Dynamics of commensal gut bacterial colonization in larval zebrafish populations

There is a constant flux of microorganisms between the guts of animals and the environment they live in. The ability of a microbe to colonize a host is influenced by microbial density, duration of exposure, movement both autonomous (motility) and externally driven (flow, diffusion), and direct and indirect transfer between host individuals. The relative importance of these transmission mechanisms is underexplored and poorly quantified, especially for commensal microbes of the intestinal microbiome. The larval zebrafish is an established model vertebrate system that allows for the controlled study of gut-associated microorganisms using optical microscopy. Here, we present an imaging-based assay to study the dynamics of colonization of larval zebrafish hosts by multiple species of fluorescently labelled bacteria. By assessing bacterial colonization in a large number of hosts, we extract statistical parameters such as colonization rate, and their dependence on temporal and spatial factors. We also show that there develop phenotypic variations between bacteria that have previously been inside zebrafish guts and those that have not, indicative of a bacterial ‘memory’.