Models of microbiome evolution incorporating host and microbial selection

Background Numerous empirical studies suggest that hosts and microbesexert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbesunder selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbesrandomly from parents and/or from the environment. Additionally, the environmental pool of available microbeswas constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation.