Fig. 5: The gut biofilm simulations with three bacterial species.

The third bacteria (red) are introduced at t = 25 h, during the two-species biofilm growth (brown and green). a Schematic of the metabolic relationships and the morphology of biofilms at t = 120 h. The notations (p) and (s) indicate the competition over metabolites produced by bacteria and bulk nutrients, respectively. The initial number of bacteria is 200, and the population of the invading bacteria is 100. The bacterial kinetics parameters are the same as the baseline simulation (Fig. 1, also refer to Supplementary Table 1). b Temporal changes of biomass and the relative abundance of brown and red bacteria within biofilms.