A more complete use of food resources and available space is achieved in the present aquaculture system, particularly in China. However, such aquaculture mode always results in high stocking density and consequently may depress the immune system (cellular and humoral immune) of piscine host and increases their susceptibility to diseases. It has been known that the gut microbe plays an important role in providing nutrients, regulating epithelial development, and instructing innate immunity. However, although more and more scientists are revealing the full pictures of these biological effects, we still know few about the characterization/mechanism of these interactions.