Environmental sources along natural cave ripening shape the microbiome and metabolome of artisanal blue-veined cheeses

Microorganisms colonising processing environments can significantly impact food quality and safety. Here we describe a detailed longitudinal study assessing the impact of cave ripening on the microbial succession and quality markers across different producers of blue-veined cheese. Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome and metabolome. The cheese microbiome was significantly determined by the microbiome of caves, which were a source of Brevibacterium, Corynebacterium, Staphylococcus, Tetragenococcus and Yaniella, among others, as demonstrated through source tracking and the characterization of 613 metagenome assembled genomes. Tetragenococcus koreensis and T. halophilus were detected at high abundance in cheese for the first time, associated with the occurrence of various metabolites, and showed high levels of horizontal gene transfer with other members of the cheese microbiome. Overall, we demonstrated that processing environments can be a source of non-starter microorganisms of relevance to ripening of artisanal fermented foods.