Analysis of Microbiota Persistence in Quebec's Terroir Cheese Using a Metabarcoding Approach

Area of Science:

• Microbiology
• Food Science
• Bioinformatics

Background:

• Metabarcoding is crucial for characterizing cheese microbiota.
• Inconsistent gene markers hinder comparisons across studies.

Purpose of the Study:

• To systematically compare bacterial (16S rDNA) and fungal (ITS) metabarcoding markers.
• To evaluate microbial ecosystem variability in Quebec terroir cheeses.
• To assess the impact of production factors on cheese microbiota.

Main Methods:

• Comparison of V3-V4 and V6-V8 regions of 16S rDNA; ITS1 and ITS2 regions of fungal ITS.
• Selection of optimal markers (V3-V4 and ITS2) based on data quality and detection capacity.
• Analysis of 32 Quebec cheese varieties over two production years using selected markers.

Main Results:

• Taxonomic profiles differed significantly based on the molecular markers used.
• V3-V4 (16S rDNA) and ITS2 (fungal ITS) were identified as optimal markers for dairy-associated microorganisms.
• Microbial variations in cheeses were primarily attributed to changes in starter/ripening cultures or cheesemaking technology, not production year.

Conclusions:

• The V3-V4 and ITS2 regions are recommended for standardized cheese microbiota metabarcoding.
• Cheese microbiota composition is largely stable between production years when technology is consistent.
• Understanding microbial shifts aids in controlling and optimizing cheese production and ripening.