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

The intestinal microbiota influences host susceptibility to <i>Campylobacter jejuni</i> (<i>C. jejuni</i>) infection. However, the interaction between specific intestinal bacteria and the <i>C. jejuni-</i>mediated host response is unclear. We established a defined consortium of bacteria to delineate <i>C. jejuni</i>-induced host responses<i>.</i> Three groups of germ-free (GF) <i>Il10</i>^-/- 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 <i>C. jejuni</i> 81-176 and 3) GF alone. The C13 + <i>C. jejuni</i> 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 <i>Escherichia</i> and <i>Paraclostridium</i> in C13 + <i>C. jejuni</i>. Fluorescence <i>in situ</i> 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 <i>C. jejuni</i> differentially modulates host gene expression compared to tissue-associated <i>Enterobacteriaceae</i>. 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.