NGS-Based Metagenomic Study of Four Traditional Bulgarian Green Cheeses from Tcherni Vit

This is the first scientific study of the unique Bulgarian Cherni Vit green cheese based on 16S and ITS2 NGS metagenomics, accomplished on the Illumina HiSeq 2 × 250 bp paired end reads in order to obtain an overview of the microbial composition. The results revealed a rich microbiota, composed of on average of 120 eubacterial and 16 fungal species. Firmicutes were represented by the families Strepotococcaceae, Lactobacillaceae and Staphylococcaceae, while the Actinobacteria were represented mainly by the genera Brevibacterium and Corynebacterium. Low counts of Proteobacteria were also detected, mainly halophiles of the genera Cobetia and Psychrobacter. Almost all (99.99%) of the detected fungi belonged to Ascomycota, represented almost equally by the families Eurotiomycetes (exclusively by Penicillium roqueforti), Saccharomycetes (mainly by the genera Debaryomyces, Pichia, Candida and Kluyveromyces) and Sordariomycetes (mostly by Scopulariopsis flava). The performed diversity analyses revealed that despite some differences, which can be attributed to environmental factors, and the time of the ripening, all of the four batches displayed very rich but similar microbiota. We found a potentially beneficial microbiota with the potential to inhibit the growth of pathogenic bacterial species, as well as to neutralize possibly produced mycotoxins, as described in numerous research on raw milk dairy products.