Observing the interplay between bacterial behaviors and the physical landscape inside the zebrafish gut

In any ecosystem, the structure of the landscape and the activities of its organisms influence one another. This is true in the vertebrate gut as well, where vast numbers of microbes cooperate, compete, and influence both normal and disease-related functions of their hosts. In gut ecosystems, however, we know little about spatial structure, bacterial behaviors, and physical forces. Most of our knowledge comes from sequencing-based studies lacking spatial or temporal information, severely limiting our ability to understand, let alone manipulate, the gut microbiome. To address this, my lab applies light sheet fluorescence microscopy to a model system that combines an in vivo environment with a high degree of experimental control: larval zebrafish with defined sets of bacterial species. I will describe this approach and experiments that have revealed how a species can manipulate intestinal mechanics to facilitate invasion; how differences in bacterial behaviors across species correlate with differences in spatial distributions; and how genetic switches and antibiotics can reveal the roles of individual behaviors such as motility in governing community outcomes. In all of these cases, the physical structure of the microbiome emerges as a major determinant of its population dynamics.