Analysis of Bacterial Diversity in Fresh Milk from Commercial Dairy Farms in Xinjiang Based on Metagenomic Sequencing

To investigate the biological characteristics of microbes in fresh milk, this study gathered fresh milk from seven large-scale dairy farms in the southern and northern regions of Xinjiang, analyzing the composition and abundance of bacterial communities in these samples through metagenomic sequencing technology. Firmicutes, Proteobacteria, and Actinobacteria were consistently identified as the dominant phyla across all samples, with stable relative abundance patterns across regions. At the genus level, the genera with the highest relative abundances were Sporosarcina, Streptococcus, and Escherichia, with relative abundances of 2.51–2.58%, 2.23–2.27%, and 1.93–1.97%, respectively. While exploring species richness, it was observed that the XN group had the most OTUs, the DR group had the fewest, and there were significant differences in community structure between the ND group and the other six groups. Further Alpha diversity analysis revealed no significant variation in Chao1 indices across the seven sample groups, highlighting a significant difference in Shannon index for ND samples, and no significant differences in Shannon indices between the CJ, JY, KT, DR, and TR samples. Shifting focus to functional potential, the top three relative abundances in the microbial metagenome KEGG functional library are biological systems, human diseases, and environmental information processing; additionally, within the CAZy (Carbohydrate-Active enZymes) database, the three most abundant categories are glycosyltransferases (GT), glycoside hydrolases (GH), and carbohydrate-binding modules (CBM). By delineating these patterns, this study demonstrates the microbial spectrum characteristics of fresh milk from southern and northern Xinjiang, China, offering a theoretical foundation for enhancing the quality of fresh milk in the area.