Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal (GI) tract with two main clinical types: Crohn's disease, which can affect any part of the GI tract, and ulcerative colitis (UC), which is limited to the colon. While early research focused primarily on the immune dysregulation and genetic susceptibilities associated with IBD, recent groundbreaking technological advances have allowed the investigation of additional factors, including diet and microbial exposures, in the onset and severity of disease. Advances in high-throughput microbial sequencing, anaerobic bacterial culturing techniques and generating germ-free mouse models have revolutionized our understanding of the microbial species associated with inflammation. While the long-standing clinical efficacy of antibiotics or surgery for Crohn's disease highlights the potential contribution of the socalled ‘IBD microbiome’ to inflammation, recent seminal studies revealed the impact of IBD-derived gut microbiota on host mucosal and systemic inflammation. This mechanistic understanding of how our ‘microbial organ’ functionally impacts both mucosal and systemic inflammatory pathways will help drive novel diagnostic and therapeutic approaches for IBD.

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