Specific microbiota drives mucosal responses in inflammatory bowel disease.

Abstract

Objectives and Study: Inflammatory bowel disease (IBD) is a chronic and currently incurable condition, which is largely comprised of two main phenotypic subtypes, Crohn's Disease and Ulcerative colitis. Abnormal immune responses to the resident gut microbiome can drive or exacerbate IBD, however, these relationships are yet to be fully elucidated. Until recently, microbiome-based studies in IBD have predominantly been restricted to high-throughput, culture-independent sequencing based analyses, typically of faecal samples. This reliance on both faecal samples and sequencing alo ne has limiting our understanding of host-microbiome interactions at the intestinal 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. Method(s): To achieve this, we established a paediatric IBD (PIBD) specific bacterial culture collection, comprising 6,416 isolates (207 distinct species, 79 putative 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. Result(s): In vitro validation of these clades demonstrates specific differences in cell cytotoxicity and inflammatory signalling in intestinal epithelial cells, that matches the colonic mucosal response measured within the clinical patient cohort. The combination of site-specific bacterial culturing, metagenomics and host transcriptomics from patient biopsies allows identification, classification and functional validation of key microbiome species, which may be harnessed in order to aid the development of therapeutics for IBD. Conclusion(s): In conclusion, this work highlights the benefits of functional clade-based bacterial analysis for the future of microbiome-based therapeutics, in the context of IBD. The Enterococcus clades identified may function as disease biomarkers or act as therapeutic candidates for a subset of IBD patients. Additionally, while these methods have allowed advancements to be made in the field of IBD, they may be employed elsewhere, with their potential use unrestricted to the gastrointestinal microbiome.