Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [10xGermfree]

Enteric neurons are essential regulators of intestinal physiology, yet their responses to varying microbial and immune environments along the intestinal tract and or during challenges remain poorly understood. Here, we regionally profile enteric neurons across gnotobiotic, allergic and parasite-infected mice. We demonstrate that timing and complexity of microbial perturbations and type 2 inflammation result in motor neuron state shifts and alter multiple functionally distinct sensory neurons, including IL-13- and leukotriene-responsive Nmu-hi cells and Grp-hi neurons, which expand in germ-free colonic tissue and interact with Grpr+ interstitial cells of Cajal. Leveraging AAV-based Perturb-seq to define genetic controllers of inhibitory motor neuron state transition, we identified Edf1 and Mitf as controllers of this program and of gastrointestinal transit time, directly linking enteric neuron states to physiology. Overall design: To understand the cellular context in which enteric neurons reside, large intestine tissues were harvested from a total of 6 mice for each group, germ free or SPF, and isolated cells were analyzed by droplet based single-cell RNA-seq.