ArticleApplied and environmental microbiology2007
Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.
Article in Applied and environmental microbiology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 216 papers, 2 of them syntheses that pooled it.
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Who cites it
216 citing papers in PubMed, 2 syntheses or guidelines pooled it, 595 citations in OpenAlex.
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- Changes in bacterial diversity associated with epithelial tissue in the beef cow rumen during the transition to a high-grain diet.Applied and environmental microbiology · 2011Trial
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- The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.Microorganisms · 2026Review
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- Development of strain specific simple sequence repeats and assessment of genetic diversity in Erwinia amylovora from marker selection to phylogenetic analysis.Scientific reports · 2025Article
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- Comprehensive Cross-Domain Taxonomic Classification of Microbiotas using Partitioned Amplification Multiplexed Amplicon Sequencing (PAMA-seq).bioRxiv : the preprint server for biology · 2025Article
- Development of a multiplex loop-mediated isothermal amplification (LAMP) method for differential detection ofMicrobiology spectrum · 2025Article
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156 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.
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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.