During the past decade, a thriving scientific interest has been raised in exploring the gut microbiome of non-westernized populations. The growing realization of the fundamental role that urbanization is playing in human health and disease, especially in non-communicable diseases, has been accompanied by the challenge of trying to understand which features of the human lifestyle and biology change as people move to cities.

Among others, scientists focus on the significant loss of gut microbial diversity and dietary traits. They appreciate various health-related potential benefits reversing these losses would implicate, and attempt to tackle industrialization’s negative impact on gut microbiota diversity, with so far positive results. Recently, a short-term rural African diet exhibited measurable changes to the microbiota and health markers (i.e., cancer risk).

Fermented foods, such as yogurt, kefir and sauerkraut, are typical examples of dietary components lost with industrialization. They have long been dietary staples in many parts of the world, yet their consumption gained popularity back only very recently as reports with potential health benefits have emerged.

A new study, carried out by researchers at Stanford University, shows that fermented-food diet may increase microbiome diversity and decrease markers of inflammation. In the same study high-fiber diet shows potential in altering gut microbiome functions and modulating immune responses.

The authors recruited 36 healthy adults, randomly split them into two groups of 18, and assigned them to increase the consumption of fiber-rich plant foods, or fermented foods. Participants in each arm were trained to gradually increase intake of their respective diets and directed to maintain a high level of consumption of either fiber or fermented foods for a total of 10 weeks.

Both groups reported significant compliance with their diets. In the high-fiber arm, including fruits, vegetables, legumes, grains, nuts and seeds, participants increased their fiber consumption from 22 to 45 g per day that is roughly triple the average American intake of fibers, without altering their intake of fermented foods. Similarly, in the high-fermented-food arm, including yogurt, kefir, fermented cottage cheese, fermented vegetables, vegetable brine drinks, kombucha, and other fermented non-alcoholic drinks, participants raised their consumption from zero to six servings of fermented foods per day, without increasing their fiber consumption.

Fermented-food diet may increase microbiome diversity and decrease markers of inflammation

Participants’ overall immune health did not change during the 10-week dietary intervention in none of the two groups, nor the primary outcome of cytokine response score. However, at the end of the 10-week high-fermented-food diet, broad serum cytokines and chemokines screening revealed significant decrease in 19 markers, including interleukin-6, a key mediator of chronic inflammation. These inflammatory compounds did not decrease in the high-fiber group.

With regards to gut microbiota, the researchers report that at baseline, there was no difference in fecal microbial diversity and structure between the two dietary groups. At the end of the intervention, in the high-fiber-diet arm, there was surprisingly no difference in microbial structure and composition compared to baseline. However, fiber intake shifted carbohydrate-processing capacity of the gut microbiota, finding in agreement with previous research. In the high-fermented foods arm, the microbial diversity significantly increased, similarly to earlier results, and remained increased for four weeks after the end of the intervention, when fermented foods intake was higher than at baseline, but lower than at the end of the 10-week period.

The latter made the researchers suggest that increased diversity likely involved ecosystem remodelling rather than an immediate reflection of consumed quantities. Therefore, they cross-checked all microbial taxa present in the fermented foods that participants consumed with the nine taxa whose relative abundance was significantly increased at the end of the high-fermented food diet. Indeed, only a very small fragment of the latter was actually detected in the fermented foods. As Justin Sonnenburg, senior author of the study, said at The New York Times “The vast majority came from somewhere else, and we don’t know where. I think there were either low-level microbes below the level of detection that bloomed, or the fermented foods did something that allowed for the rapid recruitment of other microbes into the gut environment.”

On the whole, the authors reveal significant immune health- and gut microbiota-related beneficial effects of fermented foods applying a prospective randomized multiomics approach in 36 healthy adults.



Clemente, J. C., Pehrsson, E. C., Blaser, M. J. et al. The microbiome of uncontacted Amerindians. Science Advances. 2015; 1(3):e1500183. doi: 10.1126/sciadv.1500183

Wastyk, H. C., Fragiadakis, G. K., Perelman, D. et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021; 184(16):4137-4153.e14. doi: 10.1016/j.cell.2021.06.019