Multi-omics study reveals rumen microbiome-metabolite associations with early lactation performance in dairy cows (microbiomejournal.biomedcentral.com)

• Shotgun metagenomics and untargeted LC-MS metabolomics of rumen, plasma, milk from 14 transition dairy cows with extreme ECM.
• High-yield cows enriched in Prevotella, Succinimonas, Succinatimonas, and Methanosphaera.
• Low-yield cows enriched in Alistipes, Bacteroides, Methanobrevibacter, associated with cellulose degradation and methanogenesis.
• Pan-genomic analysis revealed conserved hydrogenases and dehydrogenases in low-yield-associated microbes.
• Structural equation model identified metabolic axis from rumen microbes to plasma and milk metabolites correlating with ECM.

"This study used shotgun metagenomics and LC-MS metabolomics on rumen, plasma, and milk samples from 14 dairy cows (7 high-yield, 7 low-yield) to investigate microbial contributions to early lactation performance. High-yield cows showed increased Prevotella, Succinimonas, Succinatimonas and Methanosphaera species, enriched in genes for starch utilization and amino acid synthesis, while low-yield cows had more Alistipes, Bacteroides, and Methanobrevibacter with genes for cellulose degradation and hydrogenotrophic methanogenesis. Pan-genomic analysis revealed conservation of hydrogenases in the latter group, suggesting energy loss. A structural equation model linked Prevotella and Succinatimonas abundance to plasma chenodeoxycholic acid glycine conjugate and milk 5-methoxytryptophan, positively correlating with energy-corrected milk yield."