Résumé
INTRODUCTION: Cheeses are fermented products resulting from the complex interaction between the milk, the environment and the micro-organisms that compose them. The species found in this ecosystem originate from commercial starters, which are involved in the manufacturing and maturing processes, but also from endogenous microbial communities, which are influenced by the different cheese production practices. Although these particular communities are essential, little is known about their taxonomic and functional diversity, as well as the genetic traits of their adaptation to the cheese ecosystem.OBJECTIVE: As such, the MétaPDOcheese project – "Grand Projet de Séquençage" France Génomique (2017 – 2023) – was initiated to explore the diversity of microbial communities inhabiting the Protected Designation of Origin (PDO) cheeses at the scale of the French territory.MATERIALS AND METHODS: By analysing 146 metagenomes from three environments – i.e., milk, cheese core and rind – we review the bacterial, fungal and viral diversity of 44 PDO cheeses. A set of 373 genomes of bacterial strains isolated from cheeses were sequenced and 1119 metagenome-assembled genomes (MAGs) of good quality from the 146 metagenomes were reconstructed.RESULTS AND DISCUSSION: We show that the alpha and beta diversity are influenced by the environment, the technology used (soft, hard or semi-hard) and the type of rind (bloomy, washed or natural), with a higher abundance of i) bacteria in hard and semi-hard cheeses and ii) eukaryotes in bloomy rind and blue mold cheeses. This taxonomic profiling also highlights a positive relationship between the abundance of bacterial and viral sequences, suggesting a prevalence of bacteriophages in hard and semi-hard cheeses in particular. Moreover, the functional analysis reveals a dissimilarity between the three environments, but also between technologies/type of rind. By comparison with the reference sequences currently available in public databases, the analysis of all genomes revealed a set of 259 previously not described, and therefore potentially new, species belonging to genera of interest in the cheese ecosystem (e.g., Psychrobacter, Halomonas, Brevibacterium). Altogether, combining culturomic and metagenomic approaches has given us an access to an uncovered diversity of non-inoculated micro-organisms. In addition, from genomic and metagenomic data, we have built a catalogue of functionally and taxonomically annotated reference proteins, that includes more than 15 millions non-redundant proteins and covered the metabolic diversity of the cheese ecosystem and the 44 French PDO cheeses.CONCLUSION/PERSPECTIVES: The construction of this protein catalogue constitutes an accessible tool for future understanding of the structure and function of microbial communities in other cheese ecosystems.