Mycobiota composition through the ripening of artisanal soft cheeses ‘Torta del Casar’ and ‘Queso de la Serena’ monitored by high-throughput sequencing

• The fungal community of Queso de la Serena and Torta del Casar PDO cheeses was studied. • The ITS metabarcoding sequencing approach allowed the identification of 28 fungal species. • Y. alimentaria, Y. lipolytica, K. lactis and P. fermentans were the predominant species. • The dairy factor significantly influenced the fungal diversity of the cheese samples. This study aimed to characterise the fungal communities of the Spanish Protected Designations of Origin soft cheeses, 'Torta del Casar' and 'Queso de la Serena,' during ripening using an amplicon-based high-throughput sequencing approach. The findings contribute to a deeper understanding of the mycobiota ecology of these artisanal cheeses, providing essential insights for implementing practices to enhance their quality. The Internal Transcribed Spacer rRNA gene metabarcoding sequencing was applied to elucidate the mycobiota occurring throughout the ripening. The results showed that Yarrowia alimentaria, Yarrowia lipolytica, Kluyveromyces lactis and Pichia fermentans dominated the fungal populations in all samples, although other species such as Debaryomyces hansenii, Debaryomyces vindobonensis and Geotrichum candidum were identified in specific dairies at different ripening stages . The Protected Designation of Origin and the ripening time factors do not significantly influence the fungal diversity between different cheese samples, suggesting that minor changes in manufacturing practices between the type of cheeses have a negligible impact on mycobiota composition. By contrast, the dairy factor contributed to the variability of the fungal composition of each cheese type. Altogether, this study provides evidence of the diversity of fungi associated with traditional cheeses, highlighting the need to improve manufacturing practices to minimise variability between dairies, ensuring final quality and preserving the unique sensory characteristics that distinguish these types of Spanish artisanal cheeses.