ArticlePeerJ2017
How conserved are the conserved 16S-rRNA regions?
Article in PeerJ, 2017. 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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Who cites it
30 citing papers in PubMed.
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- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- 16S rRNA Metabarcoding Used to Identify the Etiology of Infective Endocarditis Agents.Sovremennye tekhnologii v meditsine · 2026Article
- Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.PloS one · 2026Article
- Molecular detection of hemoplasmas in domestic cats from different Brazilian regions.Revista brasileira de parasitologia veterinaria = Brazilian journal of veterinary parasitology : Orgao Oficial do Colegio Brasileiro de Parasitologia Veterinaria · 2025Article
- Research status of the relationship between microecological imbalance and lung cancer.Frontiers in microbiology · 2025Review
- Can Gut Microbiota Analysis RevealMicroorganisms · 2024Article
- Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.PloS one · 2023Article
- Evaluation of Full-Length Versus V4-Region 16S rRNA Sequencing for Phylogenetic Analysis of Mouse Intestinal Microbiota After a Dietary Intervention.Current microbiology · 2022Article
- KnotAli: informed energy minimization through the use of evolutionary information.BMC bioinformatics · 2022Article
- Expanding the Universe of Hemoplasmas: Multi-Locus Sequencing Reveals Putative Novel Hemoplasmas in Lowland Tapirs (Microorganisms · 2022Article
- Article
- Modeling Microbial Community Networks: Methods and Tools.Current genomics · 2021Review
- The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation.RNA biology · 2021Review
- An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.Scientific reports · 2021Article
- Article
- Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis.Computational and structural biotechnology journal · 2021Review
- Influence of Lab Adapted Natural Diet and Microbiota on Life History and Metabolic Phenotype ofMicroorganisms · 2020Article
- Molecular characterization of Brucella species detected in humans and domestic ruminants of pastoral areas in Kagera ecosystem, Tanzania.Veterinary medicine and science · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.
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