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

Abstract

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.

Keywords: host response; human intestinal model; intestinal physiology; multi-omics; organoids; translational research.

Fig 1

Human intestinal organoids and applications. (A) Intestinal crypts containing stem cells are isolated from resected or biopsied tissue and embedded in ECM along with organoid culture media. These cultures develop into enteroids or colonoids, depending on the intestinal segment, forming 3D cystic structures with the luminal compartment inward. The epithelial layer of these structures is typically enriched with stem cells and Paneth cells, closely resembling a crypt-like epithelium. Differentiation of enteroids and colonoids is induced by withdrawing key stem cell-supporting signals (i.e., Wnt and R-spondin1) from the culture media. (B) Research has focused on characterizing the intestinal niche microenvironment to enhance in vitro expansion and differentiation of intestinal organoids. Because human intestinal organoids preserve age- and segment-specific features of the donor tissue, they have been utilized to study the physiology of rare epithelial cell populations. (C) Human intestinal organoids are useful to study host-pathogen interactions using various platforms, such as gut-on-a-chip systems or semipermeable tissue culture inserts. The incorporation of immune cells further increases the complexity of these models. Organoids co-cultured with autologous immune cells facilitate the investigation of immune-mediated diseases and tumor biology. (D) Patient-derived organoids enable the evaluation of personalized and effective therapeutics. The integration of human intestinal organoids with multi-omics approaches empowers research from basic discovery to clinical applications. Figure created in BioRender (J. Lemme, 2025, https://BioRender.com/6mz0ng3).

Fig 2

Future directions and outstanding challenges. (A) Overview of the principal insights and conclusions presented in this minireview. (B) Summary of the key technical hurdles that remain to be addressed in the development and application of intestinal organoid models. (C) Unresolved questions and emerging areas of inquiry within the field.