Abstract:High-throughput sequencing technology has enhanced our understanding of gut microbiome and epigenetic modification, establishing the potential links between gut microbiome and epigenetic modification of host. It illuminates the development of a lot of diseases such as immune-related, metabolic, cardiovascular diseases and even cancer. Intestinal microbiome that is inseparable from human body interacts with host cells. Dysbiosis of gut microbiome may influence the status of epigenome from host. Indeed, the relationship between epigenetic regulation of host and variation of gut microbiome and its metabolites was reported responding for many diseases. Therefore, the gut microbiome could function as a diagnostic marker for certain diseases. The transplantation of healthy intestinal microbiome would re-balance dysbiosis and serve as an effective treatment strategy. Here, we gave a comprehensive introduction about how gut microbiome played direct roles in epigenetic modulation of host cells, and its indirect impact on epigenetic modification mainly through metabolites like bioactive low-molecular-weight substances and other enzymatic cofactors. Additionally, we talked about the great potentials and applied value of gut microbiome in diagnosis and treatment of related diseases.