Dynamics of colonization and phenotypic adaptations of commensal gut bacteria in larval zebrafish populations.

An organism's microbiome is assembled from the microbiotic environment that surrounds it. The likelihood of a microbe colonizing a host depends on factors such as microbial density, duration of exposure, and the microbe's ability to sense a potential host. A quantitative understanding of how these factors influence the likelihood of colonization is lacking, due in large part to the experimental challenges of controlling the source pool of colonizers and of detecting colonization state. We address this using larval zebrafish, an established model vertebrate system, implementing an imaging-based assay to study the dynamics of colonization by fluorescently labelled bacteria native to the zebrafish gut. We delineate the dependence of colonization probability on environmental bacterial concentration, and also compare colonization with the process of transmission of bacteria between host individuals. The latter reveals phenotypic adaptations that indicate 'memory' of gut residence that improves bacteria's ability to colonize a host.