Diversity and characteristics of raw milk microbiota from Korean dairy farms using metagenomic and culturomic analysis

Abstract

Bovine milk is highly nutritious, so it creates an ideal environment for the growth of microorganisms. Contamination of milk with microorganisms contributes to overall bacterial composition and has a great influence on the acidification and deterioration of milk. As dairy production and consumption have increased over the past decade, the microbial composition of milk has gained attention. In Korea, milk and milk products are rapidly gaining popularity, but studies of the bacterial composition in milk from Korean farms are limited. In the present study, we performed metagenomic analysis with high-throughput sequencing of DNA to identify bacteria in raw milk collected from 40 dairy farms in 4 different provinces in Korea: Gyeonggi-do, Chungcheong-do, Jeolla-do, and Gyeongsang-do. Representative milk bacterial communities including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria formed the core milk microbiota at the phylum level, and Pseudomonas was found to have the greatest provincial variation at the genus level. In addition, we determined the prevalence of sporeforming bacteria using two independent methods of culturomic analysis by MALDI-TOF and next generation sequencing of 16S rRNA genes, and Bacillus thermoamylovorans was identified to account for the largest proportion. We further confirmed that B. thermoamylovorans was able to survive in dairy products and potentially toxigenic using lab cheese model study and Caenorhabditis elegans as a simple host model. Our result clearly shows that specific provinces have distinct proportions of bacteria that may cause spoilage, suggesting specified farm environment management practices depending on the region. These findings can help Korean dairy farms produce safe, high-quality dairy products and develop new sanitation procedures as well as processing controls.