Intestinal organoid models as tools to interrogate the physiology of human mucosal tissues and host-microbe interactions

The intestinal epithelium serves as a critical interface between the external environment and internal tissues, coordinating nutrient absorption, immune defense, and barrier integrity. Discerning the processes that maintain gut homeostasis has been challenging due to the complexity of the intestinal microenvironment and the difficulty in accessing human tissue. The advent of human intestinal organoid technology has transformed the field by providing relevant in vitro models that recapitulate the cellular diversity and function of the gut epithelium. A recent advance involves the integration of immune cells into organoid cultures, enabling the study of epithelial-immune cell interactions in both health and disease. Furthermore, the application of cutting-edge multi-omics approaches, including transcriptomics, proteomics, and metabolomics, has enabled a deeper understanding of intestinal cell signaling, niche factors, and host-microbe dynamics. These innovations have led to breakthroughs in translational research, particularly in the field of precision medicine. This minireview highlights how intestinal organoids derived from human tissue stem cells, coupled with high-resolution omics technologies, are advancing our knowledge of intestinal physiology, host responses, and disease mechanisms. It also describes the emergence of patient-derived organoids as tools to guide personalized therapeutic strategies for conditions such as inflammatory bowel disease and cystic fibrosis. As organoid models continue to evolve, the integration of additional tissue components-such as diverse immune cell lineages, stromal elements, vasculature, neural cells, and microbiota-will more accurately replicate the intricate nature of human physiology and broaden their translational potential.