Microbiome

Linking the milk microbiome to metabolic and immune dynamics associated with subclinical inflammation during the transition period in Holstein cows

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Abstract

The transition from late gestation to early lactation is a critical period for dairy cows, characterized by profound metabolic and immune adjustments that counteract potential sub-clinical inflammation and may influence the milk microbiome. This study aimed to explore the relationships between blood metabolic and inflammation profiles and milk microbiota dynamics throughout the transition period in Holstein cows. A total of 53 animals belonging to one herd were monitored longitudinally at three time points: 60 days before calving (−60 d, pre-dry-off), 5 days after calving (+5 d), and 30 days after calving (+30 d). Animals were selected to include first- and second-parity cows calving outside periods of peak heat stress to minimize environmental confounding and ensure relatively contemporaneous groups based on expected calving dates. At each sampling, blood samples were analyzed for a comprehensive panel of 31 metabolites related to energy metabolism, liver function, oxidative stress, inflammation, innate immunity, and mineral status. Milk microbiota composition was characterized through 16S rRNA V3-V4 regions sequencing. Alpha diversity was estimated using the Shannon index to assess within-sample microbial diversity across time points, and differences between sampling points were tested using linear mixed models that included parity and time as fixed effects. Beta diversity was calculated using Bray-Curtis dissimilarity to assess differences in milk microbial composition between samples and tested for temporal effects using PERMANOVA with time and parity as factors, with permutations stratified by animal. Sparse Partial Least Squares (sPLS) analysis was used to explore associations between microbial taxa and blood biomarkers. At the family level, Corynebacteriaceae, Aerococcaceae, and Oscillospiraceae were the most abundant taxa, accounting on average for approximately 13%, 7%, and 6% of total sequences, respectively. Overall, composition remained stable across time, although Aerococcaceae markedly decreased at +5 d postpartum. Alpha diversity (Shannon index) showed minor temporal fluctuations, while beta diversity (Bray-Curtis) differed significantly across all sampling points (PERMANOVA, P Corynebacterium and Staphylococcus, reflecting differential associations between host metabolic status and milk microbiota composition. These findings point to possible interactions between milk microbiota composition and the metabolic and immune status of dairy cows during the transition period, highlighting functional relationships that warrant further validation using complementary integrative approaches.Acknowledgements. Part of the COWHOLIC project. Also, funded by the European Union.

Keywords: 2026

How to Cite:

Pegolo, S., Bisutti, V., Giannotta, G., Vanzin, A., Secchi, G., Rovetta, C., Giannuzzi, D., Bani, G., Cattaneo, L., Trevisi, E. & Cecchinato, A., (2026) “Linking the milk microbiome to metabolic and immune dynamics associated with subclinical inflammation during the transition period in Holstein cows”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285544. doi: https://doi.org/10.31274/wcgalp.23737

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