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

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