Insights into milk microbiota differences among healthy, mastitis-suspected, and subclinical mastitis cows at dairy farms in Southern Vietnam

Objectives: This study aimed to characterize and compare the milk microbiota composition among Holstein Friesian cows with healthy (HU), mastitis-suspected (MSU), and subclinical mastitis (SM) udders in Southern Vietnam. Materials and Methods: Sixty milk samples were collected from two dairy farms and classified based on somatic cell counts (SCC) into three groups: HU (<200,000 cells/ml), MSU (200,000–400,000 cells/ml), and SM (>400,000 cells/ml). Bacterial communities were profiled using Illumina MiSeq sequencing of the 16S rRNA gene. Results: The prevalence of subclinical mastitis was 46.67% (p < 0.05). The core microbiome was dominated by phyla of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes (>90%); and taxa of Moraxellaceae, Sphingomonadaceae, Enterobacteriaceae, Erysipelotrichaceae, and Streptococcaceae. Analysis revealed significant dysbiosis in the SM group, characterized by elevated relative abundances of mastitis-associated taxa (Mycobacteriaceae, Streptococcaceae, Moraxellaceae, Pasteurellaceae, and Mycoplasmataceae) compared to healthy udders (p < 0.05). Conversely, commensal taxa typical of healthy milk (Rikenellaceae, Lactobacillaceae, Sphingomonadaceae, and Opitutaceae) were significantly depleted in SM samples but remained abundant in both HU and MSU groups (p < 0.05). Notably, the microbial profile of the MSU group was statistically similar to that of the HU group (p > 0.05), with no distinct variation in key bacterial families. Principal coordinate analysis further confirmed that SM samples formed a distinct cluster separate from the HU and MSU groups. Conclusions: Subclinical mastitis drives significant shifts in the milk microbiome. However, mastitis-suspected cows retain a microbiome similar to that of healthy udders, suggesting that SCC thresholds alone may require careful interpretation in borderline cases.