Fermented foods are often associated with live cultures and probiotics. New research suggests they may also contribute something less visible but just as interesting: a significant amount of microbial protein.
In a study published in Food & Function, researchers found that proteins produced by microbes during fermentation make up a notable portion of the total protein in foods like yogurt, cheese and bread. In some cases, these microbial proteins accounted for up to 11% of total protein content and the majority of identified proteins within the food.
“We chose foods that are commonly consumed and are easily accessible at the grocery store,” said Manuel Kleiner, associate professor of plant and microbial biology at North Carolina State University. “What we found surprising is that a large proportion of protein being eaten as part of these foods is actually microbially derived.”
Fermentation relies on microorganisms such as bacteria and yeast to transform raw ingredients. During this process, microbes break down and rebuild components of the original food, including proteins. The result is not just a change in flavor and texture, but also a shift in the types of proteins present.
In the analysis, researchers examined 17 fermented foods alongside several non-fermented counterparts. Using high-resolution techniques to identify proteins, they found that microbial proteins were present across nearly all fermented foods studied, often in greater diversity than proteins from the original ingredients.
In some cases, the shift was especially pronounced. In Brie cheese, for example, most of the identified proteins were microbial rather than coming from milk. Similar patterns appeared in other dairy products and in fermented soy foods.
“I found it quite mind boggling how much of the wheat protein in a regular wheat bread is converted into yeast protein,” Kleiner said. “When we eat bread, we actually eat quite a lot of yeast.”
The findings highlight how fermentation reshapes the nutritional profile of food, not by adding protein, but by changing its composition. Researchers say these microbial proteins may have functional roles, including enzymes that break down carbohydrates or proteins that could interact with the gut environment.
However, the study did not examine how these proteins affect human health. The researchers note that further work is needed to understand whether microbial proteins influence digestion, the gut microbiome or immune responses.
The analysis was based on laboratory measurements of food composition and did not involve human participants. While the results provide a detailed look at what is present in fermented foods, they do not establish specific health effects.
Still, the findings offer a new way to think about familiar foods. Fermentation does more than preserve and flavor food. It transforms it at a molecular level, including the proteins that end up on the plate.
This study was supported by the National Institutes of Health and the European Union.