Study area and description of different sampling sites

The study was conducted in a large dairy farm (more than 1,500 cows in the stockade) in Tangshan City, Hebei Province, China (118.02°E, 39.63°N). The Milking Parlour, milk-storing hall and Sports Ground were selected as sampling sites. The sampling sites were cleaned and rinsed daily after milking, samples collected included pre-sterilized cow’s teats (C1), post-sterilized cow’s teats (C2), milking cluster (E), milk in storage tank (M1), milk in transport vehicle (M2), milk storage equipment (E2), cow dung samples (F) and cow’s drinking water (W). The samples were stored in liquid nitrogen tank for a short time after collection. Study was performed in September of 2019, and samples were taken 3 times per day, for a consecutive 5 days. The samples collected at the same day was mixed together and serve as a replicate. For each site, 5 repeats were sequenced and analyzed.