Protein sources change the gut microbiome – some drastically

A new study by researchers from North Carolina State University shows that protein sources in an animal’s diet can have major effects on both the population and function of the microscopic life within their gut. These microorganisms, known as the gut microbiome, can impact various aspects of our health. The findings could help lead to a better understanding of how to prevent and treat gastrointestinal diseases currently affecting the quality of life of millions of people globally. 

“There’s something wrong with what we’re eating today, and we are not close to knowing what that is,” said Alfredo Blakeley-Ruiz, an NC State postdoctoral researcher and co-corresponding author of a paper describing the study. “Our lab wanted to know how different diets impact what lives in the gut, and to learn something about what those microbes are doing, functionally, in response to that diet.” 

In the study, the researchers were specifically interested in how the source of protein in the diet – for example, proteins found in milk, eggs, and different plants like pea or soy – impact the gut microbiomes of mice. Mice were fed diets containing just one protein source for a week at a time, including egg whites, brown rice, soy and yeast. 

Using an integrated metagenomics-metaproteomics approach requiring high resolution mass spectrometry, the researchers found that the mice gut microbiome changed a lot over the course of the study, with some protein sources showing extreme effects.

“The composition of the gut microbiome significantly changed every time we changed the protein source,” Blakeley-Ruiz said. “The protein sources with the biggest functional effects were brown rice, yeast and egg whites.”

In examining the functional changes in the gut microbiome, the study showed that the two largest effects of dietary protein were on amino acid metabolism, which was expected by the researchers, and complex sugar degradation, which was not.

“Brown rice and egg white diets increased amino acid degradation in the mouse gut microbiome, meaning that the microbes were breaking down those proteins instead of making their own amino acids from scratch,” Blakeley-Ruiz said. “This makes intuitive sense because proteins are made of amino acids, but this is something we want to dig into more. Some amino acids can degrade into toxins and others can impact the gut-brain axis, so there are potential health implications from these diets.”

The study also showed that long chains of sugars attached to the dietary proteins, called glycans, also play a role in changing gut microbiome function. Multiple dietary protein sources, including soy, rice, yeast, and egg white, caused microbes in the gut to change the production of enzymes that break down glycans, sometimes substantially.

“This could be really meaningful, health wise,” Blakeley-Ruiz said. “In the egg white diet, in particular, one bacterium took over and activated a bunch of glycan-degrading enzymes. We then grew this bacterium in the lab and found that the glycan-degrading enzymes it produced in media containing egg white protein were similar to those produced in media containing mucin.”

Mucin is the substance that lines the inside of the gut, protecting the digestive system from things like acid and pathogens. So if bacteria are producing enzymes that, purposely or not, break down mucin, they could be damaging the intestinal lining and causing negative impacts on gut health.  

“I’m excited to explore this potential connection between the expression of glycan degrading enzymes in the egg white diet and the breakdown of mucin by the gut microbiome in future studies,” says Blakeley-Ruiz.

Manuel Kleiner, an NC State associate professor of plant and microbial biology and co-corresponding author of the paper, said the study lays the groundwork for future investigation of the effects of protein sources on the gut microbiome.

“One of the limitations of our study is that, of course, the diets are very artificial and could lead to amplified results,” Kleiner said. “But we now show that egg white has extreme effects on the microbiome. For the future, we're very interested in understanding what the mechanism of this effect is in a mixed protein diet in mice.

“Our study shows not only which bacterial species are in the gut microbiome and their abundance, but also what they are actually doing. Here, they are specifically digesting the glycans. The result is a very comprehensive picture of what really matters in the gut in terms of diet and function.”

Alexandria Bartlett, Arthur S. McMillan, Ayesha Awan, Molly Vanhoy Walsh, Alissa K. Meyerhoffer, Simina Vintila, Jessie L. Maier, Tanner Richie and Casey M. Theriot, all from NC State, co-authored the paper, which appears in The ISME Journal. 

The study was supported by the National Institutes of Health through awards R35GM138362, T32DK007737 and P30 DK034987, and by the USDA National Institute of Food and Agriculture, Hatch project 7002782. 
 
- kulikowski -

Note to editors: The abstract of the paper follows.

“Dietary protein source alters gut microbiota composition and function”

Authors: J. Alfredo Blakeley-Ruiz, Alexandria Bartlett, Arthur S. McMillan, Ayesha Awan, Molly Vanhoy Walsh, Alissa K. Meyerhoffer, Simina Vintila, Jessie L. Maier, Tanner Richie, Casey M. Theriot, Manuel Kleiner, NC State University

Published: March 21, 2025 in The ISME Journal

DOI: 10.1093/ismejo/wraf048

Abstract: The source of protein in a person’s diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices have major impacts on the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota’s metabolism, which could have major implications in the context of gut microbiota mediated diseases.