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In this thesis, we initially evaluated a wide range of reconstruction tools to determine their optimal performance in various cases. By utilizing the appropriate reconstruction tools, we successfully created a high-quality, genome-scale metabolic model for Lactobacillus delbrueckii subsp. bulgaricus, a bacterium commonly employed in yogurt production. Furthermore, we incorporated proteomic data into the model, acquired from two relevant conditions: growth on casein or amino acids. Through the incorporation of enzymatic capacity constraints into the model, we captured the emergence of glucose secretion as a system property, a phenomenon not discernible through the genome-scale model alone. Concluding our study, we introduce two innovative approaches to simulate the dynamics of co-evolved microbial communities. These methodologies are particularly suitable for species that release costly compounds into the surrounding medium due to co-evolution, as observed in the context of yogurt production. With this thesis, we have propelled the domain of systems biology as applied to the food industry, utilizing yogurt production as our focal case study.