Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

TLDR

The gut microbiota is linked to drug responses, yet drug‑microbe interactions remain understudied in clinical settings where polypharmacy and comorbidities are common. This study investigates associations between commonly used drugs and the gut microbiome. Researchers performed metagenomic sequencing of fecal samples from a population cohort and two gastrointestinal disease cohorts, comparing users and non‑users within each cohort and conducting a meta‑analysis. Nineteen of 41 drugs were associated with microbial features, with proton‑pump inhibitors, metformin, antibiotics, and laxatives showing the strongest links after adjusting for multiple medications, revealing extensive taxonomic, metabolic, and resistome changes and underscoring the need to account for drug use in microbiome studies.

Abstract

The human gut microbiota has now been associated with drug responses and efficacy, while chemical compounds present in these drugs can also impact the gut bacteria. However, drug-microbe interactions are still understudied in the clinical context, where polypharmacy and comorbidities co-occur. Here, we report relations between commonly used drugs and the gut microbiome. We performed metagenomics sequencing of faecal samples from a population cohort and two gastrointestinal disease cohorts. Differences between users and non-users were analysed per cohort, followed by a meta-analysis. While 19 of 41 drugs are found to be associated with microbial features, when controlling for the use of multiple medications, proton-pump inhibitors, metformin, antibiotics and laxatives show the strongest associations with the microbiome. We here provide evidence for extensive changes in taxonomy, metabolic potential and resistome in relation to commonly used drugs. This paves the way for future studies and has implications for current microbiome studies by demonstrating the need to correct for multiple drug use.