a, Drugs from the Prestwick Chemical Library (arranged in either 96- or 384-well format) were diluted in growth medium (usually mGAM) and pre-reduced in a Coy anaerobic chamber before inoculation with one of forty different human gut microbes. Bacterial growth was monitored for 16–24 h at 37 °C. Growth curves were acquired at least in triplicate for each drug–microbe interaction (see Methods). b, Species with a minimum relative abundance of 1% in at least one sample and a prevalence of 50% across samples (the latter estimated by rarefying to 10,000 reads mapping to taxonomic markers) were included in the set of core species. Boxplots show relative abundances of core species grouped by genus (according to NCBI taxonomy) and coloured by phylum (see key). The inner box indicates the IQR, with the median as black vertical line; the outer bars extend to the 5th and 95th percentiles; circles, outliers. To the right of the boxplots, prevalence is depicted by bars, and next to this the species diversity is shown; grey boxes indicate species represented in the screen with box widths corresponding to mean relative abundance within the genus. c, Relative abundance of genera of which at least one species was represented in the screen cumulates to 78% of the assignable fraction of reads (median across all samples, upper panel); first four boxplots show abundance within each study identified by country codes underneath (DK: Denmark; ES: Spain; US: United States; CN: China) 43,44,45,46. When directly cumulating the relative abundance of represented species the corresponding median is 60% (lower panel). Boxes span the IQR and whiskers extend to the most extreme data points up to a maximum of 1.5 times the IQR. d, Core species are shown in the order of their median abundances across all samples. Relative abundance boxplots and prevalence bars are defined as in b and grey boxes underneath indicate species screened in this study. Numbers in brackets correspond to specI cluster identifiers (version 1)47.