Microbial Evolution in Artisanal Pecorino-like Cheeses Produced from Two Farms Managing Two Different Breeds of Sheep (Comisana and Lacaune)

Abstract

"Pecorino" is a typical semi-hard cheese obtained with raw or heat-treated sheep milk using procedures to valorize the raw material's chemical and microbiological properties. In the present study, using a high-throughput method of 16S rRNA gene sequencing, we assessed the evolution of the microbiome composition from milk to Pecorino-like cheese in artisanal processes using milk from Comisana and Lacaune sheep breeds. The comparative analysis of the bacterial community composition revealed significant differences in the presence and abundance of specific taxa in the milk microbiomes of the Comisana and Lacaune breeds. Next-Generation Sequencing (NGS) analysis also revealed differences in the curd microbiomes related to dairy farming practices, which have a relevant effect on the final structure of the Pecorino cheese microbiome.

Keywords: Comisana breed; Lacaune breed; Next-Generation Sequencing (NGS); Pecorino cheese; microbiome; sheep milk.

Figure 1

Rarefaction curves for the samples of the five different farms. LSB = Lacaune Sheep Breed, CSB = Comisana Sheep Breed, Mi = milk samples, Cu = curd samples, Ch = cheese samples.

Figure 2

Comparative analysis of milk microbiomes. (A) Score plot showing principal components (PCO) 1 and 2 calculated with the abundance matrix of the CSB and LSB milk microbiota. Each symbol represents one microbiota. The plot model explains 100% of the total data variance. (B) Venn diagram showing the number of shared and unique OTUs (≥2 reads) in the CSB and LSB milk microbiotas.

Figure 3

Principal component analysis (PCA) of taxa occurring in CSB and LSB milk microbiotas based on the relative abundance distribution at the family (A) and OTU (B) levels.

Figure 4

Principal component analysis of taxa occurring in the CSB (blue symbols) and LSB (red symbols) in milk (circle), curd (square) and cheese (inverted triangle) microbiotas based on the relative abundance distribution at the family level.

Figure 5

Comparative analysis of curd microbiomes. (A) The Venn diagram shows the number of shared and unique OTUs (≥2 reads) in the CSB and LSB milk and curd microbiotas. (B) Principal component analysis (PCA) of taxa occurring in the CSB and LSB curd microbiotas is based on the relative abundance distribution at the OTU level.

Figure 6

The Venn diagrams show the number of shared and unique OTUs (≥2 reads) in the milk, curd and cheese microbiotas from the CSB (Left Panel) and LSB (Right Panel) cheesemaking processes.