A defined bacterial consortium and spatial transcriptomics highlight the complex interaction between Campylobacter jejuni and the murine intestine

Abstract The intestinal microbiota influences host susceptibility to Campylobacter jejuni ( C. jejuni ) infection. However, the interaction between specific intestinal bacteria and the C. jejuni- mediated host response is unclear. We established a defined consortium of bacteria to delineate C. jejuni -induced host responses. Three groups of germ-free (GF) Il10 -/- mice were used in this study: 1) mice colonized with a defined consortium of 13 bacterial isolates (C13) representing the four most prominent phyla in the mouse gut. 2) C13 plus C. jejuni 81-176 and 3) GF alone. The C13 + C. jejuni group induced significant intestinal inflammation and inflammatory mRNA gene expression compared to mice colonized with C13. 16S rRNA gene sequencing revealed an increased relative abundance of Escherichia and Paraclostridium in C13 + C. jejuni . Fluorescence in situ hybridization (FISH) and RNAscope integrated with spatial transcriptomics provided a high-resolution map of infection-induced gene expression, revealing localized immune responses and epithelial remodeling in defined colonic regions. Region-specific analysis further demonstrated that tissue-associated C. jejuni differentially modulates host gene expression compared to tissue-associated Enterobacteriaceae . Collectively, these findings demonstrate the potential of defined microbial consortia and spatially resolved transcriptomics to dissect the complex interplay between host, microbiota, and pathogens during enteric infection.