Systems Biology Analysis of the Effect of pH on Lactate Fermentation in Bacillus coagulans Under Mixed Carbon Sources

Environmental pH plays a crucial role in microbial metabolism. Microorganisms adapt their metabolic strategies in response to different pH conditions, which must be carefully controlled in industrial production processes to achieve desired outcomes. However, the dynamic impact of pH on hierarchical utilization of mixed carbon sources remains poorly understood. In this study, we observed that Bacillus coagulans exhibited distinct carbon source consumption rates and lactate yields at different pH levels under mixed carbon sources. We employed dynamic simulation methods using an enzyme-constrained genome-scale metabolic model, combined with transcriptomic and metabolomic data, to investigate the metabolic differences at pH 5.5, 6.0, and 6.5 conditions. The results revealed the significant flux differences in the glycolysis pathway across the tested pH conditions. Predictions also indicated that pH changes altered energy demands. Integrating omics data further revealed that under pH 5.5 conditions, a higher proportion of carbon was allocated to the phosphoketolase pathway, which provides high ATP yield. This strategy helps meet the energy demand of energy-consuming reactions that could maintain intracellular pH stability under acid stress, such as the reactions in amino acid metabolism. Consequently, we observed increased acetate production and decreased lactate production. Additionally, different pH conditions triggered a global response involving multiple metabolic pathways.