Abstract
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.
Highlights
The quality of fermented foods is determined mostly by microbial genera and species colonizing food products
High levels of milk production in dairies and the combination of raw materials from different milk producers contribute to the high microbial biodiversity of cheese and the absence of significant differences in the operational taxonomic units (OTUs) reads across production seasons
This study demonstrated that despite the application of different testing techniques, the relationships between the analyzed production periods were highly similar
Summary
The quality of fermented foods is determined mostly by microbial genera and species colonizing food products. Microorganisms are ubiquitous in the farm environment (soil, water, feed, natural fertilizers, and premises). They are present on animal skin, in animal digestive tracts, and in animal secretions (such as milk), and they colonize the surface of fodder plants. Microorganisms are found on the surface of processing lines, devices, machines, conveyor belts, pipelines, packaging, and auxiliary raw materials. They are added to products as starter cultures, and they are present on the hands of dairy plant employees [4,5]. The formation of sensory attributes is a complex biochemical process where environmental and process conditions, such as the heating temperature of the cheese slurry and the
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