Abstract
BackgroundMetabolic dependencies between microbial species have a significant impact on the assembly and activity of microbial communities. However, the evolutionary origins of such dependencies and the impact of metabolic and genomic architecture on their emergence are not clear.ResultsTo address these questions, we developed a novel framework, coupling a reductive evolution model with a multi-species genome-scale metabolic model to simulate the evolution of two-species microbial communities. Simulating thousands of independent evolutionary trajectories, we surprisingly found that under certain environmental and evolutionary settings metabolic dependencies emerged frequently even though our model does not include explicit selection for cooperation. Evolved dependencies involved cross-feeding of a diverse set of metabolites, reflecting constraints imposed by metabolic network architecture. We additionally found metabolic ‘missed opportunities’, wherein species failed to capitalize on metabolites made available by their partners. Examining the genes deleted in each evolutionary trajectory and the deletion timing further revealed both genome-wide properties and specific metabolic mechanisms associated with species interaction.ConclusionOur findings provide insight into the evolution of cooperative interaction among microbial species and a unique view into the way such relationships emerge.
Highlights
Metabolic dependencies between microbial species have a significant impact on the assembly and activity of microbial communities
A framework for modeling the evolution of species interactions To study the emergence of metabolic species interaction in bacteria we developed a computational framework that integrates models of microbial co-evolution, metabolic activity, and ecological interaction (Fig. 1)
On average, are the sets of genes retained between the two partners in each community, we found that cooperating partners were less similar to each other than independent partners, suggesting that the evolution of metabolic dependency is associated with a process of functional diversification (Additional file 1: Supporting Text)
Summary
Metabolic dependencies between microbial species have a significant impact on the assembly and activity of microbial communities. The various species that form these communities share a common environment, but rather interact with other community members in various ways including competition for extracellular nutrients, cooperation through metabolite cross-feeding, signaling, biofilm formation, and antimicrobial secretion [2, 3]. Such interactions allow community members to impact each other’s behavior and play an important role in shaping community structure and activity.
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