ArticlePloS one2009
Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 462 papers, 1 of them a synthesis that pooled it.
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Who cites it
462 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- molBV reveals immune landscape of bacterial vaginosis and predicts human papillomavirus infection natural history.Nature communications · 2022Trial
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- Shotgun metagenomic analysis of the oral microbiomes of children with noma.PLoS neglected tropical diseases · 2026Article
- Successional Trajectories of Deep Subsurface Microbiomes in Response To Experimental Dihydrogen Injection.Microbial ecology · 2026Article
- Study of the Probiotic Potential of Lactic Acid Bacteria Isolated from Artisanal Colonial Cheese and Evaluation of Microencapsulation as a Protective Method Under Simulated Gastrointestinal Conditions.Foods (Basel, Switzerland) · 2026Article
- HVRLocator: a computationally efficient tool for identifying hypervariable regions in large 16S rRNA datasets.GigaScience · 2026Article
- Resilient gut microbiome is linked to immune control in HIV-1 infection.Biology direct · 2026Article
- Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland.FEMS microbiology letters · 2026Article
- Metataxonomic insights into lactic acid bacteria diversity in artisanal coalho cheese from the Caatinga biome.PloS one · 2026Article
- Sub-community-level network analysis reveals distinct microbial dynamics in a lake littoral sediment.BMC microbiology · 2025Article
- Longitudinal analysis reveals transitions in pathogen profiles associated with mastitis in dairy cows.Veterinary research · 2025Article
- Metagenomic analysis and proteins prediction of emerging pathogens in artisanal cheese.Molecular diversity · 2025Article
402 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969-983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies.
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