Multiomics analysis of a novel American raw milk cheese (Cornerstone) and the effect of production and aging location

ABSTRACT: Cornerstone is a semihard farmstead cheese with a natural rind that was developed as an “American original.” The production of Cornerstone cheese relies on the use of unpasteurized (raw) milk, natural milk starters, and the colonization and activity of adventitious microbes native to each farmstead operation. This study describes and compares the microbial community dynamics as well as the metabolites, volatile compounds, and sensory attributes of Cornerstone cheese produced at 3 different facilities. The microbial composition of samples (n = 96) collected along the cheesemaking continuum was determined via amplicon sequencing of the bacterial 16S rRNA and fungal internal transcribed spacer genes. Despite the high bacterial diversity observed within raw milk samples, the natural milk starters produced on-site at 3 different facilities were primarily Streptococcus thermophilus and Lactobacillus delbrueckii. Microbial communities in the pastes of the resulting cheeses were similar, and ultimately attributed, to their respective natural milk starters throughout aging. The cheese rind microbiota established early and persisted throughout aging. Differential abundance analysis identified microbes uniquely abundant in cheeses produced at each facility. Beta diversity metrics indicated that bacterial communities clustered by production facility, not by aging location, whereas fungi were likely influenced by some combination of both. Aging shelves, fans, and cheese forms were identified as primary environmental sources of microbes. Descriptive sensory analysis revealed significant differences in textural attributes between cheeses but only minor differences in flavor. Volatile compounds clustered by aging day more than production location whereas there was no clear clustering by metabolites. These observations demonstrate the critical importance of natural milk starters and environmental microbes at the site of production on the structure of cheese microbial communities and the complex interplay between microbial communities, metabolic processes, and the development of sensory characteristics in cheese.