut microbiota’s environment related to fermented plant intake.

The authors also followed a subgroup of 115 subjects consuming plant and animal-based fermented foods either on a daily basis or three to five times a week. Compared to non-consumers, the gut microbiota of fermented food consumers is enriched in conjugated linoleic acid, possibly of microbial origin, and lactic acid bacteria:

  • Conjugated linoleic acid is an omega-6 fatty acid linked to health benefits, such as protection against cardiovascular diseases.
  • Lactic acid bacteria are commonly used for fermenting food staples (e.g. in milk to obtain yoghurt) and produce a wealth of beneficial metabolites. The latter include, among others, compounds that inhibit the growth of bad bacteria, as well as short-chain fatty acids and lactate that help maintain a healthy gut barrier.

This is the first study exploring the link between fermented food intake and gut microbiota composition and function in a large population. Altogether, the findings strengthen the already existing literature, showing that gut microbiota composition and function is not only an indicator of proper gut and overall health, but also of the presence of specific metabolites produced by gut microbiota.

The regular consumption of fermented foods is not linked to profound changes in gut microbiota composition; however, it can lead to modifications within the gut microbiota’s environment. This intake could promote health-promoting metabolites linked to health benefits (also sometimes referred to as postbiotics) produced by bacteria as a result of their fermentation within the gut.



Taylor BC, Lejzerowicz F, Poirel M, et al. Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome. mSystems. 2020; 5(2):e00901-19. doi: 10.1128/mSystems.00901-19.