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The intestinal tract contains over half of all immune cells and peripheral nerves and manages the beneficial interactions between food compounds and the host. Paramylon is a β-1,3-glucan storage polysaccharide from <i>Euglena gracilis</i> (<i>Euglena</i>) that exerts immunostimulatory activities by affecting cytokine production. This study investigated the signaling mechanisms that regulate the beneficial interactions between food compounds and the intestinal tract using cell type-specific calcium (Ca²⁺) imaging in vivo and in vitro. We successfully visualized <i>Euglena</i>- and paramylon-mediated Ca²⁺ signaling in vivo in intestinal epithelial cells from mice ubiquitously expressing the Yellow Cameleon 3.60 (YC3.60) Ca²⁺ biosensor. Moreover, in vivo Ca²⁺ imaging demonstrated that the intraperitoneal injection of both <i>Euglena</i> and paramylon stimulated dendritic cells (DCs) in Peyer’s patches, indicating that paramylon is an active component of <i>Euglena</i> that affects the immune system. In addition, in vitro Ca²⁺ imaging in dorsal root ganglia indicated that <i>Euglena</i>, but not paramylon, triggers Ca²⁺ signaling in the sensory nervous system innervating the intestine. Thus, this study is the first to successfully visualize the direct effect of β-1,3-glucan on DCs in vivo and will help elucidate the mechanisms via which <i>Euglena</i> and paramylon exert various effects in the intestinal tract.