A hidden confounder for microbiome studies: medications used years before sample collection

Medication usage is a known contributor to the inter-individual variability of the gut microbiome. However, medications are often used repeatedly and for long periods, a notion yet unaccounted for in microbiome studies.

 

Recently, we and others showed that not only the usage of antibiotics and antidepressants at sampling, but also past consumption, is associated with the gut microbiome. This effect can be “additive”—the more a medication is used, the stronger the impact on the microbiome.

 

Here, by utilizing retrospective medication usage data from the electronic health records and the observational Estonian microbiome cohort shotgun metagenomics data set (n = 2,509), we systematically evaluate the long-term effects of antibiotics and human-targeted medications on the gut microbiome.

 

We show that past usage of medications is associated with the gut microbiome. For example, the effects of antibiotics, psycholeptics, antidepressants, proton pump inhibitors, and beta-blockers are detectable several years after use. Furthermore, by analyzing a subcohort (n = 328) with a second microbiome characterization, we show that similar changes in the gut microbiome occur after treatment initiation or discontinuation, possibly indicating causal effects.

 

 

For more information:

Aasmets O, Taba N, Krigul KL, Andreson R; Estonian Biobank Research Team, Org E. A hidden confounder for microbiome studies: medications used years before sample collection. mSystems. Published online September 5, 2025. doi: 10.1128/msystems.00541-25