Increasing reports are suggested the control of host energy metabolism by intestinal microbes. Metabolites secreted by gut microbes are considered to be involved in the regulation of obesity by interacting with host metabolism. Bifidobacterium and Lactobacillus species are well known to play beneficial roles in the control of metabolic diseases through various mechanisms. To investigate microbe derived key substances in controlling host energy metabolism, we applied metabolomics approaches in cells and culture media of Bifidobacterium and Lactobacillus subspecies, which had beneficial effect on diet-induced obesity in mice. Using multivariate statistical analysis, some fatty acid-related molecules were selected as major substances that produced by the microbes and secreted extracellularly. The molecules were decreased in the cecum of mice fed a high fat diet. They are also reduced in the feces of obese human. In HepG2 cells, treatment of one of the substances suppressed accumulation of intracellular lipid droplets induced by palmitic acid, and at the same time, the expression of genes related to lipogenesis were suppressed. Taken together, this study implicates that the specific substance produced by gut microbes can prevent diet-induced obesity by inhibiting the cellular accumulation of lipids, and suggests the substance as a candidate of therapeutic drug for regulation of cellular lipid metabolism.