Abstract: OBJECTIVE To evaluate the function and safety risk of a strain of Enterococcus faecium isolated from probiotic products. METHODS Functional genomics and comparative genomics were used to analyze the probiotic and safety characteristics of Enterococcus faecium strains, and to assess the potential risks to human health. RESULTS The isolated strain had probiotic-related functional genes such as antibacterial activity and vitamin metabolism, as well as related functional genes such as virulence factors and drug resistance, revealing that the isolated strain had probiotic functions on the human body and had hidden safety risks. In addition, there was a high correlation between the virulence factor of this strain and the movable element(insertion sequence), and there was a potential risk of transmission. CONCLUSION Enterococcus faecium strains have potential safety risks, and further analysis of genomic and phenotypic data is needed to avoid or contain potential safety hazards of probiotic products.