Variations in methane emissions from dairy cows: associations with rumen microbial synergy and metabolic pathway divergence

<h4>Background</h4>Methane (CH₄) is a metabolic by-product of rumen microbial fermentation, contributing significantly to global warming and dietary energy loss. Elucidating the mechanisms underlying natural variation in rumen methanogenesis is essential for the development of effective CH₄ mitigation strategies. Here, we applied rumen metagenomics to identify the microbial mechanisms for differences in enteric CH₄ emissions among dairy cows.<h4>Results</h4>Enteric CH₄ emissions from 111 lactating dairy cows under normal feeding conditions were utilized to characterize the natural variation in rumen methanogenesis. Metagenomic analysis revealed that the comprehensive effects of bacteria involved in starch degradation, lactate metabolism, and volatile fatty acid biosynthesis provide distinct amounts of hydrogen for rumen methanogenesis in high-methane-producing (HMP) and low-methane-producing (LMP) cows. Ciliate protozoa were universally abundant in HMP cows (P < 0.05), whereas methanogens enrichment exhibited heterogeneity, with the dominant methanogen Methanobrevibacter exhibiting negative correlations with the other 11 methanogens (P < 0.05). Six nutrient metabolic pathways modulating methanogenesis were identified, and HMP-associated methanogenesis was further driven by upregulated formate metabolism and acetoclastic pathways (P < 0.05). Random forest model analysis screened 34 microbial genera as biomarkers for CH₄ production.<h4>Conclusions</h4>This study excluded extrinsic confounders exist for rumen microbiome and CH₄ emissions in dairy cows. These findings elucidated the causal microbial and metabolic mechanisms underlying rumen methanogenesis, providing actionable targets for microbiome-based strategies to mitigate CH₄ emissions from livestock farming.