Responses of intestinal organoids to infection by Mycobacterium avium resemble symptoms observed in Crohn’s disease

Crohn’s disease (CD) is a chronic inflammatory bowel disease (IBD) in humans. Mycobacterium avium, which causes Johne’s disease in ruminants, has been suggested as a potential CD trigger due to similar pathology. However, early epithelial responses to M. avium and their relevance to CD remain unclear. This study aimed to establish a mouse small intestinal organoid (mSIO) model of M. avium infection and assess whether the resulting epithelial and immune responses resemble CD-related inflammation. M. avium-infected mSIOs were analyzed using confocal microscopy, serial block-face scanning electron microscopy, and a macrophage co-culture system to observe bacterial localization and immune cell behavior. RNA-seq and Gene Set Enrichment Analysis (GSEA) were performed to assess transcriptional changes. Comparative transcriptomic analysis was performed against a previous published RNA-seq dataset from gut tissues of germ-free mice colonized with microbiota from CD patients. M. avium efficiently infected mSIOs, disseminated through the tissue and triggered macrophage migration and clustering around infected organoids. Transcriptomic profiling revealed strong upregulation of inflammatory genes and enrichment of pro-inflammatory pathways such as TNF-α signaling. Comparative analysis revealed significant overlap in gene expression profile between M. avium-infected mSIOs and intestinal tissues of CD-humanized mice, including shared enrichment of the IBD signaling pathway. Notably, Mmp7, involved in epithelial remodeling and inflammation, emerged as a common marker in both models. This study presents a robust mSIO model of M. avium infection that replicates key features of CD-associated inflammation. The model presents a useful tool for studying host-pathogen interactions and identifies Mmp7 as a molecular link between bacterial infection and CD-like pathology.