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Glimpses of Gut Microbes and their Physical Concerns

In any ecosystem, the physical structure of the landscape and the activities of its resident organisms influence one another. This holds in the gut as well, where legions of microbes cooperate, compete, and influence the health of their hosts. In intestinal ecosystems, however, we know little about the spatial structure, bacterial behaviors, and physical forces present, severely limiting our ability to understand and eventually engineer the gut flora. To address this, my lab applies light sheet fluorescence microscopy, an optical technique that enables high-speed, high-resolution three-dimensional imaging, to larval zebrafish, a model organism that enables a high degree of experimental control. I will describe this approach and experiments that have revealed that bacteria can manipulate intestinal mechanics to facilitate invasion, that antibiotics can cause collapses in gut populations by altering bacterial shape, and that ideas from polymer physics can help make sense of bacterial aggregation. In addition to illustrating the biophysics of the gut microbiome, I'll describe some of the broad themes of biophysics in general, and why it's such a vibrant field.

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