A digital twin of bacterial metabolism during cheese production

Cheese organoleptic properties result from complex metabolic processes occurring in microbial communities. A deeper understanding of such mechanisms makes it possible to improve both industrial production processes and end-product quality through the design of microbial consortia. In this work, we caracterise the metabolism of a three-species community consisting of Lactococcus lactis, Lactobacillus plantarum and Propionibacterium freudenreichii during a seven-week cheese production process. Using genome-scale metabolic models and omics data integration, we modeled and calibrated individual dynamics using monoculture experiments, and coupled these models to capture the metabolism of the community. This digital twin accurately predicted the dynamics of the community, enlightening the contribution of each microbial species to organoleptic compound production. Further metabolic exploration raised additional possible interactions between the bacterial species. This work provides a methodological framework for the prediction of community-wide metabolism and highlights the added-value of dynamic metabolic modeling for the comprehension of fermented food processes.