The intestinal microbiota is engaged in multiple interactions with host physiological activities, during the entire life span and contributing to the development of various health conditions, especially chronic metabolic diseases. In the last decade, numerous
studies have linked the components of the microbiota or its metabolites, such as bacterial lipopolysaccharide (LPS), short-chain fatty acids (SCFAs), secondary bile acids (BAs) to metabolic diseases including obesity and type 2 diabetes. Therefore, the potential of the intestinal microbiota in treating metabolic diseases has aroused tremendous interests. This review discusses recent progresses of the studies on gut microbiota related to host metabolic homeostasis regulations and the relevance of intestinal microbiota with respect to their roles in the treatment of metabolic diseases, such as bariatric surgery, antibiotics medicine and incretin-based therapies. The new therapeutic strategies proposed or designed for targeting or reshaping intestinal microbiota to manage metabolic diseases are also included.