Human gut microbiota is a novel concept for pathogenesis in many inflammatory disorders including inflammatory bowel disease. In the last decade, experimen- tal and clinical studies showed that gut microbiota composition is different in ulcerative colitis and Crohn’s disease. This review summarizes the gut microbiome association studies and metabolomics of gut microbiota in inflammatory bowel disease. Also, minor components of the gut microbiome (fungi, protozoa, and viruses) and IBD data are discussed. The data about probiotics, prebiotics, and synbiotics are also discussed in inflammatory bowel disease treatment and preven- tion. Finally, we need more clinical trials on this topic to understand the causative role of microbiota in inflammatory bowel disease.