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. The animal-associated microbiome, I claim, is an enticing frontier for biophysics.
Raghuveer Parthasarathy received his undergraduate degree in Physics from the University of California at Berkeley and a Ph.D. in Physics from the University of Chicago, where his dissertation work examined self-assembled nanocrystal arrays. He then returned to Berkeley as a Miller Research Fellow and postdoctoral fellow in the Department of Chemistry, exploring lipid and protein membranes. In 2006 he joined the faculty at the University of Oregon, where he is presently a Professor of Physics. His research focuses on biophysics, especially the structure and dynamics of multicellular communities, which his lab explores using techniques such as three-dimensional microscopy. His teaching primarily involves courses for non-science majors, such as a â€œbiophysics for non-scientistsâ€ class . He was born in Mysore, grew up mostly in southern California, and knows just enough Tamil to slowly read signs and elicit laughter if he tries to speak.