ArticleiMeta2024
Integrating genome- and transcriptome-wide association studies to uncover the host-microbiome interactions in bovine rumen methanogenesis.
Article in iMeta, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Microbial DNA methylation links rumen transcriptional activity to methane emission divergence in dairy cows.iMeta · 2026Article
- Host-microbial co-regulation mediates rumen volatile fatty acid production and utilization in dairy cows.Science China. Life sciences · 2026Article
- Nutritional Strategies for Methane, Nitrogen, and Phosphorus Mitigation in Ruminants: Mechanisms, Applications, and Regional Adaptations.Microorganisms · 2026Review
- Host genetic regulation of rumen 6-hydroxymelatonin reduces methane emissions in dairy cattle.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Integration of GWAS and eQTL analysis reveals regulatory CNVs for fatty acid traits in cattle.iScience · 2026Article
- A preliminary metagenomic and metabolomic investigation into the effects of Aspergillus niger cultures on microbial homeostasis and antibiotic resistance gene profiles in the rumen of fattening sheep.Journal of animal science and biotechnology · 2026Article
- Decoding the enhancer-driven regulatory network for lactoferrin across mammalian species.Zoological research · 2026Article
- Advancing climate-resilient livestock systems: Next-generation emission mitigation strategies and integrated technological innovations.Veterinary and animal science · 2026Review
- Commensal Microbiota and Reproductive Health in Livestock: Mechanisms, Cross-System Crosstalk, and Precision Strategies.Animals : an open access journal from MDPI · 2026Review
- INSIG1 parallel substitution drives lipid/sterol metabolic plasticity mediating desert adaptation in ungulates.Communications biology · 2026Article
- Comparative analysis of growth performance and rumen microbiota in Hu sheep and its three-way crossbred offspring.Frontiers in microbiology · 2026Article
- EasyAmplicon 2: Expanding PacBio and Nanopore Long Amplicon Sequencing Analysis Pipeline for Microbiome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Review
- Effects of dietary supplementation with astragalus polysaccharides on growth performance, serum parameters, and rumen microbial function of yaks.BMC microbiology · 2025Article
- Exploring genome, transcriptome, and microbiome interactions related to feed efficiency and methane emissions in Bos indicus through multi-omics network analysis.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Effects of Sea Buckthorn Polysaccharides on Rumen In Vitro Fermentation Characteristics and Microbial Composition of Hu Sheep.Microorganisms · 2025Article
- Heated drinking water in winter improves growth performance of male Hu sheep by modulating rumen quorum sensing and metabolites, and enhancing serum antioxidant capacity.Animal bioscience · 2025Article
- Host Genetic Effects and Phenotypic Landscapes of Rumen Bacterial Enterotypes in a Large Sheep Population.Animals : an open access journal from MDPI · 2025Article
- Multidimensional Phenotypic and Microbiome Studies Uncover an Association Between Reduced Feed Efficiency in Sheep During Mycoplasmal Pneumonia and Microbial Crosstalk Within the Rumen-Lung Axis.Veterinary sciences · 2025Article
- Article
Corrections and comments
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ruminal microbiota generates biogenic methane in ruminants. However, the role of host genetics in modifying ruminal microbiota-mediated methane emissions remains mysterious, which has severely hindered the emission control of this notorious greenhouse gas. Here, we uncover the host genetic basis of rumen microorganisms by genome- and transcriptome-wide association studies with matched genome, rumen transcriptome, and microbiome data from a cohort of 574 Holstein cattle. Heritability estimation revealed that approximately 70% of microbial taxa had significant heritability, but only 43 genetic variants with significant association with 22 microbial taxa were identified through a genome-wide association study (GWAS). In contrast, the transcriptome-wide association study (TWAS) of rumen microbiota detected 28,260 significant gene-microbe associations, involving 210 taxa and 4652 unique genes. On average, host genetic factors explained approximately 28% of the microbial abundance variance, while rumen gene expression explained 43%. In addition, we highlighted that TWAS exhibits a strong advantage in detecting gene expression and phenotypic trait associations in direct effector organs. For methanogenic archaea, only one significant signal was detected by GWAS, whereas the TWAS obtained 1703 significant associated host genes. By combining multiple correlation analyses based on these host TWAS genes, rumen microbiota, and volatile fatty acids, we observed that substrate hydrogen metabolism is an essential factor linking host-microbe interactions in methanogenesis. Overall, these findings provide valuable guidelines for mitigating methane emissions through genetic regulation and microbial management strategies in ruminants.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.