Common Non-Antibiotic Drugs May Harm Gut Microbiome and Raise Infection Risk: Study Shows - Video

A new study published in the journal Nature reveals that several widely prescribed non-antibiotic drugs can significantly disrupt the gut microbiome and increase the risk of gastrointestinal (GI) infections. Conducted by researchers at Yale University, the study highlights that these medications—though not intended to target bacteria—can have unintended consequences on gut health, similar to those caused by antibiotics.

While antibiotics are known to disrupt gut bacteria, this study reveals that some non-antibiotic drugs can also disturb the microbiome. In some cases, they trigger the body to produce antimicrobial agents that harm beneficial gut bacteria, weakening the gut’s natural defense and increasing infection risk.

To better understand the link between drug use and infection risk, the researchers analysed over a decade of health records and pharmacy claims from one million individuals enrolled in a universal health insurance program in Canada. They identified several non-antibiotic prescription drugs that raised the risk of GI infections to a degree comparable with antibiotics.

From their findings, the researchers selected 21 commonly used drugs for further investigation. Using a controlled laboratory setting, mice were treated with these medications, and changes in gut microbiota were analysed through faecal samples collected before and after treatment. Approximately half of the drugs tested were found to significantly alter the composition of the gut microbiome.

Among the most concerning were four specific drugs—digoxin, clonazepam, pantoprazole, and quetiapine—which not only disrupted gut bacteria but also increased the mice’s susceptibility to infections when exposed to pathogens.

These findings point to a growing need for clinicians and researchers to consider the unintended impact of non-antibiotic drugs on gut health. As medication responses vary among individuals, the study suggests the gut microbiome could play a key role in predicting and improving drug outcomes. Further research may pave the way for microbiome-friendly therapeutic strategies in the future.

Reference: Kumar, A., Sun, R., Habib, B. et al. Identification of medication–microbiome interactions that affect gut infection. Nature (2025). https://doi.org/10.1038/s41586-025-09273-8