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

A.V. Vila, V. Collij, S. Sanna, T. Sinha, F. Imhann, A.R. Bourgonje, Z. Mujagic, D.M.A.E. Jonkers, A.A.M. Masclee, J.Y. Fu, A. Kurilshikov, C. Wijmenga, A. Zhernakova, R.K. Weersma*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


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. Here, via a metagenomics analysis of population-based and disease cohorts, Vich Vila et al. study the impact of 41 commonly used medications on the taxonomic structures, metabolic potential and resistome of the gut microbiome, underscoring the importance of correcting for multiple drug use in microbiome studies.
Original languageEnglish
Article number362
Number of pages11
JournalNature Communications
Issue number1
Publication statusPublished - 17 Jan 2020


  • arthritis
  • identification
  • irritable-bowel-syndrome
  • proton pump inhibitors
  • resistance

Cite this