ArticleNAR genomics and bioinformatics2020
Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 25 citations in OpenAlex.
- Article
- Targeted assembly recovers high ammonia monooxygenase diversity in mudflat intertides.mSystems · 2025Article
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences.Microbial genomics · 2024Article
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods.Foods (Basel, Switzerland) · 2022Review
- High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS.ISME communications · 2022Article
- Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.Microbiome · 2022Article
- Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence.Microbiology spectrum · 2022Article
- Tatajuba: exploring the distribution of homopolymer tracts.NAR genomics and bioinformatics · 2022Article
- Ultra-resolution Metagenomics: When Enough Is Not Enough.mSystems · 2021Article
- Evolution of Pig Fecal Microbiota Composition and Diversity in Response to EnterotoxigenicMicroorganisms · 2021Article
- Multi-omics data integration considerations and study design for biological systems and disease.Molecular omics · 2021Review
- High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing.Nature methods · 2021Article
- Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies.Frontiers in microbiology · 2021Review
- From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the need to isolate and culture the microbes present. However, bacterial cells usually have multiple copies of this ribosomal operon, and choosing the 'wrong' copy could provide a misleading species classification. While this presents less of a problem for well-characterized organisms with large sequence databases to interrogate, it is a significant challenge for lesser known organisms with unknown copy number and diversity. Using the entire length of the ribosomal operon, which encompasses the 16S, 23S, 5S and internal transcribed spacer regions, should provide greater taxonomic resolution but has not been well explored. Here, we use publicly available reference genomes and explore the theoretical boundaries when using concatenated genes and the full-length ribosomal operons, which has been made possible by the development and uptake of long-read sequencing technologies. We quantify the issues of both copy choice and operon length in a phylogenetic context to demonstrate that longer regions improve the phylogenetic signal while maintaining taxonomic accuracy.
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What OpenQuestion holds
Registered trials
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 OpenQuestion graph.