Microbial diversity in milk from holstein dairy cattle with mastitis in Southern China using illumina MiSeq-based analysis

To evaluate the microbial population in milk from dairy cows with mastitis in Guangxi Province, China, 11 fresh milk samples were collected from cows with mastitis at a farm in the province with 1000 Holstein dairy cows. A CMT was performed on the milk samples, and they were classified by parity: A (1_th), B (2_nd), and C (3_rd). The microbial community was analyzed via deep DNA sequencing of the bacterial 16S rRNA genes using the Illumina MiSeq platform. The results revealed that there were many bacteria and fungi present in the milk samples. Ten bacterial phyla (Acidobacteria, Actinobacteria, Bacteria-unclassified, Bacteroidetes, Candidate-division-TM7, Cyanobacteria, Firmicutes, Fusobacteria, Proteobacteria, and Tenericutes) were identified. Firmicutes was the predominant phylum, followed by Tenericutes. The fungi found in the samples belonged to 2 phyla (Ascomycota and Basidiomycota). At the genus level, the most abundant bacterial operational taxonomic units (OTUs) were Enterococcus and Mycoplasma. The most abundant fungal genus was Malassezia, followed by Agaricales-unclassified. The data indicated that the predominant phylum in the milk samples was associated with climate, antibiotic resistance, and parity. In this study, we provide a theoretical foundation for research on the prevention of mastitis as well as the selection of medicine for mastitis treatment.