Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia

Simple Summary Bovine mastitis is one of the most common diseases in cattle farms in Russia. In this work we investigate a microbial composition of milk samples collected from farms of Russian Central Region. Our data revealed significant dominance of several operational taxonomic units corresponding mostly to groups of Staphylococcus aureus, Aerococcus spp. and Streptococcus spp. We identify interesting fact of Staphylococcus and Aerococcus genera seemed to be antagonistic to each other, and the disappearance of the Aerococcus genus in milk microbiota may represent a marker for its transition to a subclinical stage of mastitis. Bovine mastitis is a widespread infectious disease. In addition to the economic damages associated with reduced milk yield due to mastitis, the problem of food contamination by microorganism metabolites, in particular toxins, is also a concern. Horizontal transfer of microorganisms from animal populations to humans can also be complicated by antibiotic resistance. Therefore, bovine mastitis is relevant to the study of microbiology and veterinary medicine. In this study, we investigated the microbiome of milk samples from healthy cows and cows with different forms of mastitis from individual quarters of the udder of cows during first and second lactation. Total DNA was extracted from milk samples. The V3-V4 regions of the bacterial 16S rRNA genes from each sample were amplified to generate a library via high-throughput sequencing. We revealed significant dominance of several operational taxonomic units (OTUs) corresponding mostly to groups of Staphylococcus aureus, Aerococcus spp., and Streptococcus spp. In addition, we unexpectedly identified Streptococcus thermophilus in samples with high SCC quantities. We found some infectious agents that characterized summer mastitis. We demonstrated that in Central Russia, mastitis is associated with a wide variety of causal organisms. We observed some differences in the diversity of the two investigated farms. However, we did not find any significant difference among healthy, mastitis and subclinical samples according to their SCC status from either farms by principal component analysis. Linear discriminant analysis effect size (LEfSe) confirmed the presence of several indicator genera in farms from Moscow and the Tula Region. These results confirm the complex bacterial etiology of bovine mastitis.

Automated summary

Bovine mastitis is a common disease in cattle farms in Russia, with Staphylococcus aureus, Aerococcus spp., and Streptococcus spp. dominating the microbial composition of milk samples. Interestingly, a potential antagonistic relationship between Staphylococcus and Aerococcus genera was observed, with the disappearance of Aerococcus genus indicating a transition to subclinical mastitis. Study results highlight the complex bacterial etiology of bovine mastitis and its implications for microbiology and veterinary medicine.