Glimpses of Gut Microbes in their Physical World
In any ecosystem, the physical structure of the landscape and the activities of its resident organisms influence one another. This holds in the vertebrate 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 how bacteria can manipulate intestinal mechanics to facilitate invasion, how antibiotics can cause collapses in gut populations in a manner reminiscent of gelation transitions in soft matter physics, and more. In all these cases, the physical structure of microbial groups emerges as a major determinant of their dynamics.