Protein-packed diets are more popular than ever, but new research suggests that not all proteins are digested the same way—and this could have surprising effects on your gut and overall health.
A study from North Carolina State University, published in Food & Function, shows that proteins from different food sources vary in how well they break down in the body and how they interact with the trillions of microbes living in the gut.
While people often divide proteins into “animal” or “plant” categories, the study found that the real differences depend on the specific protein source, not just whether it comes from plants or animals.
The researchers studied purified proteins from six sources: soy, casein (a milk protein), brown rice, yeast, pea, and egg white.
They tested these proteins in two groups of mice—one with normal gut microbes and one completely free of microbes.
By tracking the proteins throughout the digestive system with advanced mass spectrometry, they could see which ones were digested, which ones escaped digestion, and how they interacted with gut bacteria.
The results were striking. Even proteins often considered highly digestible, like egg whites, were found in fecal samples, meaning some of them passed through the small intestine undigested and reached the large intestine.
There, they could serve as food for gut microbes. Brown rice protein was especially resistant, making up about half of all the protein detected in feces.
“The big takeaway is that protein digestion depends a lot on where it comes from,” said Ayesha Awan, the study’s lead author. “If a protein isn’t fully digested, it makes its way to the colon, where it can interact with gut microbes—and those interactions may not always match what you intended with your diet.”
The gut microbiota played a key role in shaping which proteins persisted. Some proteins were broken down more in mice with gut microbes, while others were enriched. This shows that the microbiota influences what happens to proteins once they reach the large intestine.
Interestingly, several proteins with biological activity—including enzyme inhibitors in soy and antimicrobial proteins in egg whites—survived digestion and were still accessible to gut microbes. The researchers suggest that these proteins could affect gut health by influencing microbial activity or altering gut physiology.
Importantly, most digestion in the small intestine happened the same way regardless of whether microbes were present, likely because microbes have less opportunity to interact there. The biggest differences appeared in the large intestine, where microbes had more time and space to interact with leftover proteins, producing metabolites that can influence health.
“These findings highlight why the source of dietary protein matters,” said Manuel Kleiner, co-senior author. “Protein isn’t just protein—it can shape gut health in ways that may be linked to conditions like inflammatory bowel disease or metabolic disorders.”
The team plans to continue studying how different proteins and their interactions with the microbiome affect long-term health outcomes.
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Source: North Carolina State University.
