Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of cheese microbiota

Microbial communities of cheeses, in particular traditional ones are very diverse, questioning their origin, safety and functional role in cheese making. Metagenomic analysis of these communities by Very High Throughput Sequencing Technology (VHTST) with short read shotgun sequencing is a promising approach for their microbial profiling and functional study. However, VHTST requires an adequate genome sequence database to assign the short reads. The objective of the present study was to constitute a reference genome catalogu suitable for short read metagenomic analysis. Bacteria isolated from dairy products, and belonging to 137 different species and 67 genera were selected, including isolates from the genera Alkalibacterium, Brochotrix, Kluyvera, Luteococcus, Marinilactibacillus and Vagococcus, for which no genome sequences were available. Draft genomes sequences were produced, and 117 among 142 were suitable for public databases and submitted, mainly at high quality level. As a proof of concept for the use of VHTST profiling, the microbial composition of the surfaces of two smear cheeses and one blue-veined cheese was analyzed with the use of these new genomes. A significant part of the cheese microbiota was composed of microorganisms that were not deliberately inoculated, including Gram-negative genera such as Pseudoalteromonas, Halomonas, Vibrio, Marinilactibacillus and Psychrobacter. The depth of this metagenomic analysis revealed the presence of strains sharing almost complete gene set with over 99.9% identity with newly sequenced strains. They may correspond to "terroir" strains that add typical values to traditional productions. The availability of the genomes sequenced in the present study and particularly those which are not deliberately inoculated, and the broaden use of VHTST will considerably extend our understanding of cheese microbiota, and of genetic determinants involved in the generation of desirable or undesirable properties.