An agent-based simulator for microbial communities’ evolution

In this work, we blueprint a Dashboard which allows users to simulate bacterial community’s evolution through a intuitive GUI. The underlying Python-coded simulator implements an agent-based model of bacterial species, nutrients and environment, allowing full customization and upgradability of the tool, due to its intrinsic modularity. Specifically, the model aims to represent discretized spaces, hosting certain number of bacteria for each species and a defined amount of nutrients characterizing the surrounding environment. Bacteria can migrate from a spatial unit into another, looking for different nutrients (i.e., metabolites) across the whole space path. Their growth and survival are governed by their metabolism, which is in turn function of the metabolites present in each specific spatial unit at a certain time point. Thus, the simulator shows how bacteria consume and produce metabolites, following species-specific metabolism rules, letting the system dynamically evolve through bacterial growth, death, spatial migration and continuous updates of the available metabolites pool.