High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses

Abstract

ABSTRACTHere, high-throughput sequencing was employed to reveal the highly diverse bacterial populations present in 62 Irish artisanal cheeses and, in some cases, associated cheese rinds. Using this approach, we revealed the presence of several genera not previously associated with cheese, includingFaecalibacterium,Prevotella, andHelcococcusand, for the first time, detected the presence ofArthrobacterandBrachybacteriumin goats' milk cheese. Our analysis confirmed many previously observed patterns, such as the dominance of typical cheese bacteria, the fact that the microbiota of raw and pasteurized milk cheeses differ, and that the level of cheese maturation has a significant influence onLactobacilluspopulations. It was also noted that cheeses containing adjunct ingredients had lower proportions ofLactococcusspecies. It is thus apparent that high-throughput sequencing-based investigations can provide valuable insights into the microbial populations of artisanal foods.