Microbial Profiles (16S rRNA amplicon) from 63 artisan cheeses from Epirus Greece

Cheese typicity reflects the unique characteristics influenced by raw ingredients used, traditional tools employed, environmental and production conditions, the cheese-making process, and the specific geographical region of origin. In the present study, the typicity of Greek cheeses was studied and compared with cheeses from various countries worldwide, on the grounds of microbiota profiles. The dataset included publicly available raw sequencing data and newly generated sequences in our laboratory from 63 Greek cheese samples, totaling 322 cheese samples, derived from seven different countries. The analysis incorporated NGS technology, with Illumina sequencing of the 16S rRNA gene hypervariable regions V3–V4, followed by a standardized analytical pipeline process. Through de novo clustering analysis, we identified four main bacterial profile clusters and nine sub-clusters and core microbiota was identified within sub-clusters. We introduced the term "Cheese Microbial Profile" (CMP) to describe stable phylogenetic bacterial assemblages. The dominant bacterial genera were Lactobacillus in CMP1, Lactococcus in CMP2 and CMP3, and Streptococcus in CMP4. Distinct cheese types exhibited a statistically significant preference for specific microbial profiles within the four clusters. However, no clear signatures of geographic origin were detected, nor were associations found between microbial communities and cheese production parameters such as cheese type, milk source, starter culture addition, or milk pasteurization. Additionally, we developed a novel model capable of accurately classifying new cheese samples into clusters and sub-clusters, based on their bacterial ecological community structure. Our findings may contribute to future efforts, in combination with multi-omic studies, to enhance the recognition of cheese typicity, authenticate and determine the geographical origin of cheeses, and improve cheese quality and safety standards.