Extended Data Fig. 1: Auxotrophs are prevalent in drug-exposed natural and synthetic microbial communities and more drug resilient.
(a) Frequency of amino acid auxotrophies across gut microbiome species, using the procedures in1. (b) Frequency of amino acid auxotrophies per gut microbiome auxotrophic species. (c) Growth, as measured by AUC, in drug exposed gut microbiome species across drug classes and metabolic background (auxotrophy vs prototrophy); n = number of drug-microbe pairs in each subset. (d) Screen setup, scoring and identification of drugs that modulate the auxotrophic composition in SeMeCos. Drug hits are identified by a high Z-score that indicates a significant shift in the SeMeCo composition compared to DMSO baseline. (e) Growth, as measured by AUC, in prototrophs and auxotrophs treated with drugs common to both the SeMeCo and gut microbiome drug screens, from Cluster 1 or 2 in the SeMeCo screen (e); n = number of drug-microbe pairs in each subset. (f) Flow cytometric analysis of the SeMeCo composition upon drug treatment, where red and blue indicate the relative increase or decrease, respectively, of a specific auxotrophic subpopulation (count of subpopulation/ total count). Median: n = 3 technical replicates within an independent experiment. Statistics by (c and f) two-sided Wilcoxon Rank Sum test, P-values are listed in the respective Source Data.
