Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing

Area of Science:

• Microbiology
• Food Science
• Genomics

Background:

• Serra da Estrela PDO cheese is a traditional Portuguese product with a long manufacturing history.
• Understanding the microbiome of traditional foods is crucial for preserving their unique characteristics and ensuring safety.

Purpose of the Study:

• To characterize the microbiome of Serra da Estrela PDO cheese and its primary raw materials: raw ewes' milk and thistle flowers (Cynara cardunculus L.).
• To investigate the influence of raw materials on the cheese's microbial composition.

Main Methods:

• Next-generation sequencing of rRNA gene amplicons (V3-V4 for bacteria, ITS2 for fungi).
• Analysis of samples from two production campaigns, including milk, thistle flowers, and cheese.
• Identification and quantification of bacterial and fungal taxa.

Main Results:

• High microbial diversity was observed in all analyzed matrices (cheese, milk, thistle), with significant differences between them.
• Over 500 taxa were identified per matrix, with distinct dominant, sub-dominant, and rare populations.
• A core microbiome of 30 taxa, including Leuconostoc, Lactococcus, Candida, Debaryomyces, and Yarrowia, was identified in the cheese.

Conclusions:

• The raw materials significantly influence the microbiome of Serra da Estrela PDO cheese.
• This characterization aids in understanding microbial dynamics and preserving the identity, quality, and safety of this traditional cheese.