Reference health
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
1 of 49 checkable references need attention · checked 2026-08-03
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
6 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.
References needing attention
does not resolve to a known work10.1128/MMBR.59.1.143-169.1995
The 48 checked references that resolve
resolves10.1093/nar/gks1219
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
resolves10.1111/j.1462-2920.2011.02599.x
Towards a taxonomy of
<i>Bacteria</i>
and
<i>Archaea</i>
based on interactive and cumulative data repositories
resolves10.1073/pnas.0906412106
Shifting the genomic gold standard for the prokaryotic species definition
resolves10.1099/ijs.0.016949-0
Notes on the characterization of prokaryote strains for taxonomic purposes
resolves10.1016/j.tim.2012.05.004
Response to Gribaldo and Brochier-Armanet: time for order in microbial systematics
resolves10.1016/j.syapm.2008.07.001
The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
resolves10.1007/978-0-387-21609-6_8
Overview: A Phylogenetic Backbone and Taxonomic Framework for Procaryotic Systematics
resolves10.1099/00207713-27-1-44
Comparative Cataloging of 16S Ribosomal Ribonucleic Acid: Molecular Approach to Procaryotic Systematics
resolves10.1111/j.1574-6976.1994.tb00132.x
Bacterial phylogeny based on 16S and 23S rRNA sequence analysis
resolves10.1128/AEM.64.12.4973-4982.1998
Flow Cytometric Analysis of the In Situ Accessibility of
<i>Escherichia coli</i>
16S rRNA for Fluorescently Labeled Oligonucleotide Probes
resolves10.1016/j.syapm.2010.08.001
Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses
resolves10.1099/00207713-46-4-939
Proposal for Two New Genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov.
resolves10.1099/ijs.0.011700-0
Brevundimonas naejangsanensis sp. nov., a proteolytic bacterium isolated from soil, and reclassification of Mycoplana bullata into the genus Brevundimonas as Brevundimonas bullata comb. nov.
resolves10.1099/00207713-51-2-667
Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes.
resolves10.1016/j.mimet.2007.02.005
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
resolves10.1371/journal.pone.0053608
Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs
resolves10.1128/AEM.71.12.7724-7736.2005
At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies
resolves10.1099/ijs.0.63589-0
International Committee on Systematics of Prokaryotes; Xth International (IUMS) Congress of Bacteriology and Applied Microbiology; Minutes of the meetings, 28 and 30 July 2002, Paris, France
resolves10.1099/ijs.0.023986-0
Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes
resolves10.1073/pnas.1120192109
Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria
resolves10.1093/nar/gks808
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
resolves10.1038/ismej.2011.109
Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers
resolves10.1038/ismej.2012.82
Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation
resolves10.1099/00207713-47-2-479
Proposal for a New Hierarchic Classification System, Actinobacteria classis nov.
resolves10.1128/AEM.03333-12
Phylogenetic Delineation of the Novel Phylum Armatimonadetes (Former Candidate Division OP10) and Definition of Two Novel Candidate Divisions
resolves10.1099/00207713-52-1-7
The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.
resolves10.1128/JB.2.2.155-164.1917
STUDIES IN THE NOMENCLATURE AND CLASSIFICATION OF THE BACTERIA II. THE PRIMARY SUBDIVISIONS OF THE SCHIZOMYCETES
resolves10.1099/00207713-29-3-245
Leptospiraceae, a New Family to Include Leptospira Noguchi 1917 and Leptonema gen. nov.
resolves10.1128/AEM.70.2.845-849.2004
New Perspective on Uncultured Bacterial Phylogenetic Division OP11
resolves10.1038/ismej.2010.87
Distribution of <i>Roseobacter</i> RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate
resolves10.1016/j.copbio.2006.05.005
The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
resolves10.1128/JB.180.18.4765-4774.1998
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
resolves10.1093/nar/gkt1209
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
resolves10.1128/AEM.02697-08
The Ultramicrobacterium “
<i>Elusimicrobium minutum</i>
” gen. nov., sp. nov., the First Cultivated Representative of the Termite Group 1 Phylum
resolves10.1093/bioinformatics/bts565
CD-HIT: accelerated for clustering the next-generation sequencing data
resolves10.1093/bioinformatics/btl446
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
The 6 references without a DOI — listed, not checked
no DOI — not checkedStackebrandt, E. & Ebers, J. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today 8, 6–9 (2006).
no DOI — not checkedCole, J. R., Konstantinidis, K., Farris, R. J. & Tiedje, J. M. in Environmental molecular microbiology (eds Liu, W.-T. & Jansson, J. K.) 1–19 (Caister Academic Press, 2010).
no DOI — not checkedLudwig, W. in Molecular Phylogeny of Microorganisms (eds Oren, A. & Papke, R. T.) 65–83 (Caister Academic Press, 2010). This chapter reports the classification of high ranks of the Bacteria and the Archaea, which is currently based on comparative analyses of rRNA and is supported by other markers and multigene approaches. The high information content and great availability in databases mostly justify the usage of rRNA gene sequences in taxonomy.
no DOI — not checkedSwellengrebel, N. H. Sur la cytologie comparée des spirochètes et des spirilles. Ann. Inst. Pasteur. 21, 562–586 (in French) (1907).
no DOI — not checkedGupta, R. S., Mahmood, S. & Adeolu, M. A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum. Front. Microbiol. 4, 217 (2013).
no DOI — not checkedR Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2014) [online]
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