Fig. 5

Representation of the use of empty compartments in studying the gut microbiota. The metabolic compartments indicated with grey squares are organized in a two-dimensional grid. Each bacterium has its own metabolic compartment. Exchange of metabolites takes place between the bacterium and its own metabolic compartment. Metabolic exchange can also take place between adjacent metabolic compartments. The metabolic compartments without any bacterium can still exchange metabolites with the adjacent compartments. In this way, metabolic gradients occur. Introduction of a time step to a grid of compartments gives the opportunity to include movement and division of bacteria. a Bacterial community at the start of a simulation, movement is indicated with black, curved arrows and division is indicated with grey arrows. b After a time step, some cells move and others divide, resulting in a different distribution of bacteria in the grid