Metagenomics-based surveillance identifies possible sources of mastitis-associated organisms in organic and conventional dairy farm environments

Mastitis is one of the most economically significant diseases of the dairy industry. Although farm environments are recognized reservoirs for mastitis pathogens, comprehensive metagenomic comparisons between organic and conventional systems remain limited. We compared the prevalence, diversity, and functional potential of mastitis-associated organisms in one organic and one conventional dairy farm in Texas using shotgun metagenomics. Of 180 samples collected from six environmental sites (teats, liners, parlor floor mats, feed areas, bedding sands, and water troughs), 126 were retained after quality-control exclusions. Taxonomic analysis revealed the prevalence of Pseudomonas fluorescens, Lactococcus garvieae, Escherichia coli, Citrobacter freundii, Enterococcus faecium, and Streptococcus parauberis. Alpha- and beta-diversity analyses indicated similar pathobiome structure between farm types, with niche-specific clustering observed for teat and liner samples. Functional annotation revealed comparable COG category distributions, with toxin-related genes representing the most abundant virulence-associated signatures, followed by lipopolysaccharide synthesis genes; adhesion and capsular polysaccharide genes were relatively more abundant on the organic farm. Metagenome-assembled genomes affiliated with key species confirmed genes related to toxin secretion, lipopolysaccharide biosynthesis, adhesion, and biofilm formation. Collectively, these farms harbored similar mastitis-associated reservoirs but differed in certain virulence-associated signatures, highlighting the need for environment-specific hygiene interventions.