The Microbiota of Edam Cheeses Determined by Cultivation and High-Throughput Sequencing of the 16S rRNA Amplicon

The aim of this study was to evaluate the microbiome of industrially produced ripened Edam cheeses by next-generation sequencing. The samples for analyses were collected in spring and autumn. Spring samples were characterized by significantly higher Lactococcus and Bacillus counts and lower counts of Enterobacteriaceae, Enterococcus, and yeasts than autumn samples. The predominant microorganisms identified by the Illumina high-throughput sequencing technology belonged to four phyla: Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes. The dominant species were starter culture bacteria. Lactobacillus rhamnosus, Lactobacillus kefiri, Lactobacillus kefiranofaciens, Lactobacillus casei, Streptococcus thermophilus, and Bifidobacterium had the highest share of microbial cheese communities. The number of γ-Proteobacteria reads was higher in autumn cheese samples. A high number of reads was also noted in the genus Clostridium. The counts of spore-forming bacteria of the genus Bacillus were higher in cheeses produced in spring. The study revealed highly similar relationships between the analyzed production periods. The present results contribute to the existing knowledge of cheese microbiota, and they can be used to improve and modify production processes based on the composition of microbial communities, as well as to improve the quality of the final product.