Lactic acid bacteria (LAB) are essential to milk fermentation, and the quality of products is strongly affected by the ability of LAB. The metabolic control of LAB contribute to stable production and improvement of qualities of milk products such as texture, flavor and function. The objective of our research is conferring unique characteristics to fermented milk products by using beneficial LAB and domestic natural resources. To accomplish our objectives, we develop LAB strains with beneficial characteristics and metabolic control technique for ripening, antioxidants production and etc, based on analysis of genome, transcriptome and metabolome in LAB. In addition, screening for domestic natural resources which can modify enzyme activity and/or gene expression of LAB, survivability and production of metabolites, such as GABA and carotenoids, are performed. Finally, we try to create high-valued fermented milk products by using beneficial LAB or combination of beneficial LAB with domestic natural resources.