Genome-scale simulations of <i>Escherichia coli</i> colony morphologies and genetic demixing

Bacterial colonies exhibit diverse morphologies that range from smooth disks to complex branched patterns. The effect of such morphological changes on evolutionary and ecological dynamics remains largely unexplored. Here, we study how environmental factors and metabolic strategies affect morphology and genetic diversity via simulations in COMETS (Computation Of Microbial Ecosystems in Time and Space). The COMETS software integrates genome-scale modeling of bacterial metabolism, nutrient diffusion, and cellular motility, which together capture the key factors that control colony morphology. Indeed, our simulations based on core metabolism of Escherichia coli showed good agreement with experimental data across nutrient and agar concentrations. We found that dendritic morphologies greatly promote genetic demixing and often produce monoclonal branches. The transition from high to low degree of genotype mixing can be controlled by tuning other external factors such as oxygen or altering cellular metabolic pathways. Taken together our findings show that realistic metabolic modeling could be essential for the understanding of population dynamics in microbial colonies.