A few commonly used non-antibiotic drugs have recently been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. We screened >1000 marketed drugs against 40 representative gut bacterial strains, and found that 24% of the drugs with human targets, including members of all therapeutic classes, inhibited the growth of at least one strain. Particular classes such as the chemically diverse antipsychotics were overrepresented. The effects of human-targeted drugs on gut bacteria are reflected on their antibiotic-like side effects in humans and are concordant with existing human cohort studies, providing in vivo relevance for our screen. Susceptibility to antibiotics and human-targeted drugs correlates across bacterial species, suggesting that non-antibiotics may promote antibiotic resistance. Our results provide a comprehensive resource for future research on drug-microbiome interactions, opening new paths for side effect control and drug repurposing, and broaden our view on antibiotic resistance.

Antibiotics are used for fighting pathogens, but also target our commensal bacteria as a side effect, disturbing the gut microbiota composition and causing dysbiosis and disease [1][2][3] . Despite this well-known collateral damage, the activity spectrum of the different antibiotic classes on gut bacteria remains poorly characterized. Having monitored the activities of >1,000 marketed drugs on 38 representative species of the healthy human gut microbiome 4 , we here characterize further the 144 antibiotics therein, representing all major classes. We determined >800 Minimal Inhibitory Concentrations (MICs) and extended the antibiotic profiling to 10 additional species to validate these results and link to available data on antibiotic breakpoints for gut microbes. Antibiotic classes exhibited distinct inhibition spectra, including generation-dependent effects by quinolones and phylogeny-independence by βlactams. Macrolides and tetracyclines, two prototypic classes of bacteriostatic protein synthesis inhibitors, inhibited almost all commensals tested. We established that both kill different subsets of prevalent commensal bacteria, and cause cell lysis in specific cases. This species-specific activity challenges the long-standing divide of antibiotics into bactericidal and bacteriostatic, and provides a possible explanation for the strong impact of macrolides on the gut microbiota composition in animals 5-8 and humans [9][10][11] . To mitigate the collateral damage of macrolides and tetracyclines on gut commensals, we exploited the fact that drug combinations have species-specific outcomes in bacteria 12 and sought marketed drugs, which could antagonize the activity of these antibiotics in abundant gut commensal species. By screening >1,000 drugs, we identified several such antidotes capable of protecting gut species from these antibiotics without compromising their activity against relevant pathogens. Altogether, this study broadens our understanding of antibiotic action on gut commensals, uncovers a previously unappreciated and broad bactericidal effect of prototypical bacteriostatic antibiotics on gut bacteria, and opens avenues for preventing the collateral damage caused by antibiotics on human gut commensals..

24Antibiotics are used for fighting pathogens, but also target our commensal bacteria as a side 25 effect, disturbing the gut microbiota composition and causing dysbiosis and disease 1-3 . 26Despite this well-known collateral damage, the activity spectrum of the different antibiotic 27 classes on gut bacteria remains poorly characterized. Having monitored the activities of 28 >1,000 marketed drugs on 38 representative species of the healthy human gut microbiome 4 , 29 we here characterize further the 144 antibiotics therein, representing all major classes. We 30 determined >800 Minimal Inhibitory Concentrations (MICs) and extended the antibiotic 31 profiling to 10 additional species to validate these results and link to available data on 32 antibiotic breakpoints for gut microbes. Antibiotic classes exhibited distinct inhibition spectra, 33including generation-dependent effects by quinolones and phylogeny-independence by β-34 lactams. Macrolides and tetracyclines, two prototypic classes of bacteriostatic protein 35 synthesis inhibitors, inhibited almost all commensals tested. We established that both kill 36 different subsets of prevalent commensal bacteria, and cause cell lysis in specific cases. 37This species-specific activity challenges the long-standing divide of antibiotics into 38 bactericidal and bacteriostatic, and provides a possible explanation for the strong impact of 39 macrolides on the gut microbiota composition in animals 5-8 and humans 9-11 . To mitigate the 40 collateral damage of macrolides and tetracyclines on gut commensals, we exploited the fact 41 that drug combinations have species-specific outcomes in bacteria 12 and sought marketed 42 drugs, which could antagonize the activity of these antibiotics in abundant gut commensal 43 species. By screening >1,000 drugs, we identified several such antidotes capable of 44 protecting gut species from these antibiotics without compromising their activity against 45 relevant pathogens. Altogether, this study broadens our understanding of antibiotic action on 46 gut commensals, uncovers a previously unappreciated and broad bactericidal effect of 47 prototypical bacteriostatic antibiotics on gut bacteria, and opens avenues for preventing the48 collateral damage caused by antibiotics on human gut commensals.49 3 MAIN TEXT 50 Medication is emerging as major contributor for changes in the composition of the human gut 51 microbiota 4,13-15 . Such severe and long-lasting changes are associated, and in some cases 52 causatively linked, to dysbiosis and a wide range of diseases 16 . Although several non-53 antibiotic drugs may also have a previously unappreciated impact on the gut microbiome 54 composition 4,16,17 , antibiotics, developed to have broad spectra and thereby target very 55 diverse pathogens, are long known to take a heavy toll on our gut flora, causing a variety of 56 gastrointestinal side-effects 18 , including Clostridioides (former Clostridium) difficile infections. 57Recently more attention has been given to this collateral damage of antibiot...