Abstract
The nutrition and flavor of cheese are generated by the microbial community. Thus, horse milk cheese with unique nutrition and flavor, an increasingly popular local cheese of the Xinjiang Uygur Autonomous Region of China, is considered to have diverse and specific bacterial community. To verify this hypothesis, horse, cow, and goat milk cheese samples produced under the same environmental conditions and manufacturing process were collected, and the 16S rRNA gene was targeted to determine the bacterial population size and community composition by real-time quantitative PCR and high-throughput sequencing. The bacterial community of horse milk cheese had a significantly larger bacterial population size, greater species richness, and a more diverse composition than those of cow and goat milk cheeses. Unlike the absolute dominance of Lactococcus and Streptococcus in cow and goat milk cheeses, Lactobacillus and Streptococcus dominated the bacterial community as the starter lactic acid bacteria in horse milk cheese. Additionally, horse milk cheese also contains a higher abundance of unclassified secondary bacteria and specific secondary bacteria (e.g., Psychrobacter, Sulfurisoma, Halomonas, and Brevibacterium) than cow and goat milk cheeses. These abundant, diverse, and specific starter lactic acid bacteria and secondary bacteria may generate unique nutrition and flavor of horse milk cheese.