Amplicon-based metagenomic characterization of the microbiome of the traditional “Bieno” cheese produced in North Macedonia

Abstract

The main goal of this study was to investigate the microbiota of the “Bieno” cheese, a traditional cheese produced only in the Republic of North Macedonia, which has never been studied before. To achieve this goal, four industrially produced brands of cheese and one artisanal batch were subjected to an amplicon-based metagenomic study focused on the eubacterial V3–V4 region of the 16S rRNA genes. The alpha-diversity analyses revealed very rich microflorae regarding the dominant species in all five analyzed samples, the differences being mainly in the group of the subdominant species, probably reflecting the local environmental microflora. Among the dominant species, representatives of the Streptococcus, Lactococcus, Bifidobacterium, Staphylococcus, and Enterococcus genera, as well as members of the Lactobacillaceae family, were found. Interestingly, the Acinetobacter johnsonii counts also placed this species within the dominant microflora. The results of the beta-diversity analyses further confirmed the hypothesis that the differences result from the subdominant microflorae. The weighted UniFrac phylogenetic clustering and the principal coordinate analysis tend to reflect the production's geographic locations. Additionally, some species present within the dominant and the subdominant taxa group indicate that the “Bieno” cheese could possess functional food properties.