Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance

Abstract

Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of 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, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically.

Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan

“…It has so far been debated if unicellular organisms would profit from a longer lifespan and if they have been selected for longevity 83 . Our study does not address this question directly, but it reveals an interesting new possibility, in the light that a vast majority of natural microbial communities contain auxotrophs 38,74 . Evolution could increase longevity by selecting for populations of cells that metabolically interact in a way that they generate a protective exometabolome.…”

“…The generation and culture of SeMeCos was performed as previously described 38 . The pH, pL, pU and pM plasmid used to generate a SeMeCo strain in the BY4741 background are described in Table S3.…”

“…Once a cell has started to uptake extracellular metabolites, its own biosynthetic pathways typically become inhibited 32,34 . As a consequence, metabolic and physiological properties that also impact ageing, such as growth rate, stress tolerance, or the formation or consumption of metabolites such as NADPH, are altered depending on the uptake of metabolites 32,[35][36][37][38] . For example, cells that uptake lysine from the environment mount better protection against oxidants, via increased pools of NADPH 37 , and cells that rely on the uptake of amino acids, including histidine, leucine, and methionine, are more drug tolerant 38 .…”

Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

“…S1E). (Yu et al, 2022) This suggested that metabolite sharing is more effective at overcoming the loss of MET17, at least when compared to the other three other auxotrophies. In order to understand the role that metabolite sharing plays in overcoming the loss of MET17 in the SeMeCo system, we recorded the metabolic profiles of SeMeCos by LC-SRM and compared these against the metabolic profiles of prototrophic communities.…”

“…We have previously generated proteomes from sorted auxotrophs and prototrophs from SeMeCo cultures (Yu et al, 2022). To distinguish auxotrophs from prototrophs, we used cosegregation of cyan fluorescent protein (CFP) with the relevant auxotrophic marker expressed from the same plasmid (PRIDE project: PXD031160).…”