Microbial Shifts in Bovine Milk Across Mastitis Severity Grades: Implications for Early Detection and Udder Health Sustainability in Tropical Dairy Systems

Subclinical mastitis remains a major barrier to sustainable milk production in tropical smallholder systems due to its asymptomatic nature and microbial complexity. This study aimed to characterize the milk microbiota across progressive mastitis scores (healthy, subclinical scores 1– 3) using full-length 16S rRNA sequencing via Oxford Nanopore Technology. Heatmap visualization of the top 50 most abundant taxa revealed distinct microbial patterns associated with disease severity. Streptococcus parauberis, Ralstonia pickettii, and Streptococcus agalactiae showed increasing abundance with higher mastitis scores, indicating their potential role in disease progression. Conversely, beneficial or commensal taxa such as Epilithonimonas vandammei and Lactococcus garvieae were more prevalent in healthy samples but decreased sharply as inflammation progressed. These microbial shifts underscore a dysbiotic transition in the milk microbiome associated with mastitis, providing insights into early biomarker discovery. Understanding microbial dynamics in milk offers a promising approach to enhancing mastitis diagnostics and supporting udder health management strategies, particularly in tropical dairy production systems striving for resilience and sustainability.