Farm-to-Fork Profiling of Bacterial Communities Associated with an Artisan Cheese Production Facility

Abstract

The various stages of the cheese-making process harbor distinct bacterial communities which may influence the sensory characteristics of artisanal cheeses. The objective of this study was to investigate the microbiota from dairy farm to final cheeses along an artisanal cheese-making continuum. Environmental and food samples were collected from 21 sites, including the dairy farm, milk, cheese plant, and finished cheeses. The microbiota of these samples were analyzed using 16S rRNA amplicon sequencing, with sequences grouped into operational taxonomic units (OTUs) by phylotype at the genus level. Alpha diversity decreased from dairy farm to finished cheese. Firmicutes was the dominant phylum, ranging from 31% to 92% between the dairy farm and finished cheeses, respectively, with Proteobacteria, Actinobacteria, and Bacteroides also present (25%, 11%, and 9% overall relative abundance, respectively). Of the 37 core OTUs (>5 reads in >80% of site replicates) observed in cheese, 32 were shared with the dairy farm. Starter-related genera (i.e., Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc) represented between 69% and 98% relative abundance in final cheeses depending on style, with the remainder likely acquired from various environmental sources on the farm and during the cheese-making process.