15/10/2025
Often patients ask why their microbiome is as bad as it is… medications are a big part of the problem. GP’s are often quick to prescribe but no one is considering the consequences.
Hot off the press: For the first time, researchers have systematically assessed the impact of long-term medication use on the gut microbiome.
This 2025 retrospective study, "A hidden confounder for microbiome studies: medications used years before sample collection," found that multiple medicines affected the gut microbiome for many years after use.
Typically, we think of antibiotics as the primary medication that alters the gut ecosystem in the long term. However, this study found that beta-blockers, benzodiazepine derivatives, glucocorticoids, PPIs, biguanides (metformin is the most widely prescribed drug in this class), and antidepressants affected the gut microbiome for several years after discontinuing use. And for many of them, the effects at the microbiome level are additive.
Overall, of the 186 drugs analyzed, 167 were found to be associated with the microbiome—affecting alpha diversity, beta diversity, or the abundance of at least one bacterial species—and 78 of those exhibited long-term effects on the gut.
Of note, benzodiazepines—nervous system depressants commonly prescribed for anxiety—impact the microbiome even more than several broad-spectrum antibiotics. The impacts of benzodiazepines and broad-spectrum antibiotics were detectable even when the drugs had not been used for over three years prior to microbiome sampling.
Read the full study at PMID: 40910778
