Linking interpersonal differences in gut microbiota composition and drug biotransformation activity

Individuals vary widely in their response to medical drugs, and growing evidence implicates the gut microbiome, together with host genetics, in this interpersonal variation. Alarmingly, bacterial drug metabolism can modify drugs’ activity and toxicity, causing altered drug response and adverse effects. However, the extent, the mechanisms and the implications for human health of microbiome drug modulation remain understudied and largely neglected in preclinical drug research. Previous works demonstrated that several drugs can be metabolized by individual gut bacteria, thus raising the question of how these results translate to complex microbial gut communities, and to what extent the interpersonal differences in microbiome composition impact microbial drug metabolism. In this study, we set up an experimental in vitro model to systematically assess the occurrence and extent of variation of drug metabolism of gut communities derived from humans and the most common preclinical animal models. The data submission contains the following 3 entry files: myCompounds.sdf: contains the list of structures (in .sdf format) of the 276 drugs used to investigate human and animal gut microbiome biodegradation community_identifiers.csv: contains the correspondance table between the ENA id assigned to each metagenomic sample, its sample name (internal to the study), the taxonomic id according to NCBI taxonomy and its corresponding scientific name. activity_summary_table: contains the table describing each drug/sample combination including drug name, sample name (corresponding to that reported in community_identifiers.csv), the threshold used to call a drug as significantly biodegraded, a True/False column to identify the combinations representing a significant biodegradation event, and the corresponding initial slope, i.e. the initial rate of biodegradation observed.