Genes carried by intestinal flora are considered as “the second genome” of humans, and intestinal flora is also reservoir of antibiotic resistance gene (ARG). Disturbance in composition and function of intestinal flora is related to multiple diseases. However, the use of antibiotics disrupts the original homeostasis of intestinal flora, intensifies spread and diffusion of ARG, increases abundance of specific ARG, and exerts adverse effects on clinical treatment. In this review, the relation of intestinal flora and drug resistance genome with antibiotics is summarized, and future research directions are prospected, aiming at providing new ideas for the research of intestinal drug resistance genome and theoretical basis for the rational use of antibiotics in clinics at the same time.

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