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Background <p>Methane (CH<sub>4</sub>) 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 CH<sub>4</sub> mitigation strategies. Here, we applied rumen metagenomics to identify the microbial mechanisms for differences in enteric CH<sub>4</sub> emissions among dairy cows.</p> Results <p>Enteric CH<sub>4</sub> 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 (<i>P</i> &lt; 0.05), whereas methanogens enrichment exhibited heterogeneity, with the dominant methanogen <i>Methanobrevibacter</i> exhibiting negative correlations with the other 11 methanogens (<i>P</i> &lt; 0.05). Six nutrient metabolic pathways modulating methanogenesis were identified, and HMP-associated methanogenesis was further driven by upregulated formate metabolism and acetoclastic pathways (<i>P</i> &lt; 0.05). Random forest model analysis screened 34 microbial genera as biomarkers for CH<sub>4</sub> production.</p> Conclusions <p>This study excluded extrinsic confounders exist for rumen microbiome and CH<sub>4</sub> 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 CH<sub>4</sub> emissions from livestock farming.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月15日

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  • Peng Jia,
  • Lifeng Dong,
  • Tao Ma,
  • Yanliang Bi,
  • Yan Tu,
  • Qiyu Diao

摘要

Background

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.

Results

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.

Conclusions

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.