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Integrative multi-omics analysis of rumen development in early-life yaks

ABSTRACT: This study investigates the developmental changes in the rumen of early-life yaks using integrative metagenomics, metabolomics, histology, fermentation profiling, and single-cell transcriptomics. Rumen fluid and epithelial tissue samples collected from yaks at 1, 6, and 12 months of age were analyzed to characterize age-associated shifts in the rumen microbiome, metabolome, and epithelial cell programs. The study aims to reveal how microbial functions, rumen metabolites, and host epithelial maturation are coordinated during postnatal rumen development.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse-phase, Liquid Chromatography MS - positive - reverse-phase

PROVIDER: MTBLS14340 | MetaboLights | 2026-04-21

REPOSITORIES: MetaboLights

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			Action	DRS
	a_MTBLS14340_LC-MS_negative_reverse-phase.txt	Txt
	a_MTBLS14340_LC-MS_positive_reverse-phase.txt	Txt
	i_Investigation.txt	Txt
	m_MTBLS14340_LC-MS_negative_reverse-phase_v2_maf.tsv	Tabular
	m_MTBLS14340_LC-MS_positive_reverse-phase_v2_maf.tsv	Tabular

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Project description:Background: Grazing yearly on pasture is a traditional practice for yaks, which cannot meet the requirements of yak products since the insufficient forage supplied in the cold season results in a long production cycle. An intensive feeding system increasing production efficiency has been selected for beef and dairy cattle. However, its impacts on yaks are less studied, and it is unclear how the rumen microbiome, rumen metabolites and the host metabolome respond to an intensive feeding system and contribute to yak growth. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the effects and regulatory mechanisms of intensive feeding system.Results: In our results, increased growth performance and rumen volatile fatty acid (VFA) concentration were observed in yaks under the intensive feeding system compared to yaks grazing on pastures. Metagenomics of the rumen microbiome revealed that species of Clostridium and Methanobrevibacter as well as Piromyces sp. E2 and Anaeromyces robustus were increased in the rumen of intensively fed yaks, interacting and contributing to amino acid and carbohydrate metabolism. The rumen of yaks grazing on pasture had more cellulolytic microbes, such as Bacteroides and Fibrobacter species. Moreover, yaks under the intensive feeding system had lower methanogen and increased methane degradation functions, suggesting that the methane emission of these yaks may be decreased. These abundant microbiomes were correlated with the pathways of “Alanine aspartate and glutamate metabolism” and “Pyruvate metabolism”. Similar with rumen VFA results, metabolomics found that intensively fed yaks had greater concentrations of metabolites related to carbohydrates. The methyl metabolites associated with methane production were greater in the rumen of yak grazing on pasture. Additionally, these changed rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally affecting yaks’ growth.Conclusions: This study compressively classifies the mechanism that an intensive feeding system benefits yak production and reveals the importance of the rumen microbiome for host metabolism and performance. These findings evidence that an intensive feeding system could be used for the yak industry.

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Integrative multi-omics analysis of rumen development in early-life yaks

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