Changes in phylotypes and composition of intestinal bacterial community affect host metabolism, inflammatory and immunogenic responses. In non-alcoholic fatty liver disease (NAFLD), small intestinal bacterial overgrowth, changes in colony composition and quantity, and increased intestinal permeability promote the development of liver inflammation and fibrogenesis through enhancing hepatic lipogenesis, causing insulin resistance and stimulating innate immune response. Identification of specific bacterial species and their products that alter metabolic status and cause sustained but low-grade inflammatory and immune responses will advance our understanding of the critical role of “gut-liver axis” in promoting the initiation and progression of non-alcoholic steatohepatitis (NASH), and exploring novel therapeutic strategies for its prevention and treatment.