Bacterial clade specific analysis identifies distinct epithelial responses in inflammatory bowel disease

Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here we combine, high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n=58) and matched controls (n=42) to investigate this relationship. Combining our novel site-specific approach with bacterial culturing, we established a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies. Phylogeny-based, clade specific metagenomic analysis identified key, functionally distinct Enterococcus clades associated with either IBD or health. Strain-specific, in vitro validation demonstrated differences in cell cytotoxicity and inflammatory signaling in intestinal epithelial cells, consistent with the colonic mucosa specific response measured in the inflammatory bowel disease patients. This demonstrates the importance of strain-specific phenotypes and considering anatomical site in exploring the dysregulated host-bacterial interactions in IBD.