Raghuveer Parthasarathy

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  Visualizing microbial population dynamics in the larval zebrafish gut
  Raghuveer Parthasarathy
  In each of our digestive tracts, trillions of microbes representing hundreds of species colonize local environments, reproduce, and compete with one another. The resulting ecosystems influence many aspects their host’s development and health. Little is known about how gut microbial communities vary in space and time: how they grow, fluctuate, and respond to perturbations. To address this, we apply light sheet fluorescence microscopy to a model system that combines a realistic /in vivo/ environment with a high degree of experimental control: larval zebrafish with defined subsets of commensal bacterial species. Light sheet microscopy enables three-dimensional imaging with high resolution over the entire intestine, providing visualizations that would be difficult or impossible to achieve otherwise. Quantitative analysis of image data enables measurement of bacterial abundances and distributions and the construction of realistic models of population dynamics. I will describe this approach and focus especially on recent experiments in which a colonizing bacterial species is challenged by the invasion of a second species. Imaging reveals dramatic population collapses driven by peristaltic activity, which differentially affects the two species due to their distinct community architectures. Our findings demonstrate that stochastic perturbations and the physical properties of the host environment can play major roles in determining population dynamics in the vertebrate gut.