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

Abstract

cHere, 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, including Faecalibacterium, Prevotella, and Helcococcus and, for the first time, detected the presence of Arthrobacter and Brachybacterium in 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 on Lactobacillus populations. It was also noted that cheeses containing adjunct ingredients had lower proportions of Lactococcus species. It is thus apparent that high-throughput sequencing-based investigations can provide valuable insights into the microbial populations of artisanal foods.

A sequencing approach targeting the 16S rRNA gene unravels the biofilm composition of spiral-wound membranes used in the dairy industry

“…and γ-Proteobacteria (Klebsiella sp., Acinetobacter sp., and Psychrobacter sp.) found on milk processing membranes could be associated with their natural presence in raw milk and their natural resistance to pasteurization since they were found in both milk and cheese rind ecosystems or in biofilms on post-pasteurization lines (Sharma and Anand 2002;Quigley et al 2012;Bokulich and Mills 2013;Quigley et al 2013). The presence of γ-Proteobacteria on milk processing membranes could be favored by the cold filtration environment (17°C, Table 1), as observed in milk ecosystems during long cold storage at 4°C, in contrast with fresh raw milk dominated by Gram-positive bacteria (such as Bacilli) at the farm (Raats et al 2011;Quigley et al 2013).…”

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

“…A comprehensive survey of about 60 Irish soft, semihard, and hard cheeses was recently performed by HTS to screen for differences in bacterial diversity according to cheese type, milk, and production technology. The structures of cheese microbiota varied according to the animal origin of the milk and the ingredients used and also differed between pasteurized and raw milk (15). It was shown that the Lactobacillus populations increased in hard cheeses compared to those in soft cheeses, indicating an effect of the level of cheese maturation on the development of lactic acid bacteria (LAB).…”

“…In addition, high salt content in some cheeses resulted in the absence of Leuconostoc and Pseudomonas. Moreover, the inclusion of ingredients such as herbs, spices, or seaweed impacted microbial composition (15). Microbial diversity can also give information on the mode of food production.…”

“…HTS is suited to such investigation, providing in-depth assessment of the location of different microbes across food matrices. Indeed, HTS has been used to highlight a significantly different structure of the microbiota in cheese and cheese rinds (15). Understanding how microbiota evolve over time is a priority in studying the microbial ecology of foods.…”

“…For example, coverage obtained from about 1,000 reads was satisfactory to determine the microbiota of some fermented soybean products (16,17). Most samples of soft, semihard, and hard Irish cheeses were adequately covered with slightly more than 1,000 reads, while cheese rinds, which have a more complex microbiota, required more sequences to be adequately studied (15). Finally, adequate coverage was reached beyond 5,000 sequences per sample of fermenting must for fermented alcoholic beverages (22,30).…”