Drugs both impact the human gut microbiota and their bioavailability is modified by gut microbes. Here, I will be presenting recent highlights from coordinated efforts at EMBL to systematically map this drug-microbiome interface, to understand its impact on the gut microbiota and on drug efficacy, to address whether communities have emergent behaviours against drugs, and to discover ways to mitigate the collateral damage of drugs, and especially of antibiotics, on gut microbes.