Variations of rumen metagenome and metabolome in dairy cows with different feed intake levels during the postpartum period

Abstract Feed intake, a critical factor for dairy cows during the postpartum period, is intricately linked to the rumen microbiome. However, the specific roles of rumen metagenome and metabolome in modulating feed intake in postpartum dairy cows remain unclear. In the current study, 20 postpartum dairy cows were divided into low feed intake ( n = 5) and high feed intake (HFI, n = 5) groups to investigate the role of ruminal microbial composition, function, and metabolism on feed intake using a combined approach of metagenomics and metabolomics. Our analysis revealed a significant enrichment of Bacteroides and Fibrobacter in HFI cows ( p < 0.05), contributing to enhanced protein and energy metabolism. Metabolomic analysis disclosed that HFI cows exhibited a higher relative concentration of rumen metabolites, such as alpha-tocopheryl acetate (fold change = 9.2, p = 0.008), linoleic acid (fold change = 5.96, p = 0.007), and leucine (fold change = 4.14, p = 0.004). Spearman correlation analysis pinpointed a positive correlation between specific microbiota ( Succinivibrionaceae and Prevotellaceae ) and metabolites involved in amino acid and peptide metabolism, fatty acid metabolism, and conjugates. Furthermore, co-occurrence network analysis showed that the unclassified_f_Succinivibrionaceae, Succinatimonas , and Ruminobacte were significantly associated with dry matter intake-associated metabotypes, including rumen metabolites involved in fatty acids and conjugates, favonoids, and gycerophosphocholines. The feed intake variation explained by the rumen microbiome, functions, and metabolites were 29.63%, 27.30%, and 33.50%, respectively. These findings provide comprehensive insights into rumen metagenomics at different feed intake levels in postpartum dairy cows, potentially guiding strategies to manipulate the rumen microbiome for feed intake and production improvement.