We face the challenge of breaking away from the production and consumption cycle that depends on fossil resources; there are high expectations for valuable compounds production using living organisms that have a low environmental impact and sustainable development. In our laboratory, we are designing new bioprocesses (fermentation processes) for future bioproduction based on understanding and rewiring the metabolic networks in living organisms, For this purpose, we tried to develop various technologies such as in silico metabolic design platform, experimental evaluation of metabolism by 13C metabolic flux analysis, computational rational enzyme design, evolutionary engineering, and multi-omics analysis. By integrating these technologies, we are aiming to understand and construct metabolic pathways (systems) and biomolecules (elements) in the new metabolic engineering.