A recent study by researchers at North Carolina State University reveals that the type of protein in an animal's diet can significantly influence both the composition and function of the gut microbiome the community of microorganisms that play a vital role in overall health. These insights could pave the way for improved prevention and treatment of gastrointestinal diseases that affect millions worldwide.

There’s clearly something off about our modern diets and we’re still far from fully understanding what that is  said Alfredo Blakeley-Ruiz a postdoctoral researcher at NC State and co-corresponding author of the study. Our goal was to explore how different protein sources shape the gut microbiome and to uncover how these microbes functionally respond to those dietary changes.

In the study researchers focused on how different dietary protein sources such as those from milk eggs and plant-based options like pea or soy affect the gut microbiome in mice. The mice were each fed a diet containing a single protein source for one week at a time including egg whites, brown rice, soy, and yeast.

By using a combined metagenomics-metaproteomics approach and high-resolution mass spectrometry, the team discovered significant shifts in the mice’s gut microbiome throughout the study with certain protein sources causing particularly dramatic changes.

The composition of the gut microbiome changed significantly each time we switched the protein source said Blakeley-Ruiz. Brown rice, yeast, and egg whites had the most pronounced functional impacts.

When examining how these changes affected microbial function the researchers found two major effects: one expected, and one surprising. As anticipated, dietary protein strongly influenced amino acid metabolism. Unexpectedly it also affected the breakdown of complex sugars.

Diets rich in brown rice and egg whites increased amino acid degradation in the gut microbiome meaning the microbes were breaking down the dietary proteins rather than synthesizing amino acids themselves Blakeley-Ruiz explained. That makes sense since proteins are built from amino acids but it raises important questions. Some amino acids can break down into toxins and others influence the gut-brain axis so these dietary effects could have significant health implications.The study also found that glycanssugar chains attached to dietary proteins can significantly influence gut microbiome function. Protein sources like soy, rice, yeast, and egg whites altered microbial enzyme production related to glycan breakdown. Notably in the egg white diet one bacterium dominated and activated several glycan-degrading enzymes. Lab tests showed these enzymes were similar to those used to break down mucin the protective lining of the gut. This suggests certain diets might unintentionally trigger gut bacteria to damage the intestinal lining potentially impacting gut health.

Source: https://news.ncsu.edu/2025/04/protein-sources-change-the-gut-microbiome/