Quantitative microbiome profiling reveals associations between ruminal microbiota shifts and accelerated milk...

Milk is a valuable source of essential nutrients for humans. In dairy cows, the rumen-the largest digestive organ-plays a critical role in supporting high productivity. The postpartum period marks a crucial transition to peak lactation, characterized by a rapid rise in milk and milk solids yield. However, the microbial mechanisms underlying this transition remain poorly understood. Previous studies of periparturient cows' rumen microbiota have primarily relied on relative microbiome profiles (RMP). Due to high false-positive rates of relative abundance (RA), RMP are unsuitable for capturing longitudinal microbial dynamics. In contrast, quantitative microbiome profiles (QMP), which focuses on absolute abundance (AA), offers a more accurate assessment of microbial community changes over time. Using QMP, we identified two distinct enterotypes (Clusters 1 and 2) across all samples, with Cluster 2 increasing progressively during lactation. Subsequently, through differential analysis, correlation analysis, and contribution assessment, we identified three genera-Succinivibrionaceae_UCG-001, Lachnospira, and Ruminococcus-were strongly associated with the rapid increase in milk yield. Among them, Succinivibrionaceae_UCG-001 showed the most significant contribution to changes in milk yield and energy corrected milk (ECM), with its abundance markedly rising as lactation progressed. Additionally, we observed that the effect of Ruminococcus on ECM may be mediated by changes in ruminal propionate e level. These findings highlight Succinivibrionaceae_UCG-001 as a key taxon driving the early lactation surge in milk production and provide novel insights into the role of the rumen microbiome in optimizing dairy performance.