The human gut harbors trillions of microbes that function as a multi-cell organ. This microbial community appears to cluster in certain types regardless of its vast number and complexity. The gut microbiota plays a key role in the host physiology since it is involed in energy breakdown, multiple host metabolic pathways, signaling, immune system balance etc. The microbiota codevelop with the host and is subject to pertubation and resilience. Changes in the composition of the gut microbiota have been associated with diverse, complex diseases including inflammatory bowel disease, metabolic disease and cancer. Therefore, microbiota-targeted early diagnosis and therapy may become possible in the near future, especially in the chemoprevention of cancer.