ArticleISME communications2023
Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses.
Article in ISME communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- Impact of the anti-inflammatory macrolide glasmacinal on the gut microbiota of healthy adults: an open-label trial.Nature communications · 2026Article
- MATRIX: rapid quantification of total and active microbial cells with single-cell phenotypes for environmental microbiomes.mSystems · 2026Article
- Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories.Ecology letters · 2026Article
- Article
- Dysbiosis of oral and gut microbiomes characterized by elevated Lactococcus in a mouse model of oral squamous cell carcinoma.NPJ biofilms and microbiomes · 2026Article
- Stronger Adaptability of Eukaryotic Communities than Prokaryotes in Seawater across an Extensive Salinity Gradient.Marine biotechnology (New York, N.Y.) · 2026Article
- Spatial Heterogeneity in Methane Biogeochemistry and Prokaryotic Community Structure in Sub-Arctic Waterbodies in Northern Canada.Environmental microbiology · 2025Article
- DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.mSystems · 2025Article
- Identification of microbial groups and functional genes associated with greenhouse gas emissions in prawn farms.Scientific reports · 2025Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.mSystems · 2025Article
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Nitrogen Redox Controls on Greenhouse Gas Production in Yedoma Taliks.Global change biology · 2025Article
- The powerbend distribution provides a unified model for the species abundance distribution across animals, plants and microbes.Nature communications · 2025Article
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- Assessment of absolute abundance in mother-infant gut microbiome using marine-sourced bacterial DNA spike-in and comparison with conventional quantification methods.Microbiome research reports · 2025Article
- Diversity of endophytic bacteria in mulberry (Frontiers in microbiology · 2025Article
- Article
- Chinese expert consensus on standard technical specifications for a gut microecomics laboratory (Review).Experimental and therapeutic medicine · 2024Review
- Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization.iMetaOmics · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
16S rRNA gene copy number (16S GCN) varies among bacterial species and this variation introduces potential biases to microbial diversity analyses using 16S rRNA read counts. To correct the biases, methods have been developed to predict 16S GCN. A recent study suggests that the prediction uncertainty can be so great that copy number correction is not justified in practice. Here we develop RasperGade16S, a novel method and software to better model and capture the inherent uncertainty in 16S GCN prediction. RasperGade16S implements a maximum likelihood framework of pulsed evolution model and explicitly accounts for intraspecific GCN variation and heterogeneous GCN evolution rates among species. Using cross-validation, we show that our method provides robust confidence estimates for the GCN predictions and outperforms other methods in both precision and recall. We have predicted GCN for 592605 OTUs in the SILVA database and tested 113842 bacterial communities that represent an exhaustive and diverse list of engineered and natural environments. We found that the prediction uncertainty is small enough for 99% of the communities that 16S GCN correction should improve their compositional and functional profiles estimated using 16S rRNA reads. On the other hand, we found that GCN variation has limited impacts on beta-diversity analyses such as PCoA, NMDS, PERMANOVA and random-forest test.
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.