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Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

https://doi.org/10.1099/ijs.0.059774-0
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31/31 checkable references clean · checked 2026-08-02

Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.

3 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.

The 31 checked references that resolve
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Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple <i>rrn</i> Operons
resolves10.1099/00207713-41-3-343
Comparative Analysis of Bacillus anthracis, Bacillus cereus, and Related Species on the Basis of Reverse Transcriptase Sequencing of 16S rRNA
resolves10.1186/1471-2180-12-302
Defining bacterial species in the genomic era: insights from the genus Acinetobacter
resolves10.1099/ijs.0.64915-0
EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
resolves10.1007/s00792-008-0194-2
Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium
resolves10.1128/JB.01202-08
A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera
resolves10.1128/JB.172.7.3609-3619.1990
Diversity and origin of Desulfovibrio species: phylogenetic definition of a family
resolves10.1038/nrmicro1236
Re-evaluating prokaryotic species
resolves10.1099/ijs.0.64483-0
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
resolves10.1186/1471-2164-14-366
Pan-genome analysis of the emerging foodborne pathogen Cronobacterspp. suggests a species-level bidirectional divergence driven by niche adaptation
resolves10.1186/1471-2180-10-154
Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae
resolves10.1093/bioinformatics/bth324
Whole-genome prokaryotic phylogeny
resolves10.1099/00207713-51-2-667
Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes.
resolves10.1099/ijs.0.038075-0
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
resolves10.1073/pnas.0409727102
Genomic insights that advance the species definition for prokaryotes
resolves10.1098/rstb.2006.1920
The bacterial species definition in the genomic era
resolves10.1371/journal.pone.0032491
Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms
resolves10.1007/s12275-011-1213-z
rRNASelector: A computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries
resolves10.1073/pnas.50.1.156
AN APPROACH TO THE MEASUREMENT OF GENETIC RELATEDNESS AMONG ORGANISMS
resolves10.1038/ismej.2011.139
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
resolves10.1186/1471-2105-14-60
Genome sequence-based species delimitation with confidence intervals and improved distance functions
resolves10.1038/nmeth.2575
Accurate and universal delineation of prokaryotic species
resolves10.1128/AEM.02953-09
Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes
resolves10.1007/s10994-011-5256-5
Classifier chains for multi-label classification
resolves10.1073/pnas.0906412106
Shifting the genomic gold standard for the prokaryotic species definition
resolves10.1016/S0168-6445(00)00040-1
The species concept for prokaryotes
resolves10.1016/S0022-2836(61)80024-7
The formation of hybrid DNA molecules and their use in studies of DNA homologies
resolves10.1099/00207713-44-4-846
Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology
resolves10.1099/ijs.0.016949-0
Notes on the characterization of prokaryote strains for taxonomic purposes
resolves10.1099/00207713-37-4-463
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics
resolves10.1111/j.1574-6968.2011.02485.x
Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence
The 3 references without a DOI — listed, not checked
no DOI — not checkedTaxonomic parameters revisited: tarnished gold standards
no DOI — not checkedReport of the ad hoc committee for the re-evaluation of the species definition in bacteriology
no DOI — not checkedInformation Retrieval
What this badge says. CiteStamped means the CHECKABLE references of this work were clean at the dated check: each resolved to a known work in a public registry, and none carried a retraction notice at that time. It says nothing about the quality, findings, or importance of the work itself, and nothing about references deposited without a DOI.

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