Emergence of alternative states in a synthetic human gut microbial community

Several human-associated microbial communities exist in multiple configurations and can change their composition in response to perturbations, remaining in an altered state even after the perturbation ends. Multistability has been previously proposed to explain this behavior for gut microbiota in particular, but has not been clearly demonstrated experimentally. Here, we first investigate the life history strategies of three common human gut bacteria to identify mechanisms driving alternative states. We then use this data to build and parameterize a kinetic model, which predicts that alternative states emerge due to phenotype switching between subpopulations of the same species. Perturbation experiments support these predictions, and confirm the existence of alternative states. Finally, simulations show that phenotype switching can also explain alternative states in larger communities. Thus, a transient perturbation combined with metabolic flexibility is sufficient for alternative communities to emerge.