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Microbiota 23 - October 2025
Dears readers,
When drugs meet microbes: a dialogue too long overlooked.
In recent years, we have become accustomed to thinking of the gut microbiota as a cornerstone of digestive and immune health, a complex organ in itself. But what happens when it meets another key player in modern medicine, drugs? This is the fascinating focus of our latest issue, expertly synthesized by Prof. Emmanuel Montassier (University of Nantes, France).
We are learning that the dialogue between gut microbes and medications is not only real, it is profoundly bidirectional. Drugs can reshape the microbiota, sometimes with long-term consequences. In turn, microbes can metabolize, activate, or inactivate medications, influencing both their efficacy and toxicity. According to studies referenced in this issue, around 24% of non-antibiotic drugs inhibit at least one commensal species, and 10–15% are metabolized by the microbiota, with possible clinical implications ranging from reduced therapeutic benefit to adverse drug reactions.
These interactions, still largely overlooked in drug development and prescribing, are now forming the foundation of a new field: pharmacomicrobiomics. By combining microbiome data with genomics and clinical information, we are on the verge of personalizing treatments in ways previously unimaginable.
In this edition, Prof. Montassier takes us through key findings, including the collateral damage of common antibiotics on gut flora, the underestimated effects of drugs like PPIs and metformin on microbial communities, and emerging strategies to preserve and restore the microbiota, ranging from microbial enzyme inhibitors to microbiota-sparing drugs and even AI-guided treatment design.
By bringing clarity to this fast-moving field, we hope to foster a broader awareness of the gut microbiota not just as a passive victim of medications, but as a therapeutic actor in its own right.
Enjoy your reading!
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Created
17 November 2025
Updated
15 December 2025