Raghuveer Parthasarathy Ph.D., University of Oregon
In each of our digestive tracts, trillions of microbes representing hundreds of different species colonize local environments, reproduce, and compete with one another. Little is known about the physical structure and temporal dynamics of gut microbial communities: how they grow, fluctuate, and respond to perturbations. To address this and investigate microbial colonization of the vertebrate gut, my lab applies 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 with other techniques. I will describe this approach and focus especially on experiments in which a colonizing bacterial species is challenged by the invasion of a second species, which leads to the decline of the first group. We find that responses of bacteria to the mechanical contractions of the gut, and to contact-mediated inter-bacterial killing, can dictate apparent competition between microbes, suggesting a major role for physical mechanisms in guiding the composition of the gut micro biota.