Strain-level multiomics analysis reveals significant variation in cheeses from different regions

Abstract

This study analyzed the microbiomes and metabolomes of four Chinese and four European cheeses using deep metagenome sequencing and liquid chromatography-mass spectrophotometry. Our results revealed great variations in the cheese microbiome and metabolome between samples, but samples originated from the same region shared a higher similarity. Deep metagenome sequencing identified four novel species (belonging to the Salinicoccus, Kocuria, and Glutamicibacter genera), and their profiles of carbohydrate-active enzymes and secondary metabolite clusters coding genes supported that these novel species were involved in cheese flavor formation. The main differential metabolites between Chinese and European cheeses were amino acids and volatile substances. Significant correlations were found between individual cheese-associated bacterial taxa (especially lactic acid bacteria) and metabolites (r > 0.6, p < 0.05), suggesting that these taxa and metabolites together shaped the cheese flavor. The cheese microbiome comprised a high proportion of phage (26.06%), providing evidence of phage infection/genome integration and horizontal gene transfer from phage to bacteria. Such processes would also modulate cheese microbiomes and thus flavor quality.