Interplay of intestinal microbiota and mucosal immunity in inflammatory bowel disease: a relationship of frenemies

Inflammatory bowel diseases (IBDs), including ulcerative colitis and Crohn’s disease, are chronic inflammatory disorders of the gastrointestinal tract. With in-depth studies on the mechanisms of the initiation and development of IBD, increasing lines of evidence have focused on the intestinal microbiota in the pathogenesis of IBD. The imbalance between the host and intestinal microbiota induces dysregulated immune response in intestinal mucosa and plays a pivotal role in the initiation of disease and ongoing bowel destruction. This review focuses on recent advances in intestinal microbiota regulation of mucosal immune response as well as novel approaches based on intestinal microbiota alterations in the diagnosis and evaluation of therapeutic response in IBD.