Fig. 1

Virtual Microbes model overview. a At the basis of the Virtual Microbe model is an artificial “metabolic universe”, describing all the possible reactions that can be catalysed. Resources (yellow and blue) are fluxed in, but building blocks (purple) and energy (red) must be synthesized to express proteins and transport metabolites across the membrane, respectively. b A Virtual Microbe only needs to express a subset of all possible reactions to be viable, and no metabolic strategy is necessarily the “right” one. c The individuals grow and reproduce on a spatial grid, and can only reproduce when there is an empty spot. Death happens stochastically or when a cell has accumulated toxicity by having excessively high concentrations of metabolites. Since only cells that have grown sufficiently are allowed to reproduce, we simulate evolution with no prior expectation