Next-generation sequencing to enhance the taxonomic resolution of the microbiological analysis of meat and meat-derived products

Meat makes up a complex environment, home to an extensive bacterial diversity that is heavily influenced by environmental conditions during processing and storage. The current review focuses on the use of next-generation sequencing methods to unravel the complex microbial communities that are present in meat environments in greater detail. Recent applications of these methods in amplicon-sequencing approaches targeting other phylogenetic marker genes than the 16S rRNA gene allowed for a better assessment of species richness in meat and the detection of many minor communities that might have previously gone underreported. With the increasing base quality of the single-molecule sequencing methods, an even improved resolution is to be expected, as high-throughput sequencing of full-length phylogenetic marker genes is on the rise.