Zebrafish harbor diverse intestinal macrophage populations including a subset intimately associated with enteric neural processes.

Intestinal macrophages are essential for gut health but remain understudied outside of human and mouse systems. Here, we establish zebrafish as a powerful model that provides superior imaging capabilities for whole-gut analysis along all dimensions (anterior-posterior and center-outer axes) for dissecting macrophage biology in gastrointestinal health and disease. We utilized high-resolution imaging to show that the zebrafish gut contains muscularis and mucosal macrophages, as well as surprisingly large subsets intimately associated with enteric neural processes. Interestingly, most muscularis macrophages span multiple gut layers in stark contrast to their mammalian counterparts typically restricted to a single layer. Using macrophage-deficient zebrafish, we found a depletion of muscularis but not mucosal macrophages, and that they may be dispensable for gross intestinal transit in adults but not during development. These characterizations provide first insights into intestinal macrophages and their association with the enteric nervous system from development to adulthood in teleosts.