Wild-type and SeMeCo yeast proteomes with microFlow-SWATH & DIANN

Proteomic analysis of FACS-sorted and unsorted auxotrophic amd prototrophic subpopulations inSelf-establishing metabolically cooperating (SeMeCo) and control wild-type yeast communities. Microbial communities are composed of cells of varying metabolic capacity and regularly include auxotrophs; cells that lack essential metabolic pathways. By analysing auxotrophs for amino acid biosynthesis pathways in microbiome data microbiome data derived from over 12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and studying auxotrophic-prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites, and in this way metabolite-enrich the community environments. Moreover, the increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels that are above the minimal inhibitory concentrations. For example, the antifungal action of azoles is greatly diminished in auxotrophs and prototrophs that uptake metabolites from a metabolically enriched environment. Our results hence show why cells are more robust to drug exposure when they interact metabolically.