Abstract

Interest in modeling microbial communities has been growing, because the resulting predictive power can impact several applications: from alternative treatments of infections to sustainable removal of environmental toxins. There are several ways to model microbial interactions and community traits. The two broad categories of modeling are agent-based models that follow the interactions among individuals versus population-level models that use the abundance of each population as the main factor that influences other populations. In both of these categories of modeling, the use of differential equations offers a path to capture major processes of interest. These processes could include interactions among microbes through diffusible metabolites or dispersal of species in the environment. Here, we first survey some of the models that employ ordinary and partial differential equations. We then focus on two particular examples: (1) an agent-based model of spatial self-organization and (2) a population-level mode of spatial coexistence to elaborate some of the implementation details.