The GI tract is the largest and most complex organ system in the human body with several different compartments and multicellular structures. Inside the GI tract, the small intestine is vital for digestion, nutrient absorption, and pathogen defense. The cell diversity, multiplex cell to cell signaling pathways, and its selective epithelial permeability has made small intestinal epithelial cells extremely difficult to be cultured as primary cells in vitro. Beginning in 2009, based on the discovery of Lgr5+ stem cells, Sato et al. successfully developed the method for long term culturing of three dimensional self-assembled organoids in which a matured cellular network was built based on cell to cell signaling and cell-ECM interactions. With the proper addition of cytokines to organoids, M cells can be induced with RANKL. Thus, organoids possessing M cells are an even more accurate model for studying antigen uptake associated with viral/bacterial infections. The general introduction of organoids formation, applications, and advantages/disadvantages are well-explained in Chapter 1.

The correct epithelial cell alignment and turnover rate, non-cancerous origins, lumen formation, and the ability of M cell and Tuft cell differentiation have made organoids the most ideal model to study epithelial cells, host-microbiome/pathogen interactions and application to studies in the fields of toxicology and nutrition. In Chapter 2, by using intestinal organoids as a health intestinal epithelium model, it showed that 50 μg/mL Bi2Te3 exerts minimum influence on shrinking crypts and disrupting lumen structure, which causes unhealthy growth. In Chapter 3, the effects of vitamin C (ascorbic acid), vitamin B3 (niacin), and microbiota differences on intestine have been studied by using four types of intestinal stem cells. In Chapter 4, by using the M cell differentiated organoids model, artificial virus-like nanocarriers (AVNs) functionalized with protein σ1 MRV receptor were created. It effectively utilizes M cells for transport across intestinal monolayers, which proven the possibility for antigen delivery through M cells into the gut-associated lymphoid tissue (GALT). In order to solve the issue of inaccessibility of lumen/apical membrane of the epithelial cells during modeling the host-microbe interactions and transport, Chapter 5 developed a method to deliver EcN to the luminal side of organoid via polymeric Ig receptor (pIgR)-mediated transcytosis.