15The trillions of microorganisms (microbiota) found within the human gut play a critical role in 16 shaping the immune system, yet these complex microbial communities are also highly sensitive 17 to numerous environmental factors. While much of the focus to date has been on dietary intake, 18 emerging data has begun to suggest that the use of pharmaceutical drugs, even those that are not 19 considered to be antibiotics, can alter the human gut microbiota with unknown consequences for 20 treatment outcomes. Here, we use a combination of in vitro, in vivo, and ex vivo methods to 21 demonstrate that the first-line therapy for rheumatoid arthritis (RA), methotrexate (MTX), has 22 off-target effects on the human gut microbiota, resulting in a significant growth advantage for 23 drug-resistant Firmicutes over the Bacteroidetes, which tend to be more sensitive. Longitudinal 24 analyses of the gut microbiotas of RA patients revealed that MTX-induced shifts in bacterial 25 relative abundance are associated with improved drug response and transplant experiments in 26 gnotobiotic mice show that these shifts lead to reduced inflammation. Together, these results 27 suggest that the mechanism-of-action of non-antibiotic drugs may be due in part to off-target 28 effects on the gut microbiota, while providing a critical first step towards explaining long-29 standing differences in drug response between patients. 30