PS1-5. Linking Microbial Profiles in Milk Somatic Cells to Feed Efficiency in Dairy Cattle.

Abstract

Feed efficiency (FE) is a complex trait with major implications for the sustainability and profitability of dairy production; however, the potential association of the milk-associated microbiota with this phenotype remains largely unexplored. Additionally, milk somatic cells (MSC) provide a minimally invasive and easily accessible means to study molecular processes within the mammary gland. Here, we investigated the differences in MSC microbiota between two divergent FE groups of Holstein cows. Eighty-five first-lactation Holstein cows (60–150 days in milk) were ranked for FE using the Canadian genomic evaluation system. The High-FE group included 30 cows, while 20 Medium-Low FE cows represented average efficiency. Milk samples were centrifuged to obtain MSC pellets, and DNA was extracted. Absolute bacterial abundance (BAC) was determined using quantitative PCR (qPCR; n = 80), while 16S rRNA gene sequencing was used to assess the relative composition of the bacterial community. The Amplicon Sequence Variants (ASVs) and taxonomic assignments were inferred using DADA2, followed by phyloseq. Alpha diversity indices (Observed, Shannon, Simpson, Fisher) and beta diversity were analyzed, and differential abundance was assessed with DESeq2 (FDR < 0.01). Functional prediction of MetaCyc pathways was performed using PICRUSt2 (FDR < 0.05). Pearson’s correlation analysis was used to explore associations across the data (phenotypic traits and ASVs). No differences associated with BAC were identified (p = 0.56) between the FE groups. Across the dataset, 397 ASVs were identified. No significant differences in alpha diversity indices were observed between FE groups (p > 0.05). Principal coordinate analysis revealed partial overlap between groups, indicating subtle shifts in the MSC microbiota composition. Two exclusive ASVs were detected in the High-FE group, belonging to the families Bacteroidaceae and Anaerovoracaceae. Differential abundance analysis identified 32 significant ASVs, with 13 upregulated in High-FE cows and 19 in Medium-Low FE cows. ASV401 (Erysipelotrichaceae) and ASV93 (Paludibacteraceae) exhibited the highest fold-change differences. Correlation analyses revealed that methane production showed the highest number of significant correlations with differentially abundant ASVs in MSC. Functional pathway analysis revealed 14 differentially abundant MetaCyc pathways between FE groups (FDR < 0.05). Notably, several differentially abundant pathways were linked to amino acid metabolism. Most were upregulated in the Medium-Low FE group, indicating higher protein turnover and metabolic costs associated with reduced efficiency, including L-tryptophan biosynthesis and ornithine degradation. In contrast, the L-methionine salvage cycle III was upregulated in High-FE cows, suggesting more efficient methionine recycling. Overall, these findings demonstrate that FE is associated with distinct microbial and metabolic profiles within the MSC fraction, despite the absence of differences in absolute bacterial abundance. This highlights potential microbiota-mediated mechanisms that may contribute to the regulation of nutrient utilization efficiency and cellular metabolism in dairy cows.