The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
Open accessAbstract
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128
Prokaryotes: The unseen majority
Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6578 · Cited by 4,871 · cited 2×
“The LTP taxonomy is distributed over four fields of information: (1) (fullname_ltp) corresponds to the species or subspecies name; (2) (high_tax_ltp) is the name of the next higher taxon above genus; (3) (type_ltp) contains information about type species that are the nomenclatural types for the higher taxa above speci…”
BackgroundThe Revised Classification of Eukaryotes
Adl, S. M., Simpson, A. G. B., Lane, C. E., Lukeš, J., Bass, D., Bowser, S. S., Brown, M. W., Burki, F., Dunthorn, M., Hampl, V., et al. (2012) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2012.00644.x · Cited by 1,680
Self-citationFederhen, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1178 · Cited by 1,436
Research works printed but not linked: 32
- 10.1126/science.276.5313.734 · DOI · Paper page
- 10.1086/303287 · DOI · Paper page
- 10.1146/annurev-marine-120709-142811 · DOI · Paper page
- 10.1525/bio.2009.59.4.7 · DOI
- 10.1016/S0966-842X(01)02257-0 · DOI · Paper page
- Amann, 1995, Phylogenetic identification and in-situ detection of individual microbial cells without cultivation, Microbiol. Rev., 59, 143, 10.1128/MMBR.59.1.143-169.1995 · doi:10.1128/mmbr.59.1.143-169.1995 · Paper page
- 10.1099/00207713-47-2-590 · DOI · Paper page
- Goodfellow M Kampfer P Busse HJ Trujillo ME Suzuki KI Ludwig W Whitman WB . Bergey's Manual of Systematic Bacteriology. New York: Springer; 2012. · DOI · Paper page
- 10.1016/j.syapm.2011.03.001 · DOI
- Parte, 2013, LPSN—list of prokaryotic names with standing in nomenclature, 42, D613
- Lapage SP Sneath PHA Lessel E Skerman V Seeliger H Clark W . International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision. Washington: ASM Press; 1992.
- Garrity GM Jonson KL Bell J Searles DB . Taxonomic Outline of the Prokaryotes. 2nd edn. New York: Springer; 2002.
- 10.1093/nar/gkm864 · DOI · Paper page
- Boone DR Castenholz RW Garrity GM Stanley JT . The Archaea and the Deeply Branching and Phototrophic Bacteria. New York: Springer; 2001.
- Brenner DJ Krieg NR Garrity GM Staley JT . The Proteobacteria. New York: Springer; 2005.
- Vos PD Garrity GM Jones D Krieg NR Ludwig W Rainey FA Schleifer KH Whitman WB . The Firmicutes. New York: Springer; 2009.
- Krieg NR Staley JT Brown DR Hedlund BP Paster BJ Ward NL Ludwig W Whitman WB . The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. New York: Springer; 2010.
- 10.4319/lo.2005.50.5.1687 · DOI · Paper page
- 10.1128/AEM.67.21.5750-5760.2001 · DOI · Paper page
- 10.1111/j.1462-2920.2007.01540.x · DOI
- 10.1080/10635150701494127 · DOI · Paper page
- 10.1111/j.1095-8312.2012.01962.x · DOI
- 10.1371/journal.pgen.0020220 · DOI · Paper page
- 10.1038/ismej.2008.101 · DOI · Paper page
- 10.1093/nar/gks1160 · DOI · Paper page
- 10.1111/j.1550-7408.2005.00053.x · DOI · Paper page
- 10.1111/j.1095-8312.2011.01624.x · DOI
- 10.1371/journal.pbio.1001419 · DOI · Paper page
- 10.1128/AEM.00062-07 · DOI · Paper page
- 10.1016/j.syapm.2008.07.001 · DOI · Paper page
- McDonald, 2011, An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea, ISME J., 6, 610, 10.1038/ismej.2011.139 · DOI · Paper page
- 10.1093/nar/gkn879 · DOI · Paper page
Cited by
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
Kumar, S., Stecher, G., & Tamura, K. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw054 · Cited by 44,059
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., & Hugenholtz, P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4229 · Cited by 3,603
Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab776 · Cited by 2,402
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303
Paramsothy, S., Kamm, M. A., Kaakoush, N. O., Walsh, A. J., van den Bogaerde, J., Samuel, D., Leong, R. W. L., Connor, S., Ng, W., Paramsothy, R., et al. (2017) · The Lancet · doi:10.1016/s0140-6736(17)30182-4 · Cited by 1,276
Metadata
- Authors
- Yilmaz, P., Parfrey, L. W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J., Ludwig, W., & Glöckner, F. O.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-11-28
- Volume
- 42
- Issue
- D1
- Pages
- D643-D648
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2103296919
- Cited by
- 3,952
- References
- 4
- FWCI
- 16.68
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. https://app.cochat.ai/papers/10.1093/nar/gkt1209
- The paper
- Yilmaz, P., Parfrey, L. W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J., Ludwig, W., & Glöckner, F. O. (2014). The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt1209
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
