Recent progresses in clinical diagnostic analyses have demonstrated the decisive influence of host gut microbiota on the status of metabolic disorders. Short chain fatty acids (SCFAs) produced by gut microbiota, in particular, are considered as a key biomarker, both of communication between gut microbiota and the host, and of impact on host metabolic homeostasis. Microbiota modulation and concomitant anti-obesity effects of probiotics have been reported by different researchers. However, the underlying modulatory functions of probiotics on gut microbiota towards host metabolic homeostasis are still not fully understood. In this study, the impact of Lactobacillus sakei CJLS03 (isolated from Korean kimchi) on obesity-related biomarkers was investigated using a diet-induced obese mouse model. Body weight increase, SCFAs, the gut microbiota and various obesity-associated biomarkers were significantly and beneficially influenced by L. sakei CJLS03 administration compared to the control groups. Analytical data on faecal samples support the role of the colonic microbial population in SCFA production. The composition of the latter may be influenced by modulation of the distal gastro-intestinal microbiota by putative probiotics such as L. sakei CJLS03.