ArticleMicrobiology spectrum2022
Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence.
Article in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Effects of a Balanced Diet and Probiotics on Blood Biomarkers and Gut Microbiota in the Elderly: A Community-Based Intervention Study.Nutrients · 2025Trial
- Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.Microbiology spectrum · 2026Article
- Article
- Complete genome dataset ofData in brief · 2026Article
- Mycobacterium tuberculosis infection disrupts gut and respiratory microbial communities and networks with incomplete restoration after two months of treatment.Gut pathogens · 2026Article
- MIrROR release 02: Expanded and refined 16S-ITS-23S rRNA operon dataset.Scientific data · 2026Article
- Cooperative siderophore use stabilizes a protective leaf microbiome.bioRxiv : the preprint server for biology · 2026Article
- Dietary Administration of a Soybean Fermented Preparation Reshapes Gut Microbial Community Structure and Colonic Mucosal Features in BALB/c Mice.Microorganisms · 2026Article
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies.Molecular ecology resources · 2025Article
- Dietary patterns drive loss of fiber-foraging species in the celiac disease patients gut microbiota compared to first-degree relatives.Gut pathogens · 2024Article
- Potentially pathogenic culturable bacteria in hemodialysis waters.BMC microbiology · 2024Article
- GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences.Microbial genomics · 2024Article
- Customized 16S-23S rDNA ITS Amplicon Metagenomics for Acetic Acid Bacteria Species Identification in Vinegars and Kombuchas.Microorganisms · 2024Article
- Soil Fertilization with Palm Oil Mill Effluent Has a Short-Term Effect on the Bacterial Diversity of an Amazonian Agricultural Land Area.Microorganisms · 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
- RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing.Frontiers in microbiology · 2023Article
- RibDif2: expanding amplicon analysis to full genomes.Bioinformatics advances · 2023Article
- Morphological and molecular characterization of bacterial endophytes from Centella asiatica leaves.Journal, genetic engineering & biotechnology · 2022Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent development of long-read sequencing platforms has enabled researchers to explore bacterial community structure through analysis of full-length 16S rRNA gene (∼1,500 bp) or 16S-ITS-23S rRNA operon region (∼4,300 bp), resulting in higher taxonomic resolution than short-read sequencing platforms. Despite the potential of long-read sequencing in metagenomics, resources and protocols for this technology are scarce. Here, we describe MIrROR, the database and analysis tool for metataxonomics using the bacterial 16S-ITS-23S rRNA operon region. We collected 16S-ITS-23S rRNA operon sequences extracted from bacterial genomes from NCBI GenBank and performed curation. A total of 97,781 16S-ITS-23S rRNA operon sequences covering 9,485 species from 43,653 genomes were obtained. For user convenience, we provide an analysis tool based on a mapping strategy that can be used for taxonomic profiling with MIrROR database. To benchmark MIrROR, we compared performance against publicly available databases and tool with mock communities and simulated data sets. Our platform showed promising results in terms of the number of species covered and the accuracy of classification. To encourage active 16S-ITS-23S rRNA operon analysis in the field, BLAST function and taxonomic profiling results with 16S-ITS-23S rRNA operon studies, which have been reported as BioProject on NCBI are provided. MIrROR (http://mirror.egnome.co.kr/) will be a useful platform for researchers who want to perform high-resolution metagenome analysis with a cost-effective sequencer such as MinION from Oxford Nanopore Technologies.
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