I decided to make a version of the abstract for my upcoming presentation at the March Meeting of the American Physical Society that (i) has a movie, and (ii) is revised slightly from the version I submitted a few months ago. My talk is one of two invited talks at a pair of focus sessions on The Physics of Microbiomes and Microbial Communities organized by Yang-Yu Liu. It’s Tuesday, March 5, 2019, 11:15 AM–11:51 AM, BCEC Room: 259A; Abstract F63.0001. Here’s the new & improved abstract:
Bacterial behaviors and the physical landscape of the zebrafish gut
In any ecosystem, the structure of the landscape and the activities of its resident 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 intestinal ecosystems, however, we know little about spatial structure, bacterial behaviors, and physical forces. The sequencing-based methods that underlie most studies of the gut microbiome are cannot provide spatial or temporal information, severely limiting our ability to understand, let alone manipulate, the gut flora. 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 antibiotics can alter the dynamics of aggregation and cause collapses in gut populations. In all these cases, the physical structure of the microbiome emerges as a major determinant of its dynamics. The animal-associated microbiome, I claim, is an enticing and underexplored frontier for biophysics.
Today’s illustration
I haven’t made a drawing for this post, but there’s a movie!
Caption: Real-time, false-color movie of a Plesiomonas species (ZOR0011) in part of the midgut of a 5-day old zebrafish. This bacterial species exists mostly in large, non-motile aggregates, but sometimes motile subpopulations are evident, as in this fish’s midgut. (The talk will feature many more movies, especially involving bacterial population collapses and antibiotic perturbations.)
The Eighteenth Elephant 