The gut microbiota is now recognized to be a key driver of mucosal inflammation in inflammatory bowel disease (IBD). Robust functional and compositional alterations of the gut microbiota have been described in IBD with a reduction in bacterial diversity, a reduction in some anti-inflammatory anaerobic bacteria, and an increase in bacteria with pro-inflammatory potential. However, despite 15 years of active research, therapeutical applications are still lacking. Recent studies have shed new light on how targeting the gut microbiota can be beneficial in IBD with fecal microbiota transplantation, next-generation probiotics, and phage therapy. Given the similarities in dysfunction and structure of the gut microbiota between IBD and other chronic conditions associated with intestinal inflammation, such as celiac disease, Familial Mediterranean Fever, or common variable immunodeficiency, common therapeutic strategies targeting the host-microbiota symbiosis may be applied in these different conditions.