Molecular characterization of bacterial communities in sheep's milk and cheese through 16S rRNA gene metabarcoding sequencing

The microbiota present in cheeses can be influenced by microorganisms present in all stages of the process, from raw materials, processing and starter cultures used in the manufacturing process. In this study, a characterization of the microbial communities of 15 milk samples and 4 different types of sheep cheese (colonial, fresh, feta and pecorino) was carried out, using the 16S rRNA sequecing. Microbial differences were identified. Milk proved to be more diverse than cheeses, when the geographical area of milk collection was evaluated, there was no significant different. The predominant genera in milk were Phyllobacterium (42.59%), Staphylococcus (29.20%), Pseudomonas (10.96%), Lactococcus (5.10%) and Acinetobacter (1.38%). Psychrotrophic bacteria like Pseudomonas and Acinetobacter are common components of the raw milk microbiota, as they are stored at low temperatures. Lactic acid bacteria (Streptococcus (73.15%), Lactobacillus (19,91%), Lactococcus (2,46%)), dominated the cheese samples, although bacteria of the genus Staphylococcus (1.74%), appeared with different relative abundances varying according to the types of cheese. This study provides new information on the bacterial diversity of sheeps milk and cheese, in addition to revealing diversity data assessed at different production farms. The characterization of bacterial communities in milk was useful to obtain information about their influence on the composition and microbiological quality of sheep cheese.