Objective Accumulating reports have suggested a coordinated association between gut microbes and host metabolisms including energy utilization and storage. In this study, we have investigated the effects of antibiotics-mediated alteration of gut microbiota on energy metabolisms in diet-induced obese mice. Methods Mice were fed HFD and antibiotics cocktail in drinking water comprised with vancomycin and bacitracin before sacrifice. Mice were tested whether body weights and obesity induced insulin resistances were affected by antibiotics or not with various approaches. Results Antibiotics significantly changed the compositions of gut microbiota and regulated insulin sensitivity. However, body weight and fat mass were retained in the absence or presence of antibiotics treatment. Further, adipose tissue and whole body inflammation, adiponectin gene expression and hepatic triglyceride levels were not affected by antibiotics treatment. Intriguingly, antibiotics treated mice contained elevated the levels of GLP-1. Since GLP-1 is a well-known gut hormone for its direct and indirect roles in the sensitization of insulin signaling, it appears that alteration of gut microbiota with antibiotics might ameliorate insulin sensitivity in obesity via GLP-1. Conclusion These data suggest the possible association of GLP-1 with the improvement of glucose homeostasis in obesity mediated by alteration of gut microbiota without adiposity change.