Resolving microbiome dynamics and host feedback mechanisms in the fruit fly gut with confocal microscopy

The gut microbiome is essential to the host, yet current methods for studying the gut microbiome rely primarily on sequencing to classify which bacterial species are present. However, this method obliterates information about the gut's microbial spatial structure which is crucial to understanding the ecological dynamics within microbiomes. In our research, we investigate the role of peristalsis, muscle contractions that drive fluid flows in the gut, in shaping the spatial organization of the gut microbiome. Since peristalsis is affected by hormone levels, we hypothesize that neurotransmitters—particularly dopamine —modulate the feedback loop between gut microbiota and the enteric nervous system. We will directly image the microbial dynamics in the crop of live fruit flies with confocal microscopy to quantify how neurotransmitter signaling affects gut microbiome composition, with implications for broader host-microbe interactions.