Background Enhancing milk nutritional quality through increased ω-3 polyunsaturated fatty acid (PUFA) content and a reduced ω-6/ω-3 PUFA ratio represents a significant opportunity for improving dairy products. While ruminal biohydrogenation substantially influences milk fatty acid (FA) composition, the specific microbial mechanisms regulating the milk fat ω-6/ω-3 PUFA ratio remain poorly characterized. This study aimed to identify key microbial taxa and metabolic pathways controlling this nutritionally relevant parameter, thereby establishing a foundation for targeted microbiome interventions to optimize milk FA profiles. Results Analysis of 95 Holstein cows revealed that rumen bacterial community composition explained 41.0% of the variation in the milk ω-6/ω-3 PUFA ratio. Comparative analysis of cows with contrasting phenotypes (high-ratio, HFR; low-ratio, LFR) demonstrated distinct FA profiles across rumen fluid, serum, and milk, with α-linolenic acid (ALA, C18:3 C9,12,15) and linoleic acid (LA, C18:2 C9,12) emerging as critical determinants. Integrated metatranscriptomic and amplicon sequencing identified members of the family Lachnospiraceae, particularly Butyrivibrio and Eubacterium genera, as central regulators of PUFA metabolism. Notably, HFR-associated microbiomes showed enrichment of FA isomerase gene transcripts. Experimental validation using isolated strains demonstrated that B. hungatei preferentially hydrogenated ALA, while Eubacterium_I efficiently metabolized LA, establishing a mechanistic basis for differential substrate biohydrogenation that influences the final ω-6/ω-3 PUFA ratio. Conclusions Collectively, these results indicate that rumen microbial community structure and transcriptional activity are closely associated with variation in the milk ω-6/ω-3 PUFA ratio. Members of Lachnospiraceae appear to contribute to substrate-specific biohydrogenation processes that may influence downstream milk FA composition. These findings provide a multi-omics framework for understanding microbiome–lipid interactions and support future efforts to develop microbiome-targeted strategies for improving dairy nutritional quality. <MediaObject ID="MOESM3"> <VideoObject FileRef="MediaObjects/40168_2026_2397_MOESM3_ESM.mp4" VideoID="1s2Lsesw8Jy7Sh15rPGY2V"> <Caption Language="En" xml:lang="en"> <CaptionContent> Video Abstract </CaptionContent> </Caption> </VideoObject> </MediaObject>

Integrated metatranscriptomics identifies Lachnospiraceae as keystone taxa regulating rumen biohydrogenation and milk ω-6/ω-3 polyunsaturated fatty acids ratio in dairy cows

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2026年4月13日

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Han Zhang,
Weimin Mao,
Zheng Lai,
Yipeng Zhu,
Jiahao Dong,
Lu Li,
Fei Xie,
Weiyun Zhu,
Junshi Shen,
Shengyong Mao

摘要

Background

Enhancing milk nutritional quality through increased ω-3 polyunsaturated fatty acid (PUFA) content and a reduced ω-6/ω-3 PUFA ratio represents a significant opportunity for improving dairy products. While ruminal biohydrogenation substantially influences milk fatty acid (FA) composition, the specific microbial mechanisms regulating the milk fat ω-6/ω-3 PUFA ratio remain poorly characterized. This study aimed to identify key microbial taxa and metabolic pathways controlling this nutritionally relevant parameter, thereby establishing a foundation for targeted microbiome interventions to optimize milk FA profiles.

Results

Analysis of 95 Holstein cows revealed that rumen bacterial community composition explained 41.0% of the variation in the milk ω-6/ω-3 PUFA ratio. Comparative analysis of cows with contrasting phenotypes (high-ratio, HFR; low-ratio, LFR) demonstrated distinct FA profiles across rumen fluid, serum, and milk, with α-linolenic acid (ALA, C18:3 C9,12,15) and linoleic acid (LA, C18:2 C9,12) emerging as critical determinants. Integrated metatranscriptomic and amplicon sequencing identified members of the family Lachnospiraceae, particularly Butyrivibrio and Eubacterium genera, as central regulators of PUFA metabolism. Notably, HFR-associated microbiomes showed enrichment of FA isomerase gene transcripts. Experimental validation using isolated strains demonstrated that B. hungatei preferentially hydrogenated ALA, while Eubacterium_I efficiently metabolized LA, establishing a mechanistic basis for differential substrate biohydrogenation that influences the final ω-6/ω-3 PUFA ratio.

Conclusions

Collectively, these results indicate that rumen microbial community structure and transcriptional activity are closely associated with variation in the milk ω-6/ω-3 PUFA ratio. Members of Lachnospiraceae appear to contribute to substrate-specific biohydrogenation processes that may influence downstream milk FA composition. These findings provide a multi-omics framework for understanding microbiome–lipid interactions and support future efforts to develop microbiome-targeted strategies for improving dairy nutritional quality.

Video Abstract