Genetic and physiological influences on the rumen microbiome and metabolic status in Holstein cows

Metabolic disorders in cows occur when physiological metabolic processes are disrupted, often due to nutritional imbalances. These disorders can significantly affect productivity, particularly in high-producing dairy breeds, such as Holsteins, especially during critical periods, including transition and early lactation. A key factor influencing nutritional efficiency is the rumen microbiome, which plays a vital role in fiber digestion, starch fermentation, and the production of VFA, as well as in microbial protein synthesis and vitamin synthesis. Given its importance in maintaining energy and nitrogen balance, this study aimed to identify associations between rumen microbiome composition and the concentration of ketone bodies and liver enzymes in the blood serum, both of which serve as markers of metabolic disorders. The bacterial phyla and genera associated with metabolic markers were further analyzed for correlations with genetic markers through a microbiome GWAS. Additionally, the study examined how parity and lactation progression (DIM) influence the rumen microbiome. The results revealed that both parity and DIM were associated with blood metabolic markers' concentration, with rumen microbiome composition varying throughout lactation and across parities. Several phyla and genera abundances were significantly associated with metabolic markers, notably Lachnospiraceae NK3A20 group, Erysipelotrichaceae UCG_006 (Firmicutes), and Bsconditabacteriales S.R1 (Patescibacteria). The microbiome GWAS identified 3 SNPs with genome-wide significance for the Elusimicrobiota, Planctomycetota, and Verrucomicrobiota phyla, as well as 10 significant SNPs for the Asteroleplasma and Succinivibrio genera. The mean SNP-based heritability for phyla associated with metabolic markers was 0.287, with several taxa exhibiting heritability estimates above 0.2. This study highlights that specific ruminal bacteria are associated with the energy balance and metabolic status of cows, in relation to parity and DIM. Moreover, some of these bacteria are influenced by host genetic factors and could potentially be modified through selective breeding.