By George Citroner
What protein you put on your plate—whether it’s egg whites, brown rice, or soy—reshapes your gut microbiome, potentially influencing everything from digestive health to brain function, according to a new study.
“There’s something wrong with what we’re eating today, and we are not close to knowing what that is,” Alfredo Blakeley-Ruiz, a postdoctoral researcher at NC State and study author, said in a statement.
The findings reveal that certain protein sources may even damage the protective lining of your gut, challenging conventional wisdom about “healthy” food choices.
Different Proteins, Different Microbiomes
The study, recently published in The ISME Journal, focused on how different protein sources could affect the gut microbiome of mice.
The mice were fed diets containing only one protein source for one week at a time—egg whites, brown rice, soy, and yeast.
“The composition of the gut microbiome significantly changed every time we changed the protein source,” Blakeley-Ruiz said in a statement. The biggest effects on the function of these microbes came from a diet of brown rice, yeast, and egg whites.
“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,” he stated.
This process could have health implications because some amino acids can turn into toxins, and others can influence the gut-brain connection, according to Blakeley-Ruiz.
The researchers were particularly concerned about effects on the protective gut lining. Certain bacteria that flourished on the egg white diet produced enzymes that break down mucin, a protective barrier that lines the gut.
Blakeley-Ruiz pointed out that the breakdown of mucin could damage our gut lining and harm gut health by making the gut more vulnerable to inflammation or infection.
“We don’t usually think of protein as something that shapes the gut microbiome, but it absolutely does,” Alyssa Simpson, a digestive health dietitian in Phoenix, Arizona, who was not involved with the study, told The Epoch Times.
Beyond Plant vs. Animal Protein
What surprised the researchers most was that the amino acid composition of proteins wasn’t the key factor driving these changes.“I always thought about protein as mainly strings of amino acids, so how would it really make much of a difference for the microbiome what protein we consume?” Manuel Kleiner, NC State associate professor of plant and microbial biology and co-corresponding author of the study, told The Epoch Times.
“We found that the amino acid composition was not relevant for the massive impacts we saw,” he continued. What mattered was what type of proteins were less or more digested when the food reached the colon, and another thing that mattered was what molecules were attached to these proteins.
“One thing that our findings do underscore is that thinking about plant versus animal protein, when thinking about health consequences of different protein sources, may be overly simplistic,” Kleiner said. “In terms of impacts on the microbiota, there are sources from both plants and animals that lead to major shifts in the microbiota, so it really is more about the specific protein source.”
The brown rice diet led to a significant increase in proteins capable of producing indole, a compound often generated in the gut during plant digestion. The egg white diet resulted in a slight increase in proteins involved in producing gamma-aminobutyric acid (GABA), a neurotransmitter. Both indole and GABA have anti-inflammatory properties and can influence gut and brain function.
While the mouse digestive system and microbiome have some marked differences from the human one, past studies have shown “over and over again” that overall trends in how diet and other “interventions” impact the microbiome are similar between humans and mice, Kleiner told The Epoch Times.
He added that he’s now working on a follow-up study where they’ll investigate if similar effects are observed in human volunteers who consume a protein supplement from a specific source.
Balancing Your Protein Intake
Dietitians suggest that the new study findings reinforce the importance of dietary diversity.Plant-based proteins, which are high in fiber, have been shown to improve human gut health, Emily Feivor, a registered dietitian at Northwell Long Island Jewish Forest Hills, told The Epoch Times. However, she cautioned that in those already living with a gastro-intestinal (GI) disorder, “added fiber from plant-sources, may cause additional GI distress.”
Simpson added that generally, proteins from plants like legumes, grains, and seeds tend to support a healthier gut environment because they come with fiber and polyphenols that feed beneficial bacteria. “Animal proteins can still be part of a gut-friendly diet,” she noted. “But balance is key.”
People with gut disorders like irritable bowel syndrome or leaky gut may be more vulnerable to shifts in their microbiome based on protein choices. Simpson explained that in these cases, eating too much of certain animal proteins, especially without enough fiber, can encourage bacteria that drive inflammation or gut lining damage.
“People with kidney disease also need to be thoughtful, since high-protein diets can strain kidney function,” Simpson said.
While the study suggests that diets high in egg whites might promote bacteria that could damage the gut lining—which might help explain why some population studies have associated higher egg consumption with increased mortality rates—the researchers emphasize that real-world diets involve combinations of foods with fats, fibers, and other nutrients that could influence these microbial responses.
The study’s broader implication is clear: protein source diversity matters, and understanding the functional changes in gut bacteria—not just which species are present—is crucial for developing dietary strategies that promote gut health.