Imaging Bacterial Population Dynamics in the Zebrafish Intestine
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Every animal harbors a large community of microbes, the microbiota. Of particular importance is the intestinal microbiota, which plays a crucial role in the development and homeostasis of its animal host. Over the last several years researchers have been able to catalogue the diversity of bacterial species present in the microbiota. However, we lack an understanding of the spatial and temporal dynamics of these communities. The work in this dissertation aims to fill, in part, this gap in our knowledge. We use larval zebrafish (Danio rerio), an optically transparent model organism, which can be reared germ-free. Zebrafish are inoculated with fluorescently-tagged bacteria, allowing us to image the bacterial populations of the intestine. Imaging is accomplished using a home-built light sheet fluorescence microscope. This recently developed approach makes it possible to image biological samples with a speed, field of view, and level of phototoxicity unmatched by other techniques. Using this technique we are able to image the entire bacterial population of the zebrafish intestine, the first time this has been accomplished for a vertebrate intestine. Using computational image analysis we are able quantify the bacterial load in an intestine as a founding population of tens of bacteria grows to tens of thousands. We image the early colonization dynamics of Aeromonas veronii in the intestine and have found that there is heterogeneity in the growth dynamics of this species, in which populations of clusters of bacteria grow faster than individual bacteria. We further find that this growth rate is not surface-mediated but results from a higher bulk growth of this population. We have also undertaken studies to investigate the dynamics of interspecies competition. Established populations of A. veronii are challenged with a population of Vibrio, a species which is known to outcompete A. veronii in the intestine. We find that these two species respond dramatically differently to environmental perturbations from the host, with A. veronii experiencing random population collapses to which Vibrio is relatively immune. These observations point the way towards discovering how the physical environment of the host can shape competition in the microbiota. This dissertation includes previously published and unpublished co-authored material.