Dynamic metagenome-scale metabolic modeling of a yogurt bacterial community

Genome-scale metabolic models and flux balance analysis (FBA) have been extensively used for modeling and designing bacterial fermentation. However, FBA-based metabolic models that accurately simulate the dynamics of coculture are still rare, especially for lactic acid bacteria used in yogurt fermentation. To investigate metabolic interactions in yogurt starter culture of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus, this study built a dynamic metagenome-scale metabolic model which integrated constrained proteome allocation. The accuracy of the model was evaluated by comparing predicted bacterial growth, consumption of lactose and production of lactic acid with reference experimental data. The model was then used to predict the impact of different initial bacterial inoculation ratios on acidification. The dynamic simulation demonstrated the mutual dependence of S. thermophilus and L. d. bulgaricus during the yogurt fermentation process. As the first dynamic metabolic model of the yogurt bacterial community, it provided a foundation for the computer-aided process design and control of the production of fermented dairy products.

Automated summary

In this study, a dynamic metagenome-scale metabolic model was built to investigate metabolic interactions between Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in yogurt fermentation. The model, which integrated constrained proteome allocation, was validated by comparing predicted bacterial growth, lactose consumption, and lactic acid production with experimental data. The dynamic simulation revealed the mutual dependence of S. thermophilus and L. d. bulgaricus during yogurt fermentation. This dynamic metabolic model of the yogurt bacterial community provides a foundation for computer-aided process design and control of fermented dairy product production.