The pill that might be relieving your heartburn but killing your gut microbes

Why drugs commonly used against heartburn harm your gut microbiome

Proton pump inhibitors (PPIs) such as omeprazole are frequently used to treat heartburn – often without medical necessity. However, regular use can disrupt the delicate balance of the gut microbiome, thereby increasing the risk of Clostridioides difficile infections and chronic diseases such as obesity and diabetes.

A recent study led by CMFI Board Member Lisa Maier shows that it is not the active ingredient itself, but the sustained increase in pH in the intestine that affects key microbes. In bioreactor experiments, the researchers demonstrated that a permanently elevated pH value alters the composition of the microbiome and weakens its protective function against pathogens such as C. difficile – whereas omeprazole alone had no direct effect.

The results make it clear that a shift in the intestinal environment caused by PPIs can have far-reaching consequences. People who regularly suffer from heartburn should therefore also consider lifestyle changes – to protect the microbiome and maintain their own health in the long term.

Libera Lo Presti from CMFI wrote a “Behind the Paper” post for the Research Communities blog by Springer Nature.

Springer Nature - Behind the Paper

Publication:

Schumacher J, Müller P, Sulzer J, Faber F, Molitor B, Maier L. (2025) Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model. Gut Microbes. 17(1):2519697. doi: 10.1080/19490976.2025.2519697.