Antagonistic drug interactions protect commensal Bacteroidaceae from macrolides via an RND-type efflux pump.

Antibiotics are essential to modern medicine, but their broad-spectrum activity can unintentionally disrupt the gut microbiota. This collateral damage may be alleviated by antagonistic drug interactions, in which specific compounds used in combination therapies selectively protect beneficial gut microbes from antibiotic activity. Using efflux pump inhibitors, transcriptomic and proteomic analyses, and targeted gene deletions, we show that a variety of non-antibiotic pharmaceuticals-from diverse therapeutic classes and at sub-inhibitory concentrations-can protect multiple Bacteroidales species from macrolide antibiotics. In Bacteroidaceae, this protection is mediated by a resistance-nodulation-division (RND)-type efflux pump, which is induced by the non-antibiotic drug but not by macrolides alone. Notably, protection persists even after the non-antibiotic drug is removed, and prolonged exposure results in stable macrolide resistance that is dependent on the RND-type efflux pump. Our findings illustrate how non-antibiotic drugs can inadvertently activate otherwise silent detoxification systems in gut microbes, uncovering resistance mechanisms that arise without antibiotic selection or gene transfer. While this can be harnessed to protect the microbiome during antibiotic therapy, it also reveals hidden resistance phenotypes that may escape detection in standard antimicrobial resistance assays.