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). Mycobacterium avium, which causes Johne’s disease in ruminants, has been suggested as a potential CD trigger due to shared pathology, but early epithelial responses remain unclear. This study established a mouse small intestinal organoid (mSIO) model of M. avium infection to assess CD-related inflammation. Infected mSIOs were examined by confocal microscopy, block-face scanning electron microscopy, and macrophage co-culture to track bacterial localization and immune cell behavior. The data give unprecedent dynamic and super high resolution insights in the responses of gut cells to mycobacterial infection. RNA-seq with GSEA revealed strong induction of inflammatory genes and enrichment of pro-inflammatory pathways. Comparative analysis with CD-humanized mouse data showed overlapping gene expression and enrichment of the IBD signaling pathway. Notably, Mmp7, which can be linked to epithelial remodeling and inflammation, was a common marker in both models. This study presents a robust mSIO model of M. avium infection that recapitulates features of CD-associated inflammation both with high-resolution imaging and transcriptomics and identifies Mmp7 as a potential molecular link between infection and CD-like pathology.