Genome to Production: A Multiscale Model for Bioprocess Design

Bioprocesses are inherently multiscale, spanning intracellular metabolism to production-scale reactors. Simulation models that integrate these scales offer potential strategies to study the effect of changing metabolic states and enable efficient integration of biological knowledge gathered from lab-scale experiments. In this study, we demonstrate the potential of such simulation model towards the production of mevalonate, an important pharmaceutical drug compound produced through fermentation of a fungal species Aspergillus terreus. We integrate a genome-scale metabolic model of the organism with a plant-wide simulation model for the bioprocess that encompasses several upstream and downstream unit operations. Through this integration, we identify potential targets for metabolic engineering towards increased product flux and simultaneously estimate the associated oxygen requirements. This framework serves as a foundation for developing digital twins of bioprocesses that bridges strain engineering with process design and operations.