Metagenomics of pasteurized and unpasteurized gouda cheese using targeted 16S rDNA sequencing

Abstract

Background: The microbiome of cheese is diverse, even within a variety. The metagenomics of cheese is dependent on a vast array of biotic and abiotic factors. Biotic factors include the population of microbiota and their resulting cellular metabolism. Abiotic factors, including the pH, water activity, fat, salt, and moisture content of the cheese matrix, as well as environmental conditions (temperature, humidity, and location of aging), influence the biotic factors. This study assessed the metagenomics of commercial Gouda cheese prepared using pasteurized or unpasteurized cow milk or pasteurized goat milk via 16S rDNA sequencing.

Results: Results were analyzed and compared based on milk pasteurization and source, spatial variability (core, outer, and under the rind), and length of aging (2-4 up to 12-18 months). The dominant organisms in the Gouda cheeses, based on percentage of sequence reads identified at the family or genus levels, were Bacillaceae, Lactococcus, Lactobacillus, Streptococcus, and Staphylococcus. More genus- or family-level (e.g. Bacillaceae) identifications were observed in the Gouda cheeses prepared with unpasteurized cow milk (120) compared with those prepared with pasteurized cow milk (92). When assessing influence of spatial variability on the metagenomics of the cheese, more pronounced differences in bacterial genera were observed in the samples taken under the rind; Brachybacterium, Pseudoalteromonas, Yersinia, Klebsiella, and Weissella were only detected in these samples. Lastly, the aging length of the cheese greatly influenced the number of organisms observed. Twenty-seven additional genus-level identifications were observed in Gouda cheese aged for 12-18 months compared with cheese only aged 2-4 months.

Conclusions: Collectively, the results of this study are important in determining the typical microbiota associated with Gouda cheese and how the microbiome plays a role in safety and quality.

Keywords: 16 s rDNA; Cheese; Dairy; Gouda; Metagenome; Unpasteurized milk.

Fig. 1

Rarefaction curves of all commercial Gouda cheeses assessed in this study

Fig. 2

Percentage of bacterial genera in Gouda cheese based on milk pasteurization and source. The reads from all cheese sampling locations (core, inside, just under the rind) were included

Fig. 3

Bacterial kronographs of core (a), under the rind (b), and inside (c) locations of the commercial Gouda cheese

Fig. 4

Bacterial genera in commercial unpasteurized Gouda cheese from the same manufacturer based on aging length