Bacterial cohesion predicts spatial distribution in the larval zebrafish intestine

Are there general biophysical relationships governing the spatial organization of the gut microbiome? Despite growing realization that spatial structure impacts microbial ecological dynamics, it is unclear in any animal gut whether structure is governed by predictive, unifying rules, of if it results from contextual, species-specific behaviors. I’ll present work that explores this question through light sheet fluorescence microscopy of live, larval zebrafish that are raised germ-free and then associated with model microbial communities consisting of fluorescently tagged, symbiotic bacteria. Through comparative study of seven different species in isolation, we uncovered an unexpected and striking correlation between bacterial cohesion—the degree to which bacteria auto-aggregate—and position along the length of the intestine. We propose that this relationship emerges from the mechanical response of communities to flows generated by peristaltic contractions, and test this idea with genetic and antibiotic perturbations that modulate bacterial cohesion. The generality of this phenomenon points to bacterial cohesion as an ideal target for precision microbiome engineering.