Investigation of seasonal microbiome changes in raw milk between conventional and organic farming practices

Raw milk microbiota is influenced by farming practices, environmental exposure, and seasonal changes. This study investigated how organic and conventional dairy farming practices influence the microbial composition of raw milk over a 1-yr period. Milk and environmental samples were collected quarterly from 7 dairy farms (4 organic and 3 conventional) in Oregon and analyzed using microbiome sequencing. Across all seasons, the microbial community of raw milk was largely similar between organic and conventional farms, with Escherichia-Shigella being the most abundant genus. Aerobic plate counts were significantly higher in conventional raw milk during winter and summer. Organic milk showed greater seasonal variation in α diversity (Shannon index 1.81 ± 0.40 in winter to 1.01 ± 0.34 in fall), whereas conventional milk remained more stable. No significant β diversity differences were observed between farming types. Shared microbial taxa between raw milk and environmental sources varied by season and farming type, reflecting the influence of confinement and grazing. For example, Romboutsia was more abundant during grazing seasons in organic farms, whereas Clostridium sensu stricto 1 appeared uniquely in conventional milk in winter. These seasonal and housing-related trends highlight how farm management shapes milk microbiota.