ArticleApplied and environmental microbiology2013
Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity.
Article in Applied and environmental microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 199 papers, 1 of them a synthesis that pooled it.
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Who cites it
199 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Prenatal Maternal Stress and Infant Gut Microbiome in Human and Animal Studies: A Comprehensive Systematic Review.Developmental psychobiology · 2026Pooled it
- Variations in oral microbiota associated with oral cancer.Scientific reports · 2017Trial
- Expanding the geographic and host range of moss-nostocacean symbioses in central Europe.Oecologia · 2026Article
- Unraveling yeast diversity in food fermentation using ITS1-2 amplicon-based metabarcoding.Microbiology spectrum · 2026Article
- Interpreting oral microbiome research in clinical dentistry: terminology, limitations and clinical implications.British dental journal · 2026Review
- Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes.bioRxiv : the preprint server for biology · 2026Article
- Cultivar and tree age jointly shape rhizosphere bacterial diversity and community assembly in Macadamia integrifolia.Applied microbiology and biotechnology · 2026Article
- Modular RNA:DNA Nanostructures Enable Nanopore Profiling of rRNA Processing and rRNA Variants.ACS nano · 2026Article
- Multidimensional Differences and Driving Mechanisms of Bacterial Communities in Urban and Rural Rivers Across China.Microorganisms · 2026Article
- Artificial lagoon project alters archaeal diversity, community assembly, and potential activity around a nearshore island: insights from an annual cycle.Applied and environmental microbiology · 2026Article
- Pathogenic bacterial species and the microbiome of cat fleas (Ctenocephalides felis) inhabiting flea-infested homes.PloS one · 2026Article
- Characterization of the atmospheric microbiome in a semi-rural area of Central Europe using flow cytometry.ISME communications · 2026Article
- [Comparison of 16S rRNA gene hypervariable regions V3-V4 and V4 sequencing results of gut microbiota in obese children with non-alcoholic fatty liver disease].Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2025Article
- Intratumoral microbiome: a crucial regulating factor in development and progression of colorectal cancer.Molecular biomedicine · 2025Review
- Investigating microbiota differences across chronic pancreatitis, influenced by lifestyle and genetic determinants.BMC gastroenterology · 2025Article
- Nasal microbiota dysbiosis and functional alterations in children with adenoid hypertrophy: potential biomarkers and post-surgical microbial recovery.Applied microbiology and biotechnology · 2025Article
- Seasonally and niche-differentiated diversity of active, dormant and dead microbes in coastal waters and surface sediments.Communications biology · 2025Article
- SyFi: generating and using sequence fingerprints to distinguish SynCom isolates.Microbial genomics · 2025Article
- Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.mSystems · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
139 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Ever since Carl Woese introduced the use of 16S rRNA genes for determining the phylogenetic relationships of prokaryotes, this method has been regarded as the "gold standard" in both microbial phylogeny and ecology studies. However, intragenomic heterogeneity within 16S rRNA genes has been reported in many investigations and is believed to bias the estimation of prokaryotic diversity. In the current study, 2,013 completely sequenced genomes of bacteria and archaea were analyzed and intragenomic heterogeneity was found in 952 genomes (585 species), with 87.5% of the divergence detected being below the 1% level. In particular, some extremophiles (thermophiles and halophiles) were found to harbor highly divergent 16S rRNA genes. Overestimation caused by 16S rRNA gene intragenomic heterogeneity was evaluated at different levels using the full-length and partial 16S rRNA genes usually chosen as targets for pyrosequencing. The result indicates that, at the unique level, full-length 16S rRNA genes can produce an overestimation of as much as 123.7%, while at the 3% level, an overestimation of 12.9% for the V6 region may be introduced. Further analysis showed that intragenomic heterogeneity tends to concentrate in specific positions, with the V1 and V6 regions suffering the most intragenomic heterogeneity and the V4 and V5 regions suffering the least intragenomic heterogeneity in bacteria. This is the most up-to-date overview of the diversity of 16S rRNA genes within prokaryotic genomes. It not only provides general guidance on how much overestimation can be introduced when applying 16S rRNA gene-based methods, due to its intragenomic heterogeneity, but also recommends that, for bacteria, this overestimation be minimized using primers targeting the V4 and V5 regions.
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