Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia

Abstract

Bacteria often grow as communities in intricate spatial arrangements on surfaces and interact with each other through the local exchange of diffusible molecules. Yet, our understanding of how these metabolite exchanges shape the properties of the communities remains limited. Here, we study synthetic communities of Escherichia coli amino acid auxotrophs interacting through the obligate exchange of amino acids. We genetically engineer these strains to alter their amino acid leakage and uptake abilities. We then characterise the spatial arrangement and composition of the communities when grown on a surface and compare these to qualitative predictions of a previously developed analytical model for cells growing in two dimensions. Our experiments provide empirical validation of the model’s central hypothesis: higher uptake rates reduce sector widths and promote mixing, while increased leakage rate of an amino acid increases the frequency of the strain benefiting from this amino acid. We thus extend the relevance of this simplified model to more complex, three-dimensional systems, while also identifying its limitations. Our findings provide critical insights into microbial community dynamics and establish a predictive framework for designing and engineering microbial consortia.