Fermented foods and the gut microbiome

By Jeffrey Letourneau

Bread, cheese, beer. What do these products have in common besides their massive popularity? They are all produced with the help of microbes such as bacteria and yeast. These helpful microbes cause bread to rise, cheese to acquire its flavor, and beer to have alcohol, by carrying out chemical reactions collectively known as fermentation.

Humans have been fermenting food for millennia. Fermentation can extend the life of food products, enhance nutritional value, and create new flavors. Today, commonly consumed fermented products include wine, sauerkraut, pickles, kimchi, kombucha, yogurt, miso, and many more. Just about anything can be fermented – meat, fish, milk, fruit, beans, etc. Common types of microbes used in fermentation include lactic acid bacteria (LAB), acetic acid bacteria (AAB), and yeast (which are fungi, not bacteria). How does consuming these microbes affect the tens of trillions already living in our guts?

A recent study by researchers at the University of California, San Diego provided new insights into this question. The study, led by PhD Candidate Bryn Taylor, in the lab of Dr. Rob Knight, sought to test whether regular consumption of fermented foods caused changes in gut microbiome composition (the types of microbes present) and function (the chemicals the microbes are producing). Previous studies have identified certain chemicals that are beneficial to health, such as lactic acid and some vitamins, in fermented foods. This is the first study to look at the effects of consuming fermented foods on the gut microbiome in a large number of participants. To achieve this large sample size, the authors analyzed stool samples from 6,811 participants from the American Gut Project.

Participants completed diet surveys to assess frequency of fermented food consumption. This enabled the researchers to separate participants into groups based on how often they ate fermented foods. They considered participants to be “consumers” if they reported eating fermented foods at least occasionally (1-2 times/week) and “non-consumers” if they reported eating fermented foods rarely (less than once/week) or never.  Of the thousands of participants involved in the study, 115 were specifically recruited for either frequent or very rare fermented food consumption, and these participants provided samples over a long period of time to assess changes within individuals. This cohort was given an additional survey to further assess which specific fermented foods they consumed.

In terms of gut microbiome composition, there were no differences in overall diversity between consumers and non-consumers. However, there were differences at the level of specific microbes, and these differences appeared to be dose-dependent, meaning the effects were more pronounced the more often one ate fermented foods. When specific microbes common in fermented foods consumers were assessed, these included some species previously thought to be beneficial to gut health such as Faecalibacterium prausnitzii. Consumers also had higher proportions of fermented-food associated microbes such as Lactobacillus acidophilus. This finding supports previous work demonstrating that microbes in some fermented foods like cheese can make it through the gastrointestinal tract alive.

Another interesting finding pertains to the metabolites gut microbes produced. Overall, the types of chemicals present changed more day-to-day than community composition. Fermented food consumers had increased lipid metabolism and specifically increased levels of conjugated linoleic acid (CLA), which may have health benefits. CLA has previously been found in higher concentrations in people who ate more plants. However, in this cohort, stratifying on plant consumption did not reveal an enrichment of CLA. The researchers also found that CLA levels were correlated with the abundance of some known CLA producers such as Eubacterium rectale and Bifidobacterium adolescentis, supporting the effect of fermented foods on CLA.

The authors note that the variations observed between groups were subtle, which may be due to the fact that even in frequent consumers, fermented foods probably constitute a relatively small proportion of the diet. All study participants were from the United States, where fermented food consumption is relatively low, so it is possible that there a greater effect could be observed in other cohorts. The present study did not look at health outcomes, so conclusions about whether the subtle observed changes in microbes and metabolites benefit the host cannot be made.

In general, it is important to note that most of the microbes in fermented foods are undefined and unstudied, so there is no guarantee of a health benefit. In many fermented foods, such as beer, wine, and soy sauce, microbes are killed by baking or pasteurization. Still, fermentation can provide benefits such as enhanced vitamin content and greater digestibility, not to mention exciting new flavors like the umami of soy sauce or notes of chocolate in a glass or red wine. Since some have argued that a lack of exposure to particular microorganisms during early childhood may contribute to allergies and immune disorders, making fermented foods cheap and accessible could be a way to mitigate some aspects of modern industrialized life that adversely affect the gut microbiome.

Overall, this study demonstrated that fermented food consumption subtly alters the composition of the gut microbiome and the chemicals that gut microbes produce. Furthermore, the increased CLA concentration in fermented food consumers hints at a health benefit, although the present study comes short of directly establishing such a benefit. This is an exciting and ongoing area of research, and future studies in the field will help us better understand the impacts of different fermented foods and the microbes used in their production.

Peer-edited by Erin Coffman