ArticleFrontiers in microbiology2016
Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches.
Article in Frontiers in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Comparative metataxonomic analysis of total, viable, and active rumen microbial communities under methane-mitigated conditions.Environmental microbiome · 2026Article
- Rumen Microbiota, Predicted Metabolic Pathways, and Fermentation Parameters Exhibit Production-System-Specific Associations in Cattle and Goats.Microorganisms · 2026Article
- Phytosterols improve feed efficiency in yaks by enriching rumen Succiniclasticum.Animal microbiome · 2026Article
- Responses of rumen bacterial microflora to aflatoxin B1 challenge: potential roles of AHLs/AI-2 mediated quorum sensing.Animal microbiome · 2026Article
- Metatranscriptomics uncovers diet-driven structural, ecological, and functional adaptations in the rumen microbiome linked to feed efficiency.ISME communications · 2026Article
- Short- and long-term dietary supplementation as well as withdrawal of the enteric methane inhibitor 3-nitrooxypropanol reveal distinct effects on the rumen microbial community.Journal of animal science and biotechnology · 2025Article
- Dietary modulation of the rumen microbiome drives the expression of metabolic and methanogenic pathways inmSphere · 2025Article
- Refining microbial biomarker identification in rumen microbiome studies: a viability PCR-based approach.Applied and environmental microbiology · 2025Article
- Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin.Nature communications · 2025Article
- Assessment of fecal bacterial viability and diversity in fresh and frozen fecal microbiota transplant (FMT) product in horses.BMC veterinary research · 2024Article
- Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes.BMC microbiology · 2024Article
- Structural and functional analysis of the active cow rumen's microbial community provides a catalogue of genes and microbes participating in the deconstruction of cardoon biomass.Biotechnology for biofuels and bioproducts · 2024Article
- Process conditions affect microbial diversity and activity in a haloalkaline biodesulfurization system.Applied and environmental microbiology · 2024Article
- From transients to permanent residents: the existence of obligate aerobic microorganisms in the goat rumen.Frontiers in microbiology · 2024Article
- Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant.Interface focus · 2023Article
- Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data.Frontiers in microbiology · 2023Article
- Evolving understanding of rumen methanogen ecophysiology.Frontiers in microbiology · 2023Review
- First Steps into Ruminal Microbiota Robustness.Animals : an open access journal from MDPI · 2022Review
- The Effects of Breed and Residual Feed Intake Divergence on the Abundance and Active Population of Rumen Microbiota in Beef Cattle.Animals : an open access journal from MDPI · 2022Article
- Expressions of resistome is linked to the key functions and stability of active rumen microbiome.Animal microbiome · 2022Article
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Authors and funding
6 authors.
Funding
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Abstract
Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data.
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