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The host–microbe interaction is critical for intestinal homeostasis. By‐products from microbial metabolism of unabsorbed dietary components have been studied increasingly as potential contributors to health and disease. In vitro fermentation systems provide a way to simulate microbial activity and by‐product production of the colon using human fecal samples. Objectives of the study were to determine how clarified supernatants from two different fermentation conditions affect markers of cell proliferation, differentiation, barrier function, and immune function in a human‐induced pluripotent (iPSC) colon organoid model. SCFA and BCFA's of the supernatants were analyzed and were similar to known in vivo concentrations. Molecular results showed 25% of the clarified supernatant from batch fermentation led to a more physiological intestinal phenotype including increased markers of differentiation, including alkaline phosphatase, chromogranin A, SCFA transport monocarboxylate transporter‐1, (6.2‐fold, 2.1‐fold, and 1.8‐fold, respectively;  p  < 0.05). Mucin production (mucin‐2, mucin‐4) was increased in cells treated with 25% supernatant, as observed by confocal microscopy. In addition, increased tight junction expression (claudin‐3) was noted by immunofluorescence in 25% supernatant‐ treated cells. A dose–response increase in barrier function was observed over the 72‐h time course, with a twofold increase in transepithelial electrical resistance (TER) in the 25% group compared to the control group ( p  < 0.05). To further investigate host effects, clarified supernatants from a continuous multistage fermentation representing the ascending (AC), transverse (TC), and descending (DC) colonic domains were utilized and some regional differences were observed including increased markers of inflammation (IL‐1β, 6.15 pg/ml; IL‐6, 27.58 pg/ml; TNFα, 4.49 pg/ml;  p  < 0.05) in DC‐treated samples only. Overall, clarified supernatants represent a valuable model to examine effects of microbial by‐products on host intestinal development and function and future efforts will be designed to further understand microbial communities and metabolites, along with additional host response measures.

Human iPSC colon organoid function is improved by exposure to fecal fermentates