Analysis of Raw Milk Microbiota from Different Sources using High-throughput Sequencing
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Abstract:
Second-generation high-throughput sequencing was used in this study to analyze the bacterial diversity of raw milk samples and predict their functions. A total of 23 raw milk samples were collected from four regions, Beijing, Hebei, Inner Mongolia, and Tianjin, during different seasons. Genomic DNA was sequenced using Illumina MiSeq sequencing platform for the V3-V4 "variable regions" of 16SrRNA. Using the RDP classifier database, the community distribution, relative abundance, and metabolic pathways of the functional genes of bacteria in raw milk were analyzed. The bacteria in raw milk can be divided into 33 phyla and 732 genera. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are the main phyla, and their average relative abundances account for 99.37 % of the total number of microorganisms. The dominant genera are Pseudomonas and Acinetobacter, with a sum of average relative abundance of 60.55 %. There are differences in the structural composition and relative abundance of the microbial communities in the raw milk samples collected from different seasons and regions. The relative abundances of Pseudomonas and Aeromonas are significantly different during different seasons (p<0.05). Finally, amino acid metabolism, carbohydrate metabolism, and membrane transportation are the main metabolic pathways of bacteria in raw milk.
