Microbiota changes in rumen and milk corresponding to dietary protein intake in transition dairy cows

During the transition period in dairy cows, the incidence of disease increases due to a negative energy balance affecting both the metabolic and immune health status. Limiting milk production at the beginning of lactation improves the metabolic status of cows. However, past strategies tested to achieve this reduction either negatively affected milk yield for the rest of the lactation or were difficult to implement on large-scale dairy farms. This study evaluated the impact of a temporary reduction in MP supply during the transition period on the rumen and milk microbiota and their metabolic composition. Treatment cows (n = 5) were fed 80% of their MP needs (MP80) from 14 d before calving to 14 d after calving, before being switched to a 100% MP diet (MP100) for an additional 14 d. Control cows (n = 6) were fed MP100 for the entire experiment. Samples of rumen content and milk were taken in the immediate postpartum phase (PP) on d 2 and 7, as well as after dietary change in the experimental recovery phase on d 21 and 28 postpartum. All samples were extracted for DNA and analyzed using shotgun metagenomic sequencing (Illumina NovaSeq). Milk samples were additionally analyzed for composition, and rumen fluid was analyzed for short-chain fatty acids and ammonia-N. Significant changes to the microbial composition were almost exclusively associated with the effect of day of sampling, with the exception being the family Micrococcaceae, which was found to be differentially abundant in the MP100 compared with the 80% group in PP milk samples. This study used a metagenomics approach to understanding the impact of altered protein supply on rumen and milk microbiota, to better understand impacts on these separate ecosystems.