ArticlePloS one2012
A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 147 citations in OpenAlex.
- Full-length 16S rRNA nanopore sequencing enables species resolution ofGut microbes · 2026Article
- The Prokaryotic Community of Hypersaline Soils from the Odiel Saltmarshes: Culturomics Versus Metagenomics.Life (Basel, Switzerland) · 2026Article
- Transcriptome Analysis Reveals the Potential Mechanism of MAP34-B TargetingMicroorganisms · 2026Article
- Nested PCR to optimizeMicrobiology spectrum · 2025Article
- Comparative analysis of metagenomic next-generation sequencing for pathogenic identification in clinical body fluid samples.BMC microbiology · 2025Article
- Review
- Broad-range amplification and sequencing of theJournal of clinical microbiology · 2024Article
- Molecular identification and GC-MS analysis of a newly isolated novel bacterium (Lysinibacillus sp. VCRC B655) for mosquito control.Molecular biology reports · 2024Article
- A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5.Foods (Basel, Switzerland) · 2024Article
- Macroevolutionary Dynamics in Micro-organisms: Generalists Give Rise to Specialists Across Biomes in the Ubiquitous Bacterial Phylum Myxococcota.Molecular biology and evolution · 2024Article
- Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach.ISME communications · 2023Article
- Modularity and diversity of target selectors in Tn7 transposons.Molecular cell · 2023Article
- Microbial Diversity Biased Estimation Caused by Intragenomic Heterogeneity and Interspecific Conservation of 16S rRNA Genes.Applied and environmental microbiology · 2023Article
- Article
- Molecular identification of nontuberculous mycobacteria using the rpoB, argH and cya genes analysis.AMB Express · 2022Article
- Analysis ofMicrobiology spectrum · 2022Article
- Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.Microbiome · 2022Article
- Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive PhyllospheremBio · 2022Article
- Comparison of Actinobacteria communities from human-impacted and pristine karst caves.MicrobiologyOpen · 2022Article
- Effect of vaginal flora on clinical outcome of frozen embryo transfer.Frontiers in cellular and infection microbiology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 16S rRNA gene is the gold standard in molecular surveys of bacterial and archaeal diversity, but it has the disadvantages that it is often multiple-copy, has little resolution below the species level and cannot be readily interpreted in an evolutionary framework. We compared the 16S rRNA marker with the single-copy, protein-coding rpoB marker by amplifying and sequencing both from a single soil sample. Because the higher genetic resolution of the rpoB gene prohibits its use as a universal marker, we employed consensus-degenerate primers targeting the Proteobacteria. METHODOLOGY/PRINCIPAL
findingsPyrosequencing can be problematic because of the poor resolution of homopolymer runs. As these erroneous runs disrupt the reading frame of protein-coding sequences, removal of sequences containing nonsense mutations was found to be a valuable filter in addition to flowgram-based denoising. Although both markers gave similar estimates of total diversity, the rpoB marker revealed more species, requiring an order of magnitude fewer reads to obtain 90% of the true diversity. The application of population genetic methods was demonstrated on a particularly abundant sequence cluster. CONCLUSIONS/SIGNIFICANCE: The rpoB marker can be a complement to the 16S rRNA marker for high throughput microbial diversity studies focusing on specific taxonomic groups. Additional error filtering is possible and tests for recombination or selection can be employed.
Indexed as
Identifiers
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.