Targeted Neuronal Activation of the Gastrointestinal Tract Shapes the Environment of the Gut in Mice

The enteric nervous system (ENS) integrates cues from the brain and from local signals in the gut to coordinate responses that shape the intestinal milieu. Tools to study, and knowledge of, the ENS lag behind brain research. Herein, we deploy novel recombinant adeno-associated viral (rAAV) vectors with enhanced tropism for the gut to map and activate enteric neurons with spatial and temporal resolution. rAAV-mediated fluorescent labelling coupled with whole-tissue clearing methods in the small intestine and colon of mice enables efficient and thorough characterization of the neuronal architecture of the ENS. We also delivered designer receptors exclusively activated by designer drugs (DREADDs) to specifically activate gut neurons that express choline acetyltransferase (ChAT+) and tyrosine hydroxylase (TH+). Targeted activation of ChAT+ or TH+ neuronal populations associated with the gastrointestinal (GI) tract altered the intestinal transcriptome of mice, host and microbial proteome, metagenome, and fecal metabolome. We reveal previously unknown and broad roles for neurons in modulating intestinal physiology, mucosal immunity, and gut microbiome structure, and propose novel interactions for the ENS such as regulating fungal colonization and shaping of bile acid profiles. Experimental tools and rich datasets with multi-parameter characterization of the gut ecosystem may enable further study of the ENS.