High-Throughput Sequencing Reveals Bacterial Diversity in Raw Milk Production Environment and Production Chain in Tangshan City of China

Raw milk is a nature media of microbiota that access milk from various sources, which constitutes a challenge in dairy production. This study characterizes the relationship between the raw milk quality and the bacteria diversity at different sampling sites in dairy farms, aiming to provide a strong scientific basis for good hygienic practices and optimized procedure in milk production. High-throughput sequencing of 16S rRNA V3-V4 region was used to analyze the components, abundance and diversity of 48 bacterial population sampled from 8 different sites in dairy farm: pre-sterilized cow’s teats (C1), post-sterilized cow’s teats (C2), milking cluster (E), milk in storage tank (M1), transport vehicle (M2), storage equipment (E2), cow’s dung samples (F) and drinking water (W). Firmicutes account for predominantly 32.36% (C1), 44.62% (C2), 44.71% (E), 41.10% (M1), 45.08% (M2), 53.38% (F) of all annotated phyla. Proteobacteria accounts for 81.79% in W group and Actinobacteria 56.43% in E2 group. At the genus level, Acinetobacter was the most abundant genus that causes bovine mastitis, Acinetobacter and Arthrobacter were dominant in C1, C2, and E groups, Kocuria in E2 group and Arcobacter in W group. E, C1, and C2 group have very similar bacterial composition, and M1 and M2 demonstrated similar composition, indicating that the milking cluster was polluted by the environment or contact with cow udders. Bacterial population composition in different sampling sites identified by NGS reveals a correlation between the bacteria communities of raw milk production chain and the quality of raw milk.