Microbiome

Investigation of Relationship Between Milk Somatic Cell Associated Microbiota and Feed Efficiency in Dairy Cattle

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Abstract

Abstract Text:Feed efficiency (FE) is a complex trait with major implications for dairy sustainability and profitability. However, the association between the milk-associated microbiome, which reflects host metabolic status, and this phenotype remains largely unexplored. In parallel, milk somatic cells (MSC) provide a minimally invasive means to study molecular processes within the mammary gland. This study aimed to investigate the differences in MSC microbiome 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 (V3-V5 region) was used to assess the relative composition of the bacterial community. The Amplicon Sequence Variants (ASVs) and taxonomic assignments were inferred using DADA2. Alpha diversity indices (Observed, Shannon, Simpson, Fisher) and beta diversity were analyzed using phyloseq, and differential abundance was assessed with DESeq2 (FDR 0.05). Principal coordinate analysisrevealed partial overlap between groups, indicating subtle shifts in the MSC microbiome composition. Two ASVs were uniquely significantly detected in the High-FE group, belonging to the families Bacteroidaceae and Anaerovoracaceae. Differential abundance analysis identified 32 significant ASVs (FDR Erysipelotrichaceae) and ASV93 (Paludibacteraceae) exhibited the highest fold-change values, with log-fold changes of -2.39 and 2.53, respectively. 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 microbiome-mediated mechanisms that may contribute to the regulation of nutrient utilization efficiency and cellular metabolism in dairy cows.

Keywords: 2026

How to Cite:

Asselstine, V., Baes, C., Cánovas, à., Gebim Polizel, G., Guan, L., Jahnel, R., Miglior, F., Santana, M. & Schenkel, F., (2026) “Investigation of Relationship Between Milk Somatic Cell Associated Microbiota and Feed Efficiency in Dairy Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287270. doi: https://doi.org/10.31274/wcgalp.24252

Rights: 1