Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing

The production of sheeps milk cheese has grown in recent years since it is a high value-added product with excellent properties. As such, it is necessary to provide data on the microbiota and organoleptic characteristics of this product, as well as the influence of these microorganisms on public health. Thus, the aim of the present study was to characterize the microbial community of different types of sheep cheeses using high-throughput sequencing of the 16S rRNA gene. The study was conducted with four groups of cheese: colonial, fresh, feta, and pecorino (n = 5 samples per group). The high-throughput 16S rRNA amplicon sequencing revealed 55 operational taxonomic units in the 20 samples, representing 9 genera of the two bacterial phyla Firmicutes and Proteobacteria. The predominant genera in the samples were Streptococcus and Lactobacillus. When evaluating alpha diversity by the indexes of Simpson, Chao1, Shannon, and Skew no significant differences were observed between the groups. Evaluating of the beta diversity using Bray-Curtis dissimilarity, the group of colonial cheeses presented a significant difference when compared to the feta (q = 0.030) and pecorino groups (q = 0.030). Additionally, the fresh group differed from the pecorino group (q = 0.030). The unweighted Unifrac distance suggests that the colonial cheese group differed from the others. Moreover, the feta cheese group differed from the fresh group. The distance-weighted Unifrac suggests that no significance exists between the groups. According to this information, the microbiota characterization of these cheese groups was useful in demonstrating the bacterial communities belonging to each group, its effects on processing, elaboration, maturation, and public health.