ArticleApplied and environmental microbiology2023
Microbial Diversity Biased Estimation Caused by Intragenomic Heterogeneity and Interspecific Conservation of 16S rRNA Genes.
Article in Applied and environmental microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Yeasts on Tree Gum: Taxonomic, Genetic and Phenotypic Diversity.Environmental microbiology reports · 2026Article
- Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes.bioRxiv : the preprint server for biology · 2026Article
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- Quantification of the absolute abundance of the jejunal mucosa-associated microbiota of pigs using spike-in control.Microbiome research reports · 2026Article
- Spatial Heterogeneity in Methane Biogeochemistry and Prokaryotic Community Structure in Sub-Arctic Waterbodies in Northern Canada.Environmental microbiology · 2025Article
- Streptomyces shaoguanensis sp. nov.: elucidating the mechanisms of efficient chicken feather degradation and its potential for biofertilizer development.Microbial cell factories · 2025Article
- Cervicovaginal microbial features predictInfection and immunity · 2025Article
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- Crop genotype modulates root rot resistance-associated microbial community composition and abundance of key taxa.Environmental microbiome · 2025Article
- Seepage area of the cold seep exhibits strong homogeneous selection on prokaryotic community assembly and supports high depth variability of both archaeal and bacterial communities.Microbiology spectrum · 2025Article
- CABO-16S-a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples.NAR genomics and bioinformatics · 2025Article
- The impact of biotic and abiotic interactions on Candidatus Kouleothrix bulking in a full-scale activated sludge anaerobic-anoxic-oxic plant in Japan.Scientific reports · 2025Article
- Application ofISME communications · 2025Article
- Unveiling the impact of 16S rRNA gene intergenomic variation on primer design and gut microbiome profiling.Frontiers in microbiology · 2025Article
- DNA metabarcode analyses reveal similarities and differences in plant microbiomes of industrial hemp and medicinalFrontiers in microbiology · 2025Article
- Genome assembly ofFrontiers in microbiology · 2025Article
- Regulation of the Rhizosphere Microenvironment by Arbuscular Mycorrhizal Fungi to Mitigate the Effects of Cadmium Contamination on Perennial Ryegrass (Microorganisms · 2024Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The 16S rRNA gene has been extensively used as a molecular marker to explore evolutionary relationships and profile microbial composition throughout various environments. Despite its convenience and prevalence, limitations are inevitable. Variable copy numbers, intragenomic heterogeneity, and low taxonomic resolution have caused biases in estimating microbial diversity. Here, analysis of 24,248 complete prokaryotic genomes indicated that the 16S rRNA gene copy number ranged from 1 to 37 in bacteria and 1 to 5 in archaea, and intragenomic heterogeneity was observed in 60% of prokaryotic genomes, most of which were below 1%. The overestimation of microbial diversity caused by intragenomic variation and the underestimation introduced by interspecific conservation were calculated when using full-length or partial 16S rRNA genes. Results showed that, at the 100% threshold, microbial diversity could be overestimated by as much as 156.5% when using the full-length gene. The V4 to V5 region-based analyses introduced the lowest overestimation rate (4.4%) but exhibited slightly lower species resolution than other variable regions under the 97% threshold. For different variable regions, appropriate thresholds rather than the canonical value 97% were proposed for minimizing the risk of splitting a single genome into multiple clusters and lumping together different species into the same cluster. This study has not only updated the 16S rRNA gene copy number and intragenomic variation information for the currently available prokaryotic genomes, but also elucidated the biases in estimating prokaryotic diversity with quantitative data, providing references for choosing amplified regions and clustering thresholds in microbial community surveys.
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