The role of the gut microbiota in the pathogenesis of inflammatory bowel disease (IBD) is well established. For this reason, the gut microbiota is now recognized as a promising treatment target in Crohn’s disease, pouchitis and ulcerative colitis .Antibiotics and probiotics are increasingly components of IBD management. In this presentation, Prof Sartor reviews data that support the use of serologic markers to predict the clinical aggressiveness of these diseases. Abnormal profiles of enteric bacteria are present in patients with Crohn’s disease, Ulcerative Colitis and, most notably, in pouchitis. Prof Sartor presents data from animal models, showing that proliferation of aggressive bacteria promotes colitis in genetically susceptible mice and rats. Conversely, the proliferation of certain bacterial subsets is protective. In patients with IBD, there is an abnormal balance between aggressive and protective bacterial. Future IBD treatments can aim to correct this dysregulated balance between protective and pro-inflammatory resident intestinal microbial components.