FIG 1.

Simulating multi-omic data with a dynamic multispecies genome-scale framework. (A) Community species abundances throughout a single 10-species simulation run. Abundances were quantified in units of microbial biomass. In this simulation, community composition was initialized with a high relative abundance of Eubacterium rectale. For visual clarity, only every eighth time step is illustrated. Species abundances at the final time point (highlighted with larger colored circles) were used for calculating species-metabolite correlations. (B) Cumulative secretion and uptake of acetate by each community member, throughout the same simulation run as that illustrated in panel A. Acetate was synthesized by several species and consumed by E. rectale over the course of the simulation. Cumulative fluxes at the final time point (highlighted with larger colored circles) were used for calculating species contributions to metabolite variation. The bottom plot illustrates the resulting environmental concentration of acetate at each time point. The metabolite concentration at the final time point (highlighted with a larger black triangle) was used for calculating species-metabolite correlations.