Quantitative mapping of drug effects on microbiota and homology-driven competitive remediation of dysbiosis

While the impact of non-antibiotic drugs on gut bacteria is well-known, their mechanisms of action remain poorly characterized, and effective mitigation strategies for drug-induced dysbiosis are still limited. Here, we screened bacterial-derived drug-target protein homologs (BDTPHs) mapped to 63 target proteins and 107 associated drugs to quantify “drug-BDTPH-bacterium” interactions. These interactions were validated by co-culture experiments using 10 drugs and 25 strains, enzyme assays, and genetic perturbation in the Escherichia coli strain. Ex vivo and in vivo testing with six drugs showed that over 50% of affected genera exhibited high drug affinity, indicating microbiota alterations through the "drug-BDTPH-bacterium" axis. Leveraging this quantitative interaction framework, we identified a strain of Bifidobacterium animalis to competitively bind to methotrexate through high-affinity BDTPH, thereby effectively remediating gut microbiota dysbiosis in vivo. Our findings elucidate a mechanism of non-antibiotic drug effects on bacterial growth, and suggest a universal homology-based competition strategy to restore drug-disrupted microbiota.