Lower bounding variability in microbiome acquisition and exponential growth

Microbiome composition 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. We examine two factors that contribute to variability in microbiome composition: (i) hosts are constantly exposed to microbial species that may or may not colonize their gut, and (ii) intrinsic variability in microbial division timing compounds to produce macroscopic variability in exponentially growing systems. Data from microbiome assembly in fruit flies and growth experiments in E. coli, S. aureus, and L. minor empirically demonstrate that replicates of identically prepared experimental systems are nonetheless variable. We employ theoretical microscopic models that lower bound the variability associated with these processes and show they are consistent with experiments. These findings yield design principles for microbiome-based therapies, while also placing limits on their efficacy.