"Drivers of within- and between-host diversity during stochastic microbial community assembly"Marrec, LoïcThe composition of host-associated microbial communities differs within and between individuals. Experiments have shown that both within- and between-host diversity may emerge during the community assembly. To better identify the mechanisms under which this diversity emerges, we build a model accounting for two events: the dispersal of microbes from a microbial pool to hosts, and intra-host division. For the minimal case of two strains, we combine analytical and numerical approaches to quantify the probability that the strains co-exist. After showing why stochasticity matters in microbial community assembly, we demonstrate that the timescales associated with dispersal and intra-host division play a crucial role in the emergence of within- and between-host diversity. In particular, if the dispersal timescale is much longer than the intra-host division timescale, most hosts are colonized with only one strain. Conversely, if the dispersal timescale is much shorter than the intra-host division timescale, most hosts are colonized with both strains. We consider additional cases in which both strains have different dispersal and intra-host division rates and determine how these two traits shape the diversity of microbial communities during their assembly. Our work shows how stochasticity, timescales, and traits jointly shape within- and between-host diversity during microbial community assembly, allowing for a better understanding of microbiome formation. |
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