Metagenomic Analysis of Bacterial Diversity in Milk of Mastitis Cows from Farms with Different Milking Management

Most cases of mastitis are caused by bacteria that infect the udder through the milk ducts causing inflammation. The
objective of this study was to identify the bacteria that cause mastitis in farms that apply different milking management. Mastitis testing using the California Mastitis Test (CMT) was conducted on 132 quarters of milk samples from 33 cows in three farms with different milking management practices. The 3 positive samples from each farm were taken and analyzed for metagenomics in the laboratory. The V1-V9 regions of the 16S ribosomal RNA gene were amplified using primers 27F and 1492R under specific polymerase chain reaction conditions for bacterial identification. DNA concentration was determined using both NanoDrop spectrophotometers and Qubit fluorometer. Library preparations were conducted using Kits from Oxford Nanopore Technology. Primary data were obtained using MinKNOW version
23.04.5. The results of metagenomic analysis of mastitis cow milk samples from farms with different milking management were dominated by bacteria from the Firmicutes and Proteobacteria phylum. Streptococcus agalactiae was
the dominant bacteria causing mastitis in Kemiri farm and UPTD BPBPTDK, while Lactococcus lactis was the dominant bacteria causing mastitis in UPT farm. Kemiri farm had the highest diversity of bacteria in milk compared to
the other two farms. The same 56 bacterial species were found on all three farms. Different milking management
practices on the three farms showed different bacterial diversity and causes of mastitis