ArticleMicrobiome2018
Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem.
Article in Microbiome, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 169 papers, 2 of them syntheses that pooled it.
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Who cites it
169 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Functional Redundancy Enables Stable Treatment Performance Across Taxonomically Diverse Dairy Wastewater Microbiomes.Environmental microbiology reports · 2026Pooled it
- Bacillus drives functional states in synthetic plant root bacterial communities.Genome biology · 2025Pooled it
- Full-length 16S rRNA nanopore sequencing enables species resolution ofGut microbes · 2026Article
- MATRIX: rapid quantification of total and active microbial cells with single-cell phenotypes for environmental microbiomes.mSystems · 2026Article
- TIPP-SD: A new method for species detection in microbiomes.PLoS computational biology · 2026Article
- Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.Biology · 2026Review
- Effects of heat-assisted sample desiccation on microbiome surveys.Environmental microbiome · 2026Article
- Shared stream-lake patterns in diversity, rRNA-based activity and community assembly of bacteria and microeukaryotes under distinct hydrological regimes.FEMS microbiology ecology · 2026Article
- Stronger Adaptability of Eukaryotic Communities than Prokaryotes in Seawater across an Extensive Salinity Gradient.Marine biotechnology (New York, N.Y.) · 2026Article
- Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.The ISME journal · 2026Article
- Antibiotic resistance genes detected in lichens: insights from Cladonia stellaris.Annals of botany · 2026Article
- Dissolved organic matter specialization drives temporal dynamics of simplified bacterial communities in a microcosm experiment.ISME communications · 2026Article
- Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.Microbiome · 2025Article
- Effects of Vacuum-Heat-Assisted Sample Desiccation on Microbiome Surveys.Molecular ecology resources · 2025Article
- Comparative analysis of illumina and oxford nanopore sequencing platforms for 16S rRNA profiling of respiratory microbial communities.Scientific reports · 2025Article
- SyFi: generating and using sequence fingerprints to distinguish SynCom isolates.Microbial genomics · 2025Article
- What lurks in the dark? An innovative framework for studying diverse wild insect microbiota.Microbiome · 2025Article
- Systems Biology Applications in Revealing Plant Defense Mechanisms in Disease Triangle.International journal of molecular sciences · 2025Review
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities.Environmental microbiome · 2025Article
109 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases. However, the accuracy of those predictions has not been independently assessed. Here, we systematically evaluate the predictability of 16S GCNs across bacterial and archaeal clades, based on ∼ 6,800 public sequenced genomes and using several phylogenetic methods. Further, we assess the accuracy of GCNs predicted by three recently published tools (PICRUSt, CopyRighter, and PAPRICA) over a wide range of taxa and for 635 microbial communities from varied environments. We find that regardless of the phylogenetic method tested, 16S GCNs could only be accurately predicted for a limited fraction of taxa, namely taxa with closely to moderately related representatives (≲15% divergence in the 16S rRNA gene). Consistent with this observation, we find that all considered tools exhibit low predictive accuracy when evaluated against completely sequenced genomes, in some cases explaining less than 10% of the variance. Substantial disagreement was also observed between tools (R
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