Abstract: This study aimed to fully demonstrate the microbial diversity in dairy products from Xinjiang, China and to compare the microbial community composition of raw and fermented milk from different animal species. The composition and structure of bacterial communities in bovine milk, camel milk, mare’s milk, caprine milk, fermented cow milk, fermented camel milk and koumiss from Kizilsu Kirghiz and Tacheng regions of Xinjiang were analyzed based on high-throughput sequencing of the V4-V5 region of the 16S rDNA. A total of 539 557 effective sequences and 379 OTUs were obtained. The results showed that the Shannon-Wiener diversity index for raw milk was higher than that for fermented milk. The microbiota of raw and fermented milk were significantly different. Two bacterial phyla, Firmicutes and Proteobacteria, dominated the microbiota of all seven dairy products, and Proteobacteria dominated the microbiota of raw milk, while Firmicutes was the predominant phylum in fermented milk. At the genus level, Pseudomonas was dominant in cow milk, Escherichia-Shigella was the major bacterial population in camel milk, Leuconostoc was the most abundant bacteria in mare’s milk, Lactococcus was the dominant bacteria in goat milk samples, and Lactobacillus dominated the microbiota of yogurt, camel yogurt and koumiss. The microbiota in raw and fermented milk from different animals were significantly different, and the abundances of environmental bacterial and pathogenic bacteria (or conditional pathogenic bacteria) in raw milk were highest. The results of this study would provide preliminary data of the microbial diversity in dairy products to assess their effect on the health of Xinjiang minorities.

Key words: dairy product, microbial diversity, high-throughput sequencing