Ryu, E. P.; Keller, C. A.; Nichols, R. G.; Tran, H. N.; Brocious, P. R.; Harris, L. R.; Koltun, W. A.; Yochum, G. S.; Davenport, E. R.

Host genetics shapes gut microbiome composition, yet the physiological mechanisms underlying this relationship remain poorly understood. Characterizing associations between host gene expression and the mucosal microbiome offers a promising route to identifying the host pathways and microbial taxa most likely to interact physiologically. However, existing investigations have been conducted primarily in acute disease contexts and within the colon, leaving host-microbiome associations outside of acute inflammatory contexts and those in undersampled regions such as the terminal ileum poorly characterized. To address these gaps, we profiled paired host gene expression from full-thickness resections and mucosal microbiome data, both from macroscopically non-inflamed tissue from Crohn's disease patients undergoing surgery across three intestinal sites: terminal ileum (n = 32), cecum (n = 35), and right colon (n = 30). Using a multi-level analytical framework including Procrustes analysis, sparse canonical correlation analysis, and elastic net regression, we identified significant associations between the mucosal transcriptome and microbiome. Intestine-wide, genes enriched in immune and intestinal barrier integrity pathways were associated with heritable taxa including Fusicatenibacter, consistent with patterns observed in microbiome genome-wide association studies. Region-specific analysis identified the terminal ileum as a distinct site of host-microbiome interaction, with associations involving metabolic and barrier-related pathways not observed in the large intestine. Notable terminal ileum-specific associations included PCDH20 with Faecalitalea and ACAT1 with Lactococcus, implicating epithelial barrier maintenance and host-microbiome metabolic interactions, respectively. These findings advance our understanding of the physiological basis of host-microbiome interactions across the intestine.