Dynamics of thermophilic starters in PDO Comté cheese: Insights from viability qPCR

In Comté cheese production, Streptococcus thermophilus and thermophilic lactobacilli (Lactobacillus delbrueckii and Lactobacillus helveticus) drive acidification and early fermentation. This study investigated their dynamics during ripening in cheeses from two factories, over two production periods, using culture-based counts, qPCR, and PMAxx-based viability-qPCR (v-qPCR). Two starter types were compared: a natural whey starter (NWS) and a defined S. thermophilus strain starter (control). Thermophilic starters persisted throughout ripening, but their dynamics varied with cell type (culturable, total, viable), species, and starter type. Culturable counts declined by 3-6 log units during ripening. S. thermophilus maintained high total and viable levels (≈7-8 log gu/g of cheese), with minimal discrepancies between qPCR and v-qPCR results in control cheeses, indicating a predominantly viable population. In contrast, L. delbrueckii and L. helveticus showed marked viability losses, with discrepancies of up to 3 log units between total and viable counts by the end of ripening, suggesting a higher increase in non-viable lactobacilli compared to S. thermophilus. Starter type significantly influenced S. thermophilus culturability and viability, with the control strain maintaining higher levels over time, suggesting the importance of strain composition in the starter. No effect was observed on lactobacilli culturability. It was only observed for total and viable L. helveticus, depending on the period. v-qPCR effectively quantified viable thermophilic starters and revealed that culture-based methods underestimated viable populations. The persistence of thermophilic starters in multiple physiological states, influenced by the starter type, questions their potential functional role in flavor and texture development during cheese maturation.