Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease, is a chronic and 
relapsing inflammatory disorder of the intestine. Although its incidence is increasing globally, the 
precise etiology remains unclear and a cure for IBD has yet to be discovered. The most accepted 
hypothesis of IBD pathogenesis is that complex interactions between genetics, environmental factors, 
and the host immune system lead to aberrant immune responses and chronic intestinal inflammation. 
The human gut harbors a complex and abundant aggregation of microbes, collectively referred to as 
the gut microbiota. The gut microbiota has physiological functions associated with nutrition, the 
immune system, and defense of the host. Recent advances in next-generation sequencing technology 
have identified alteration of the composition and function of the gut microbiota, which is referred 
to as dysbiosis, in IBD. Clinical and experimental data suggest dysbiosis may play a pivotal role in 
the pathogenesis of IBD. This review is focused on the physiological function of the gut microbiota 
and the association between the gut microbiota and pathogenesis in IBD. In addition, we review the 
therapeutic options for manipulating the altered gut microbiota, such as probiotics and fecal 
microbiota transplantation.