Résumé
Protected Designation of Origin (PDO) cheeses are considered as high quality, non-standardised products. Our objective was to decipher the drivers of microbiota in milks and the associated cheeses, and their relationships to geography, farming and cheese processing practices. We characterised the bacterial and fungal communities in 1,145 cheeses and 390 milks from 44 French PDO, using 16S rRNA and ITS2 gene sequencing. A total of 820 bacterial species and 333 fungal species were identified in cheeses. Species assemblages differed depending on human drivers, dairy species, and geographical area, thus demonstrating the contribution of regional know-how to shaping the cheese microbiota.