Antibiotics are useful for treating infections caused by bacteria, but they have negative effects on the host body. The goal of this study was to determine whether antibiotics alter the metabolic phenotype of the host. We found that taking antibiotics reduced the diversity and richness of gut microbiota and affected the composition of the microbiome, which in turn altered the metabolic profiles of plasma and fecal samples. Additionally, plasma and fecal metabolites and gut microbiota genera showed a significant association. The most significant pathways related to the gut dysbiosis induced by antibiotics including purine, pentose, and glucuronate metabolism, histidine, ascorbate and alternate, lysine degradation, and fatty acid biosynthesis. The relationship between gut microbiota and altered metabolites of plasma and feces provides information about bacterial action, which is useful for designing new microbiota-based disease prevention and treatment interventions.