ArticleScientific reports2021
Establishment and assessment of an amplicon sequencing method targeting the 16S-ITS-23S rRNA operon for analysis of the equine gut microbiome.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 51 citations in OpenAlex.
- From Diet to Disease: The Role of the Gut Microbiome and Microbial Metabolites in Horses.Veterinary sciences · 2026Review
- Primer-Less Species Identification Throughout Fungal (International journal of molecular sciences · 2026Article
- Microbiota-derived metabolite landscapes modulate Fusobacterium fitness and colorectal cancer cell behaviour.Gut pathogens · 2026Article
- Article
- Third-generation RNA Amplicon Sequencing Reveals the Dynamics of Microbial Communities in the Tidal Reach of a Subtropical Estuary.Microbial ecology · 2026Article
- MIrROR release 02: Expanded and refined 16S-ITS-23S rRNA operon dataset.Scientific data · 2026Article
- Review
- High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons.Microbiome · 2025Article
- Minimal disruption of equine gut microbiota by intravenous cephalothin treatment.The Journal of veterinary medical science · 2025Article
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- Improving the profiling of wheat bacterial and fungal endophytic communities-a PCR clamping approach.Frontiers in microbiology · 2025Article
- Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.International journal of microbiology · 2025Article
- Correlation of fecal microbiome dysregulation to synovial transcriptome in an equine model of obesity associated osteoarthritis.Annals of translational medicine · 2024Article
- Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization.iMetaOmics · 2024Review
- Algicidal bacteria-derived membrane vesicles as shuttles mediating cross-kingdom interactions between bacteria and algae.Science advances · 2024Article
- GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences.Microbial genomics · 2024Article
- Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.Frontiers in microbiology · 2024Article
- PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences.Frontiers in bioinformatics · 2024Article
- The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling.Applied and environmental microbiology · 2023Article
- Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing.Scientific reports · 2023Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial communities are commonly studied by using amplicon sequencing of part of the 16S rRNA gene. Sequencing of the full-length 16S rRNA gene can provide higher taxonomic resolution and accuracy. To obtain even higher taxonomic resolution, with as few false-positives as possible, we assessed a method using long amplicon sequencing targeting the rRNA operon combined with a CCMetagen pipeline. Taxonomic assignment had > 90% accuracy at the species level in a mock sample and at the family level in equine fecal samples, generating similar taxonomic composition as shotgun sequencing. The rRNA operon amplicon sequencing of equine fecal samples underestimated compositional percentages of bacterial strains containing unlinked rRNA genes by a fourth to a third, but unlinked rRNA genes had a limited effect on the overall results. The rRNA operon amplicon sequencing with the A519F + U2428R primer set was able to detect some kind of archaeal genomes such as Methanobacteriales and Methanomicrobiales, whereas full-length 16S rRNA with 27F + 1492R could not. Therefore, we conclude that amplicon sequencing targeting the rRNA operon captures more detailed variations of equine microbiota.
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