Will a High-Protein Diet Mess With Your Microbiota?

Protein gets a lot of hype in the world of weight management. When cutting calories, high-protein diets can keep hunger at bay and improve metabolic outcomes in those with overweight and obesity. But what impact does a high-protein diet have on gut health in the long-term? To help answer this question, we’re going to take a closer look at a position paper hot off the press from the Clinical Nutrition journal. 


The authors reviewed dietary intervention studies on humans, including recent data from the MyNewGut European research project, to weigh the costs and benefits of high-protein diets (HPDs) for weight loss and the gut microbiota – i.e., the bacteria, viruses, and fungi that live in our intestinal tracts. 

Weight Loss

“Ad libitum” studies—where volunteers consume as much food as they want on either a HPD (providing 25–30% of total calorie intake from protein) or moderate-protein control diet—have found that volunteers on a HPD naturally eat less food (and thus lose more weight) than controls. Worth noting, however, is that researchers reported a return to initial body weights among many participants in the long-term. 

Another type of HPD intervention studies reviewed manipulated the proportion of protein consumed by participants while maintaining constant caloric intakes across groups. These studies generally found little to no effect of HPDs on weight loss when calories were kept constant, suggesting that calorie intake (not macronutrient distribution) is the main determinant for weight management. 

Gut Health

The protein we consume isn’t entirely digested by our small intestines, so small amounts of nitrogenous compounds (undigested proteins, peptides, and amino acids) move into the large intestine where bacterial enzymes act on them. When a HPD is consumed, a proportionately greater amount of nitrogenous compounds enter the large intestine, modifying the activity of gut microorganisms. Results showed HPDs have a limited effect on the composition (variety of species) of the gut microbiota when calorie and fiber intake are not modified. HPDs in short- and medium-term studies also showed no increased potential harm for genetic mutation or cell damage. In 3-weeks’ time, an increased consumption of protein did appear to alter normal expression of genes known to be involved in maintenance of a healthy rectal mucosa (or lining), which could be linked to inflammation. These effects seem to depend on the type of protein in the diet, with high animal protein intake linked to higher incidence of inflammatory bowel disease and relapse.

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“Two studies have shown that a high amount of animal protein intake is associated with increased inflammatory bowel disease incidence and relapse.”

Blachier, François et al.


Potential confounders include differences in calorie and fiber intake across studies, two factors known to have a big impact on the gut microbiota composition, thus making it tricky to know for sure how protein intake directly impacts the gut.

Bottom Line

HPDs can yield efficient weight loss along with calorie restriction by curbing hunger but, due to potential weight regain and possible negative effects on the microbiota, the authors of this paper caution against recommending long-term HPDs for weight loss purposes at this time. A dietitian can recommend the best diet to meet your individual needs. To learn more, book a free consultation with us today. 

Ryan Stallard