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Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

https://doi.org/10.1016/j.tim.2020.05.019
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi
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Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast
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Evolutionary trends in animal ribosomal DNA loci: introduction to a new online database
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Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny
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Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene
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Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates
inferredcites →https://doi.org/10.1016/j.tig.2019.07.006openalex-snapshot
Mechanisms of rDNA Copy Number Maintenance
inferredcites →https://doi.org/10.1016/j.tim.2019.06.003openalex-snapshot
Making the Most of Trait-Based Approaches for Microbial Ecology
inferredcites →https://doi.org/10.1038/ismej.2015.191openalex-snapshot
Decreases in average bacterial community rRNA operon copy number during succession
inferredcites →https://doi.org/10.1038/ismej.2017.119openalex-snapshot
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
inferredcites →https://doi.org/10.1038/nature24621openalex-snapshot
A communal catalogue reveals Earth’s multiscale microbial diversity
inferredcites →https://doi.org/10.1038/nbt.2676openalex-snapshot
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
inferredcites →https://doi.org/10.1038/nbt.3601openalex-snapshot
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.160openalex-snapshot
Exploiting rRNA operon copy number to investigate bacterial reproductive strategies
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Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean
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Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
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Best practices for analysing microbiomes
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Mycobiome diversity: high-throughput sequencing and identification of fungi
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Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
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Complete, closed bacterial genomes from microbiomes using nanopore sequencing
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The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
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Regulation of ribosomal DNA amplification by the TOR pathway
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Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life
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Ribosomal DNA stability is supported by many ‘buffer genes’—introduction to the Yeast rDNA Stability Database
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BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1093/nar/gku1201openalex-snapshot
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
inferredcites →https://doi.org/10.1093/nar/gkw110openalex-snapshot
More than 10% of yeast genes are related to genome stability and influence cellular senescence via rDNA maintenance
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The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
inferredcites →https://doi.org/10.1098/rspb.2017.0425openalex-snapshot
Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error
inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
inferredcites →https://doi.org/10.1101/gr.258640.119openalex-snapshot
Accurate and complete genomes from metagenomes
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Diversity in a hidden world: potential and limitation of next‐generation sequencing for surveys of molecular diversity of eukaryotic microorganisms
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The Amount of Ribosomal RNA Genes in Tetrahymena pyriformis in Different Physiological States
inferredcites →https://doi.org/10.1111/j.1462-2920.2007.01364.xopenalex-snapshot
Phylogenetic identity, growth‐response time and rRNA operon copy number of soil bacteria indicate different stages of community succession
inferredcites →https://doi.org/10.1111/mec.14995openalex-snapshot
Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles
inferredcites →https://doi.org/10.1126/sciadv.aax8787openalex-snapshot
The global-scale distributions of soil protists and their contributions to belowground systems
inferredcites →https://doi.org/10.1126/science.1179044openalex-snapshot
Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity
inferredcites →https://doi.org/10.1126/science.1256688openalex-snapshot
Global diversity and geography of soil fungi
inferredcites →https://doi.org/10.1126/science.1261359openalex-snapshot
Structure and function of the global ocean microbiome
inferredcites →https://doi.org/10.1128/aem.00905-17openalex-snapshot
Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity
inferredcites →https://doi.org/10.1128/aem.01179-06openalex-snapshot
The Mosaic Nature of Intergenic 16S-23S rRNA Spacer Regions Suggests rRNA Operon Copy Number Variation in Clostridium difficile Strains
inferredcites →https://doi.org/10.1128/aem.01282-13openalex-snapshot
Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity
inferredcites →https://doi.org/10.1128/aem.01298-08openalex-snapshot
Quantification of Diatom and Dinoflagellate Biomasses in Coastal Marine Seawater Samples by Real-Time PCR
inferredcites →https://doi.org/10.1128/aem.01574-06openalex-snapshot
Gene Copy Number Polymorphisms in an Arbuscular Mycorrhizal Fungal Population
inferredcites →https://doi.org/10.1128/aem.02627-17openalex-snapshot
The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
inferredcites →https://doi.org/10.1128/aem.66.4.1328-1333.2000openalex-snapshot
rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria
inferredcites →https://doi.org/10.1128/aem.70.11.6670-6677.2004openalex-snapshot
Life History Implications of rRNA Gene Copy Number in Escherichia coli
inferredcites →https://doi.org/10.1128/jb.170.2.605-610.1988openalex-snapshot
Instability of rRNA operons in Bacillus subtilis
inferredcites →https://doi.org/10.1128/jcm.02073-08openalex-snapshot
Strain-Dependent Variation in 18S Ribosomal DNA Copy Numbers in Aspergillus fumigatus
inferredcites →https://doi.org/10.1139/g02-103openalex-snapshot
The correlation between rDNA copy number and genome size in eukaryotes
inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.102003.152620openalex-snapshot
The Functional Significance of Ribosomal (r)DNA Variation: Impacts on the Evolutionary Ecology of Organisms
inferredcites →https://doi.org/10.1186/1745-6150-4-13openalex-snapshot
Massive comparative genomic analysis reveals convergent evolution of specialized bacteria
inferredcites →https://doi.org/10.1186/2049-2618-2-11openalex-snapshot
CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction
inferredcites →https://doi.org/10.1186/s40168-018-0420-9openalex-snapshot
Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
inferredcites →https://doi.org/10.12688/f1000research.16817.2openalex-snapshot
Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon
inferredcites →https://doi.org/10.1371/journal.pbio.1001419openalex-snapshot
CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms
inferredcites →https://doi.org/10.1371/journal.pbio.2005849openalex-snapshot
EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution
inferredcites →https://doi.org/10.1371/journal.pcbi.1002743openalex-snapshot
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
inferredcites →https://doi.org/10.1371/journal.pgen.1007006openalex-snapshot
DNA replication stress restricts ribosomal DNA copy number
inferredcites →https://doi.org/10.1371/journal.pone.0056413openalex-snapshot
Chromosome Copy Number Variation and Control in the Ciliate Chilodonella uncinata
inferredcites →https://doi.org/10.1371/journal.pone.0057923openalex-snapshot
The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses
inferredcites →https://doi.org/10.1371/journal.pone.0087624openalex-snapshot
Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers
inferredcites →https://doi.org/10.1534/g3.119.400771openalex-snapshot
Challenges and Approaches to Genotyping Repetitive DNA
inferredcites →https://doi.org/10.2183/pjab.90.119openalex-snapshot
Ribosomal RNA gene repeats, their stability and cellular senescence
inferredcites →https://doi.org/10.3168/jds.2008-1417openalex-snapshot
Rumen ciliated protozoa decrease generation time and adjust 18S ribosomal DNA copies to adapt to decreased transfer interval, starvation, and monensin
inferredcites →https://doi.org/10.3389/fphar.2017.00840openalex-snapshot
Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample
inferredcites →https://doi.org/10.3390/genes10050345openalex-snapshot
Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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First report on genetic characterization, cell‐surface properties and pathogenicity ofLactococcus garvieae, emerging pathogen isolated from cage‐cultured cobia (Rachycentron canadum)
inferred← citeshttps://doi.org/10.1128/mbio.00294-21openalex-snapshot
Effect of HIV/HAART and Other Clinical Variables on the Oral Mycobiome Using Multivariate Analyses
inferred← citeshttps://doi.org/10.1128/msystems.00285-25openalex-snapshot
Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members
inferred← citeshttps://doi.org/10.1128/msystems.00399-24openalex-snapshot
Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling
inferred← citeshttps://doi.org/10.1128/spectrum.01052-22openalex-snapshot
MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis
inferred← citeshttps://doi.org/10.1136/gutjnl-2022-327952openalex-snapshot
Fungi and cancer
inferred← citeshttps://doi.org/10.1186/s10086-025-02187-zopenalex-snapshot
Analysis by next-generation sequencing of bacterial communities in Japanese cedar logs buried for 2 years for ground improvement
inferred← citeshttps://doi.org/10.1186/s12915-025-02328-2openalex-snapshot
Universal orthologs infer deep phylogenies and improve genome quality assessments
inferred← citeshttps://doi.org/10.1186/s13717-024-00550-4openalex-snapshot
Biogeographic shifts in the microbial co-occurrence network features of three domains across complex environmental gradients in subtropical coastal waters
inferred← citeshttps://doi.org/10.1186/s40168-021-01111-zopenalex-snapshot
The allometry of cellular DNA and ribosomal gene content among microbes and its use for the assessment of microbiome community structure
inferred← citeshttps://doi.org/10.1186/s40168-023-01693-wopenalex-snapshot
Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.1186/s40168-026-02484-9openalex-snapshot
Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach
inferred← citeshttps://doi.org/10.1186/s42523-021-00134-zopenalex-snapshot
Defining gut mycobiota for wild animals: a need for caution in assigning authentic resident fungal taxa
inferred← citeshttps://doi.org/10.1371/journal.pone.0303697openalex-snapshot
Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes
inferred← citeshttps://doi.org/10.17169/refubium-42938openalex-snapshot
Revisiting soil fungal biomarkers and conversion factors: Interspecific variability in phospholipid fatty acids, ergosterol and rDNA copy numbers
inferred← citeshttps://doi.org/10.21203/rs.3.rs-4006805/v1openalex-snapshot
Evaluating the Efficiency of 16S-ITS-23S operon Sequencing: A Comparison of Primer Pairs, Sequencing Platforms, and Taxonomic Classifiers
inferred← citeshttps://doi.org/10.24072/pci.microbiol.100007openalex-snapshot
Towards a more accurate metabarcoding approach for studying fungal communities of fermented foods
inferred← citeshttps://doi.org/10.24072/pcjournal.321openalex-snapshot
Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods
inferred← citeshttps://doi.org/10.3354/ame02003openalex-snapshot
Exploring the diversity of microeukaryotic communities in New England tide pools
inferred← citeshttps://doi.org/10.3389/fmars.2022.878803openalex-snapshot
Coupling Imaging and Omics in Plankton Surveys: State-of-the-Art, Challenges, and Future Directions
inferred← citeshttps://doi.org/10.3389/fmars.2023.1306336openalex-snapshot
Metabarcoding and microscopy characterization of phytoplankton from frontal areas of the Argentine Sea
inferred← citeshttps://doi.org/10.3389/fmed.2024.1488377openalex-snapshot
Predicting cancer-related mycobiome aspects in gastrointestinal cancers: a systematic review
inferred← citeshttps://doi.org/10.3389/fmicb.2022.969230openalex-snapshot
Metabarcoding of mycetangia from the Dendroctonus frontalis species complex (Curculionidae: Scolytinae) reveals diverse and functionally redundant fungal assemblages
inferred← citeshttps://doi.org/10.3389/fmicb.2022.969799openalex-snapshot
Does filter pore size introduce bias in DNA sequence-based plankton community studies?
inferred← citeshttps://doi.org/10.3389/fmicb.2024.1360488openalex-snapshot
Comparative metabarcoding and biodiversity of gut-associated fungal assemblages of Dendroctonus species (Curculionidae: Scolytinae)
inferred← citeshttps://doi.org/10.3389/fmicb.2026.1813833openalex-snapshot
Soil algae in arable land: changes in the genotypic community composition across time points and farming systems—a pilot study
inferred← citeshttps://doi.org/10.3389/fpls.2026.1872093openalex-snapshot
A beta-tubulin-based qPCR assay for monitoring of Peronospora variabilis and disease progression in quinoa
inferred← citeshttps://doi.org/10.3390/applmicrobiol2030036openalex-snapshot
Cambisol Mycobiome in a Long-Term Field Experiment with Korean Pine as a Sole Edificator: A Case Study
inferred← citeshttps://doi.org/10.3390/biology12020268openalex-snapshot
A TaqMan® Assay Allows an Accurate Detection and Quantification of Fusarium spp., the Causal Agents of Tomato Wilt and Rot Diseases
inferred← citeshttps://doi.org/10.3390/dna5010013openalex-snapshot
Estimating Carbon Biomass Using DNA: Phytoplankton as a Case Study
inferred← citeshttps://doi.org/10.3390/f15061008openalex-snapshot
Phylogenetic Diversity, Host Specificity, and Distribution of the Wood-Decaying Fungus Phellinotus teixeirae in Western Colombia’s Seasonally Dry Tropical Forest
inferred← citeshttps://doi.org/10.3390/ijms24109005openalex-snapshot
Cytogenetics Meets Genomics: Cytotaxonomy and Genomic Relationships among Color Variants of the Asian Arowana Scleropages formosus
inferred← citeshttps://doi.org/10.3390/ijms27125372openalex-snapshot
Genomic and Metabolomic Comparisons Provide New Insights into Plant Cell Wall Degradation, Mating Diversity and Secondary Metabolites in Brown and White Commercial Hypsizygus marmoreus Varieties
inferred← citeshttps://doi.org/10.3390/jmse10121967openalex-snapshot
A CHEMTAX Study Based on Picoeukaryotic Phytoplankton Pigments and Next-Generation Sequencing Data from the Ulleungdo–Dokdo Marine System of the East Sea (Japan Sea): Improvement of Long-Unresolved Underdetermined Bias
inferred← citeshttps://doi.org/10.3390/jof7020146openalex-snapshot
Characterization of Kazachstania slooffiae, a Proposed Commensal in the Porcine Gut
inferred← citeshttps://doi.org/10.3390/microorganisms11051185openalex-snapshot
Effect of Anthropogenic Disturbances on the Microbial Relationship during Bioremediation of Heavy Metal-Contaminated Sediment
inferred← citeshttps://doi.org/10.48130/jzser-0026-0012openalex-snapshot
Efficient enrichment of ciliate sequences using a phylum-specific one-step amplicon approach
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653906openalex-snapshot
Additional file 1 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653909openalex-snapshot
Additional file 2 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653912openalex-snapshot
Additional file 3 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653915openalex-snapshot
Additional file 4 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653918openalex-snapshot
Additional file 5 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653921openalex-snapshot
Additional file 6 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653924openalex-snapshot
Additional file 7 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653927openalex-snapshot
Additional file 8 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653930openalex-snapshot
Additional file 9 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653933openalex-snapshot
Additional file 10 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653936openalex-snapshot
Additional file 11 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653939openalex-snapshot
Additional file 12 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653942openalex-snapshot
Additional file 13 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653948openalex-snapshot
Additional file 14 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653951openalex-snapshot
Additional file 15 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.6084/m9.figshare.26653954openalex-snapshot
Additional file 16 of Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
inferred← citeshttps://doi.org/10.64898/2025.12.01.25341376openalex-snapshot
Exploratory Deep Phenotyping of Early Antidepressant Treatment Effects in a Longitudinal, Double-Blind, Randomized, Controlled, Parallel-Group Pre-Post Design – a Study Protocol from Research Consortium OptiMD
inferred← citeshttps://doi.org/10.64898/2026.06.17.732913openalex-snapshot
Ecological inference and contaminant detection from fungal microbiome data with q2-fungal-traits
inferred← citeshttps://doi.org/10.70675/08139f8fz39d4z4ae8za747z2d4c4f46a6b1openalex-snapshot
Effet des pratiques culturales sur le mycobiote racinaire et la mycorhize à arbuscules chez le blé
inferred← citeshttps://doi.org/10.70675/15f32752za04dz46adz8598z70a702c527faopenalex-snapshot
Symbioses mycorhiziennes des orchidées épiphytes
inferred← citeshttps://doi.org/10.70675/a418fdd9z2683z4a7azbbc1zcb3046791a01openalex-snapshot
Role of the microbiome in the rhizosphere functioning of different grapevine rootstocks and influence on scion growth
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