Genome‐scale reconstruction of the metabolic network in Streptococcus thermophilus S‐3 and assess urea metabolism

Abstract

BACKGROUNDStreptococcus thermophilus is an important strain widely used in dairy fermentation, with distinct urea metabolism characteristics compared to other lactic acid bacteria. The conversion of urea by S. thermophilus has been shown to affect the flavor and acidification characteristics of milk. Additionally, urea metabolism has been found to significantly increase the number of cells and reduce cell damage under acidic pH conditions, resulting in higher activity. However, the physiological role of urea metabolism in S. thermophilus has not been fully evaluated. A deep understanding of this metabolic feature is of great significance for its production and application. Genome‐scale metabolic network models (GEMs) are effective tools for investigating the metabolic network of organisms using computational biology methods. Constructing an organism‐specific GEM can assist us in comprehending its characteristic metabolism at a systemic level.RESULTSIn the present study, we reconstructed a high‐quality GEM of S. thermophilus S‐3 (iCH492), which contains 492 genes, 608 metabolites and 642 reactions. Growth phenotyping experiments were employed to validate the model both qualitatively and quantitatively, yielding satisfactory predictive accuracy (95.83%), sensitivity (93.33%) and specificity (100%). Subsequently, a systematic evaluation of urea metabolism in S. thermophilus was performed using iCH492. The results showed that urea metabolism reduces intracellular hydrogen ions and creates membrane potential by producing and transporting ammonium ions. This activation of glycolytic fluxes and ATP synthase produces more ATP for biomass synthesis. The regulation of fluxes of reactions involving NAD(P)H by urea metabolism improves redox balance.CONCLUSIONModel iCH492 represents the most comprehensive knowledge‐base of S. thermophilus to date, serving as a potent tool. The evaluation of urea metabolism led to novel insights regarding the role of urease. © 2023 Society of Chemical Industry.

Investigating the Role of β-Disodium Glycerophosphate and Urea in Promoting Growth of Streptococcus thermophilus from Omics-Integrated Genome-Scale Models

“…The M17-β group and the M17 group demonstrated similar trends of pH decline, but the final pH of the M17-β group was lower than that of the M17 group. The pH of the UM17 group, however, showed a trend of initially rising, and then falling, which is consistent with the phenomenon observed in the CDM [5].…”

“…however, showed a trend of initially rising, and then falling, which is consistent with the phenomenon observed in the CDM [5].…”

“…These results outperformed those obtained from Flux Balance Analysis (FBA). Furthermore, the model predicted a positive reaction flux for F 0 F 1 -ATPase in the UM17 group, suggesting that this reaction can indeed generate ATP-a finding consistent with our previous conclusions on urea metabolism [5]. Although the prediction accuracy of REMI has significantly improved compared to FBA, there is still a deviation between the predicted value and the experimental value.…”

“…The proliferative effect of urea on S. thermophilus has been confirmed in our previous studies, where the addition of urea to a chemically defined medium (CDM) significantly increased the biomass of S. thermophilus S-3 [5]. This is beneficial for the high-density cultivation of S. thermophilus.…”

“…Cell dry weight was determined by weighing. All methods were based on previously established methods [5].…”