Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

Abstract Sheep’s milk and cheese represent unexplored reservoirs of microorganisms’ genetic and metabolic diversity. This study aimed to characterize the microbial communities of milk and cheese from sheep of Lacaune breed, produced in the South Region of Brazil. Milk samples (n = 15) from three dairy farms and four types of cheese (fresh, colonial, feta-type, and pecorino-type; n = 20) were subjected to partial 16S rRNA gene sequencing. Streptococcus spp. and Lactobacillus spp. were the dominant taxa (core microbiota) of cheeses, while Phyllobacterium spp. and Staphylococcus spp. were the most prevalent genera in milk. Regarding milk samples, no differences in alpha diversity were observed between the analyzed farms. However, beta diversity analysis revealed that milk collected on Farm 1 differed from the others. These differences may be associated with sheep feeding, mammary gland diseases, and the milking practices used. Upon analyzing cheese samples, significant differences in both alpha and beta diversity were observed between the different cheese types, suggesting that processing and maturation conditions are important for shaping cheese microbiota. Notably, other bacterial groups—including decomposers and potentially pathogenic microorganisms to humans—were observed in some of the analyzed cheeses. This study expands our knowledge of the bacterial composition of sheep's milk and cheese found in different geographic regions.