How do organisms acquire their gut microbiomes?

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Synopsis

Gut microbiome composition--the ecosystem of bacteria that resides within our guts--influences host health, but we do not yet fully understand how microbiomes are assembled, nor how the vast diversity of microbiome compositions across individuals is maintained. A key aspect that contributes to variability in microbiome composition is that hosts are constantly exposed to microbial species that may or may not colonize their gut, leading to a combinatorially large number of possible microbiome compositions. We quantify this variability with data from microbiome assembly experiments in fruit flies, then characterize the process of stochastic microbiome assembly with mathematical models. Our findings yield design principles for microbiome-based therapies, while also placing limits on their efficacy.