Abstract
Background: Bacterial mastitis in cows is a huge challenge to the dairy cattle breeding and production industry. This study examined the relationship between mastitis and bacterial diversity at different sampling sites in dairy farms. Methods: High-throughput sequencing of 16S rRNA V4 region was used to analyze the abundance and diversity of bacterial population sampled from seven different sites in a dairy farm, named healthy cow milk (N), cow milk from a mastitis cow (C), perimammary (T), milk collecting cup (B), turntable surface (P), feces (F) and bedding material (W). Result: In total, 2757356 reads were obtained from the sequencing results, which were annotated to 29 phyla, 67 classes, 166 orders, 295 families, 696 genera and 306 species. In all samples, Proteobacteria and Firmicutes were the dominant microflora, while Oscillospira-UCG-005 and Atopostipes were the dominant genera in different proportions, indicating certain differences in bacterial flora structure among different samples. Furthermore, alpha diversity analysis revealed high richness and diversity among different samples.