SRA

Abnormal immune response to the resident gut microbiome can drive or exacerbate inflammatory bowel disease (IBD). Until recently, microbiome studies in IBD have predominantly been restricted to high-throughput, culture independent sequencing, typically of faecal samples, limiting the elucidation of host-microbiome interactions at the site of disease. Here we define key IBD associated, functional bacterial clades from within the patient microbiome by combining shotgun metagenomic sequencing, bacterial culturing and host transcriptomic analysis with detailed experimental validation. To achieve this, we established a paediatric IBD (PIBD) specific bacterial culture collection, comprising 6,416 isolates (207 distinct species, 54 novel), cultured from 286 mucosal biopsies (58 PIBD and 42 control patients). This resource, coupled with novel, high-resolution, culture-based shotgun metagenomic sequencing (231 samples) and matched host transcriptomics (231 samples) across three biopsy sites (terminal ileum, caecum, rectum) identified key, functionally distinct Enterococcus subclades associated with IBD state. In vitro validation of these clades demonstrates specific differences in cell cytotoxicity and inflammatory signalling in intestinal epithelial cells that matches the colonic mucosa response measured within the patient cohort. The combination of site-specific bacterial culturing, metagenomics and host transcriptomics from patient biopsy allows identification, classification and functional validation of key microbiome species and highlights the benefits for functional clade based analysis for the future of microbiome-based therapeutics.