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

Abstract

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.

The resistome of the food chain: A One Health perspective

“…The literature contains numerous studies that demonstrate the circulation of a large diversity of known ARGs in the food chain, including several ARGs of critical importance (Alexa et al., 2024; Guron et al., 2019; Sequino et al., 2024; Vieira et al., 2023). According to the existing evidence, the major carriers of ARGs in food and associated environments are members of the ESKAPEE group and other closely related taxa, with notable examples including Pseudomonas , Acinetobacter and Staphylococcus .…”

“…According to the existing evidence, the major carriers of ARGs in food and associated environments are members of the ESKAPEE group and other closely related taxa, with notable examples including Pseudomonas , Acinetobacter and Staphylococcus . Moreover, a considerable proportion of the ARGs present in the food chain have been associated with mobile genetic elements, indicating the potential for their transfer within the complex gut ecosystem (Alexa et al., 2024; Walsh et al., 2020; Wind et al., 2021).…”

“…Alexa et al. (2024) investigated the resistome evolution of blue‐veined cheeses during ripening and reported that raw milk and associated processing environments are a rich reservoir of AMR determinants, mainly associated with resistance to tetracyclines, aminoglycosides and beta‐lactams and harboured mainly by members of the Enterobacteriaceae family. Various ARG‐carrying contigs were classified by Alexa et al.…”