Metagenomics of Idiazabal cheese: elucidating the microbiota, its impact on cheese quality and safety, and factors affecting its composition

Abstract The present doctoral thesis was conducted within the Lactiker Research Group (UPV/EHU), which focuses on the quality and safety of animal-origin foods, particularly the Protected Designation of Origin Idiazabal cheese. This cheese, produced in small artisanal dairies in the Basque Country from Latxa or Carranzana raw ewe milk, undergoes a minimum 60-day ripening period. Raw milk cheeses, compared to those produced from pasteurized milk, are known for their rich aroma due to microbial dynamics during production. However, limited information exists on the microbiota of raw ewe milk cheeses, including Idiazabal cheese, and its subsequent impact on cheese quality and safety. Therefore, this thesis aimed (1) to characterise the microbiota of Idiazabal cheese and how it evolves by amplicon sequencing, (2) to explore its impact on cheese quality (gross composition, free fatty acids, and volatile compounds) and safety parameters (biogenic amines and antimicrobial resistances) determined by several approaches, and (3) to investigate key production factors (including herd feed, teat skin, dairy surfaces, and processing ingredients) affecting the microbial composition of raw ewe milk and Idiazabal cheese, and its genetic potential in terms of quality and safety by shotgun sequencing. Results revealed significant differences in the microbiota among producers, which affected cheese quality and safety parameters, and were related to microbial niches in dairy environments. This research contributes valuable novel insights not only for the scientific community, as information on raw ewe milk cheeses is limited, but also for Idiazabal cheese producers, facilitating improvements in the quality and safety of the final product.