Fig. 3

Metabolizing patterns of gut microbes from the best predictions of MicrobeRX. a General overview of drug distribution with the top best predictions for humans (blue), gut microbiota (orange), and both (gray). The top best predictions correspond to the high-confidence prediction (confidence score cutoff of ≥ 1.2) with the highest confidence score per drug–microbe pair. b The metabolic landscape of 6,286 strains included in MicrobeRX and what they can metabolize. The highest confidence scores for the prediction of each drug are plotted, showing both chemo-specific (group 1) and taxa-specific (group 2, strains of Bacillus cereus in the plot) metabolism patterns, as well as drugs that can be extensively metabolized (group 3). The heatmap is ordered based on clustering the drugs by the top best confidence score. The y-axis is organisms arranged alphabetically by phylum. The horizontal colored bars at the top of both plots indicate the drug superclass chemical classification and the anatomical therapeutic chemical (ATC) classification level 1. The molecules in the gray boxes exemplify the chemo-, taxa-, and extended-metabolism patterns. An example of the substructure modified during metabolism is colored in red