Watching Gut Microbes Swim, Stick, and Survive*

In your gut, as in the gut of every animal, legions of microbes cooperate, compete, and influence their host’s health. Conventional approaches for studying the intestinal microbiome reveal its constituent species and their constituent genes, and suggest biochemical networks that govern microbial activities. While such approaches have yielded profound insights, they are largely blind to the spatial structure, individual behaviors, and physical forces present in the gut -- factors that, as in every ecosystem, should be major determinants of function. 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, how antibiotics can cause collapses in gut populations by altering bacterial community morphology, and how the host immune system might sense bacterial activity. In all these cases, the physical structure of microbial groups, especially their aggregation state and its coupling to intestinal transport, emerges as a major determinant of microbial population dynamics.