Investigation of Host–Microbe–Parasite Interactions in an In Vitro 3D Model of the Vertebrate Gut

Abstract In vitro models of the gut–microbiome axis are in high demand. Conventionally, intestinal monolayers grown on Transwell setups are used to test the effects of commensals/pathogens on the barrier integrity, both under homeostatic and pathophysiological conditions. While such models remain valuable for deepening the understanding of host–microbe interactions, often, they lack key biological components that mediate this intricate crosstalk. Here, a 3D in vitro model of the vertebrate intestinal epithelium, interfaced with immune cells surviving in culture for over 3 weeks, is developed and applied to proof‐of‐concept studies of host–microbe interactions. More specifically, the establishment of stable host–microbe cocultures is described and functional and morphological changes in the intestinal barrier induced by the presence of commensal bacteria are shown. Finally, evidence is provided that the 3D vertebrate gut models can be used as platforms to test host–microbe–parasite interactions. Exposure of gut–immune–bacteria cocultures to helminth “excretory/secretory products” induces in vivo‐like up‐/down‐regulation of certain cytokines. These findings support the robustness of the modular in vitro cell systems for investigating the dynamics of host–microbe crosstalk and pave the way toward new approaches for systems biology studies of pathogens that cannot be maintained in vitro, including parasitic helminths.