Fig 1.
Intended workflow when using McComedy.
The modeler designs an individual-based model (IBM) by selecting process modules under consideration of the research question and the current understanding of the system. The parameter values that are necessary for the simulation of the selected processes are set by the modeler, e.g. according to experimental data or literature. The resulting IBM generates spatiotemporally explicit data of the modeled microbial system.
Fig 2.
McComedy can reproduce the results of experiments and simulations by Mitri et al. [17] both quantitatively and qualitatively.
Top views on colonies at different initial resource (nutrient) concentrations and degree of heterozygosity over the distance to the inoculum. The unit xLB is defined as the fold-concentration of LB medium. Blue and green colors on colony images indicate the two bacterial strains. White circles on the colony images indicate the inoculum. Red circles indicate where the demixing area begins. Analyses with McComedy were conducted after 45 simulated hours of growth. A: Stylized recreation of top views on colonies at different resource concentrations according to Figures 2a and 4a in [17]. B: Stylized recreation of the heterozygosity over distance from inoculum and corresponding demixing distances at different resource concentrations according to Figures 2c and 4b in [17]. Axis labels of distances are not shown as they varied between experimental and simulation results and were of no consequence for the qualitative pattern. C: Representive top views on colonies at different resource concentrations in the McComedy IBM. D: Heterozygisity over distance from inoculum and estimated demixing distances at different resource concentrations in the McComedy IBM. Images A and B were recreated due to copyright issues. Refer to Figures 2 and 4 in [17] to view the original data.
Fig 3.
Increased diffusion resulted in an increased demixing distance.
Simulations were performed with McComedy. Analysis after 39 simulated hours of growth. A: Top views on representative colonies as simulated using McComedy using different resource diffusion constants. Blue and green colors on colony images indicate the two bacterial strains. White circles on the colony images indicate the size of the inoculum. Red circles indicate where the demixing area begins. B: Heterozygosity over distance from inoculum and estimated demixing distance at different resource diffusion constants.
Fig 4.
McComedy reproduces qualitative results of experiments and simulations by Momeni et al. [16].
Vertical cross-section views on layers of yeast cells grown on media supplemented with lysine and adenine (+ LA) and on media without these resources (- LA). Red and green color indicates the two cooperative yeast strains, blue color indicates the non-cooperative yeast strain. Simulations performed with McComedy were visualized after 6 generations. A, C, E: Representative cross-sections of yeast cells grown with supplemented lysine and adenine (+LA) in the experiment, original IBM, and McComedy IBM, respectively. B, D, F: Representative cross-sections of yeast cells grown without lysine and adenine (-LA) in the experiment, original IBM, and McComedy IBM, respectively. Scale bar: 100 μm. Images A, B, C, D adapted from [16].
Fig 5.
McComedy reproduces quantitative results of simulations by Momeni et al. [16].
The quantitative metrics were assessed for yeast cells grown on media supplemented with lysine and adenine (+ LA) and on media without these resources (- LA). A, B: Association index of the two cooperative strains ( with
) and the non-cooperators C←L in the original IBM and McComedy IBM, respectively. C, D: Abundance ratio between the cooperators
and the non-cooperators C←L in the original IBM and McComedy, respectively. Note the logarithmic scales of the vertical axes. Images A, C adapted from [16].
Fig 6.
Reduced resource release rates increase abundance and intermixing of cooperators but also their generation time.
Simulations were performed with McComedy with varied resource release rates and all other parameter values corresponding to scenario without supplemented lysine and adenine (- LA) in Fig 5. At low resource release rates, not all simulated communities achieved six generations. Numbers indicate how many of the initial 10 simulations contributed to the data visualized in the same color, starting from the respective X-position. Ribbons indicate the standard deviation. A: Association index of the two cooperative strains ( with
) and the non-cooperators C←L. B: Abundance ratio between the cooperators
and the non-cooperators C←L. C: Mean time until respective generation time is reached. One generation corresponds to the biomass doubling time of the simulated community.
Table 1.
Process modules currently available in McComedy.
The columns SOM (Spatial organization model, Mitri et al. [17]) and CM (Cooperation model, Momeni et al. [16]) indicate with an ‘X’ which process modules were integrated in the corresponding McComedy models. A more detailed description of each process module is provided in the ODD protocol (S1 Text).