Microbial communities associated with animals and plants (i.e., microbiomes) are implicated in the day-to-day functioning of their hosts. However, we do not yet know how these host-microbiome associations evolve. In this paper, we develop a computational framework for modelling the evolution of microbiomes. The models we use are neutral, and assume that microbes have no effect on the reproductive success of the hosts. Therefore, the patterns of microbiome diversity that we obtain in our simulations require a minimal set of assumptions relating to how microbes are acquired and how they are assembled in the environment. Despite the simplicity of our models, they help us understand the patterns seen in empirical data, and they allow us to build more complex hypotheses of host-microbe dynamics.
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