Fermented Foods Contain More Microbial Protein Than Expected

A new North Carolina State University study examining the proteins found in fermented foods like yogurt, cheese and bread found that a surprisingly large number, and percentage, of microbial proteins contribute to their overall protein content. These microbes have long been used in traditional fermentation processes and are widely associated with the beneficial or probiotic nature of these fermented foods.

The findings highlight the role of microbial proteins in shaping the nutritional and potential health impacts of fermented foods and could also help pave the way to engineering fermented foods with specific microbial profiles that enhance their beneficial effects.

NC State researchers were interested in teasing out how microbial fermentation changes the protein composition of foods and which microbial proteins are ultimately consumed as part of these changed foods.

Using a metaproteomics approach, the researchers combined high-resolution liquid chromatography and mass spectrometry to identify all the food- and microbial-derived proteins in 17 fermented and three non-fermented foods. Dairy milk, tofu and wheat bread comprised the non-fermented foods, while the fermented foods included the fermented derivatives of these substrates such as yogurt, brie cheese, sour cream, plain yeast bread, sourdough bread, tempeh, miso and soy sauce.

The striking results showed that microbial proteins contributed up to 11% of the total protein content and up to 60% of the total number of identified proteins in fermented foods.

Manuel Kleiner, an NC State associate professor of plant and microbial biology and co-corresponding author of a paper describing the work, found the results surprising.

“We chose foods that are commonly consumed and are easily accessible at the grocery store,” Kleiner said. “What we found surprising is that a large proportion of protein being eaten as part of these foods is actually microbially derived.

“I found it quite mind boggling how much of the wheat protein in a regular wheat bread is converted into yeast protein, for example,” Kleiner added. “When we eat bread, we actually eat quite a lot of yeast.”

Interestingly, the proportion and diversity of microbial proteins were much higher than the food substrate proteins in five of the fermented foods analyzed. In Brie cheese, for example, out of the 1,573 different proteins present, 1,023 proteins, or 65%, were microbial proteins. This pattern was observed in almost all dairy products studied.

“This shows that microorganisms not only contribute to the fermentation process itself but also to the overall nutritional and functional profile of fermented food by converting substrate proteins into microbial proteins,” said Ayesha Awan, an NC State Ph.D. candidate and co-corresponding author of the paper. “These results offer future areas for investigation beyond the known probiotic effects of fermented foods, as the microbial proteins consumed as part of these foods may influence the host immune response or interact with the gut microbiota.”

Awan said that next steps in the research could include studying the impacts of fermented food proteins on the gut microbiome of mice to better understand the possible associated health benefits.

Reference:  Winkler L, Awan A,  Rideout N.et al. Assessing the diversity and functional profile of the “microbial proteome” in fermented foods. Food Funct. 2026. doi: 10.1039/D5FO05039A 

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