ArticleMicrobiome2019
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 papers.
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Who cites it
180 citing papers in PubMed.
- Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.Journal of animal science and biotechnology · 2026Article
- Divergent residual feed intake is associated with distinct fecal microbiota in early fattening Hanwoo steers.Journal of animal science and technology · 2026Article
- A total infectome framework for resolving complex disease etiology in aquaculture.Advanced biotechnology · 2026Article
- Article
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Mechanisms Underlying the Impact of Feed-to-Gain Ratio Differences on Nutrient Metabolism in Simmental and Simmental × Hereford Crossbred Cattle Fed a Low-Energy Diet.Animals : an open access journal from MDPI · 2026Article
- Eucommia ulmoides leaves improving growth by regulating the rumen microbiome in sheep.BMC microbiology · 2026Article
- Dietary L-Citrulline Supplementation Promotes Rumen Development and Modulates the Microbiota-Metabolome Axis in Suckling Hu Lambs.Animals : an open access journal from MDPI · 2026Article
- Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.Journal of animal science and biotechnology · 2026Article
- Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.Microbiome · 2026Article
- RuSpacer: a CRISPR spacer database derived from ruminant-associated prokaryotes for virome analysis.Scientific reports · 2026Article
- Phytosterols improve feed efficiency in yaks by enriching rumen Succiniclasticum.Animal microbiome · 2026Article
- Effects of Dietary Non-Fibrous Carbohydrate to Neutral Detergent Fiber Ratio on Apparent Digestibility, Fecal Microbiota, and Plasma Metabolomics in Yili Horses.Animals : an open access journal from MDPI · 2026Article
- Integrated metabolome and microbiome analysis deciphers the effects of resveratrol and β-hydroxy-β-methylbutyric acid on jejunal function under different protein levels in Tibetan sheep.Microbiology spectrum · 2026Article
- Meat Quality Differences Between Ganan Tibetan Sheep and Tianzhu Tibetan Sheep Using Metabolomics and Rumen Microbiota Analyses.Microorganisms · 2026Article
- The impact of dietary supplementation with tannic acid on the digestion of nutrients, rumen microflora, rumen fermentation, and methane production in Liuyang black goats.Animal bioscience · 2026Article
- Effects ofBiology · 2026Article
- Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.Microbiome · 2026Article
- Longitudinal long-read microbiome profiling in a canine model reveals how age, diet, and birth mode shape gut community dynamics.mSystems · 2026Article
- From association to intervention: Muribaculaceae driven SCFAs production enhances boar semen quality via inflammation alleviation.NPJ biofilms and microbiomes · 2026Article
120 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
backgroundMicroorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.
resultsRumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.
conclusionsMetatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.
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