Fig. 2: Simulations based on an agent-based and metabolic model capture overall colony expansion dynamics.

a–c The different cell growth and maintenance modes included in our model: aerobic growth and maintenance on glucose (a), anaerobic growth and maintenance on glucose (b), and aerobic growth and maintenance on acetate (c). Anaerobic consumption of glucose by cells is accompanied by acetate excretion indicated by the red arrow in (b). Even under aerobic growth on glucose, cells still excrete a small amount of acetate (not indicated) due to overflow metabolism which is also included in our model. d Illustration of the computational domain comprising of the colony, agar, and air sub-domains with appropriate boundaries between the sub-domains. e A template reaction-diffusion equation used to model the spatiotemporal dynamics of metabolite concentrations. f Illustration of agent-based model features involving individual cell growth, division, and movement. The forces experienced by the cells arise from cell-cell, cell-agar interaction as well as surface tension. g–l Dynamics of (1 + 1)-dimensional agent-based simulations of colony expansion for different initial glucose concentrations in agar. Simulations start with a single cell on top of an agar region with dimensions of ~10 mm×8 mm. The cross-sectional profile of a simulated colony with 10 mM (g), 20 mM (h), and 30 mM (i) initial concentration of glucose in agar, at various times (coded by color) of colony development. j–l The radius (μm) (j), height (μm) (k), and number of cells (l) in simulated colonies plotted against the time (h) post-inoculation. j–l Brown, cyan and black symbols represent simulations with 10 mM, 20 mM and 30 mM initial glucose concentration in agar respectively.