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What is LPSN?
LPSN is the List of Prokaryotic Names with Standing in Nomenclature: a curated reference database for the names of prokaryotes—bacteria and archaea—maintained at DSMZ. It was founded in 1997 by Jean P. Euzéby and is a free-to-use service. It is recognized as a Global Core Biodata Resource and an ELIXIR Core Data Resource, and is supported by the ICSP.
Its core purpose is nomenclature, not identification. It tells you whether a name is validly published and correctly formed, which matters when a name changes or when different publications use competing names. Beyond names, it holds related information such as etymology, collections and nomenclatural categories, and offers an API and downloads.
What you can do with it
- Check a name's standing. Confirm whether a prokaryotic name is validly published before using it in a paper, patent, culture collection record or clinical report.
- Browse by rank. Move through the hierarchy from domain and kingdom down to phylum, class, order, family, genus and species, including rarely used categories.
- Trace nomenclatural detail. Look up etymology, type information and collection links rather than relying on a single search-engine result.
- Search systematically. Use the advanced search when you need to filter by rank or category instead of guessing a name.
- Work at scale. Use the API or downloads when you need to reconcile many names across a database, lab information system or sequence metadata set.
Who it suits
Microbiologists, taxonomists, journal editors and patent examiners use it to settle naming questions. Clinical and public-health laboratories may instead want the List of Recommended Names for bacteria of medical importance, which LPSN cites separately—useful when a strictly correct name would confuse routine diagnostic reporting. Bioinformatics teams should prefer the API or downloads over manual browsing for bulk work.
A practical next step: if you have a name in hand, search it directly and check its standing and etymology; if you have a list, use the API or downloads so your records stay consistent. The site also provides citation guidance, which is worth following when you publish.
How do I search for a prokaryotic name using LPSN?
Use LPSN's browse hierarchy or its name search to find a prokaryotic name, then read the record for the nomenclatural status and the original publication details. The site is organised around the taxonomic ranks of domain, kingdom, phylum, class, order, family, genus and species, so you can either drill down through those ranks or jump straight to a name if you already know what you are looking for.
Two practical routes
- Browse by rank. Start at a broad rank and narrow down. This suits exploratory work, such as checking which genera sit in a family or confirming the correct spelling of a taxon above genus level.
- Search by name. Use the search when you have a candidate name, including one you suspect is a synonym or has been reclassified. LPSN's value here is that it covers nomenclatural information rather than only current taxonomy.
An advanced search is also available for more targeted queries, and the site provides downloads and an API if you need to work with many names at once rather than one at a time.
What to check on a record
- The standing in nomenclature — whether the name is validly published and whether it is a correct name or a synonym.
- The etymology, which LPSN exposes as its own category and which is useful when you need to explain or verify a name's derivation.
- The original publication and the type information, so you can cite the name correctly.
- Whether the name appears in the List of Recommended Names for bacteria of medical importance, which is a separate curated list with its own citation.
The last point matters in clinical and diagnostic work: nomenclature changes can disrupt laboratory reporting, and that list exists specifically to offer stable names for medically important bacteria.
A concrete scenario
Suppose a clinical microbiology report uses a genus name you do not recognise. Search the name in LPSN. If the record shows it as a synonym, follow the link to the currently correct name and check the publication that proposed the change. That gives you both the replacement name and a citable reference for explaining the switch to colleagues.
Next step
If you only need a single name, go straight to the name search. If you are building a list of names for a project, use the downloads or API instead, and cite LPSN appropriately — the site gives separate citation guidance for the medical names list and for other uses, including the API. For broader taxonomic context alongside LPSN, the NCBI Taxonomy database at NCBI and the Bergey's Manual Trust at Bergey's Manual Trust are useful companions, though neither replaces LPSN for nomenclatural standing.
How do I cite LPSN in a scientific publication?
Cite LPSN according to which part of the resource you used. The site itself distinguishes two cases: the List of Recommended Names for bacteria of medical importance has its own citation, while other uses — including the API — take the general LPSN/TYGS paper.
Which citation to use
| What you used | Citation to give |
|---|---|
| The List of Recommended Names for bacteria of medical importance | Göker, M., Christensen, H., Fingerle, V., Kostovski, M., Margos, G., Moore, E.R.B., Oren, A., Patrick, S., Reischl, U., Vázquez-Boland, J.A. (2025). List of Recommended Names for bacteria of medical importance: report of the Ad Hoc Committee on Mitigating Changes in Prokaryotic Nomenclature. Int J Syst Evol Microbiol, 75:6943; DOI: 10.1099/ijsem.0.006943 |
| Any other aspect of LPSN, including the API | Freese, H.M., Meier-Kolthoff, J.P., Sardà Carbasse, J., Afolayan, A.O., Göker, M. (2026). TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity. Nucleic Acids Research, 54, D884–D891; DOI: 10.1093/nar/gkaf1110 |
Practical points
- The two citations are not interchangeable. If your paper's nomenclature follows the medical-importance list, citing only the general paper leaves that specific source unattributed.
- Add the access date and the URL for the record you consulted, since nomenclature status can change as names are validated or corrected. The stable address is LPSN.
- Check the target journal's style for database citations. Many journals want the database name, version or access date, and URL in the reference list or in the text.
- If you used a nomenclatural opinion, a collection entry, or downloaded data, say so in your methods; a reader reproducing your work needs to know which LPSN layer you relied on.
A useful next step: before submission, open the LPSN record for each name you cite and confirm its current standing, then store the access date alongside your reference manager entry. That single habit prevents most nomenclature-related correction requests at proof stage.
What does 'standing in nomenclature' mean for a prokaryotic name?
"Standing in nomenclature" means a prokaryotic name has been validly published and is therefore legitimate for use in the international code-governed literature. A name with standing is the correct, citable label for a taxon; a name without it is effectively a proposal that has not cleared the formal publication requirements.
What gives a name standing
For prokaryotes, the key steps are:
- Valid publication — the name must appear in a publication that the rules recognise, with a description or reference to a type strain.
- Compliance with the International Code of Nomenclature of Prokaryotes — formation, priority, and typification rules must be followed.
- Entry on the approved list — the name is recorded in a maintained register, which is where LPSN comes in.
Why it matters in practice
If you are writing a paper, a clinical report, or a culture-collection record, using a name with standing avoids ambiguity. A name that lacks standing may still be in circulation, but it is not the nomenclaturally correct one, and journals or databases may reject or flag it.
How LPSN fits
LPSN is a curated register of prokaryotic names with standing in nomenclature. It lets you check whether a name is validly published, see its rank and classification, and trace nomenclatural details. It is a free service and a Global Core Biodata Resource, maintained at DSMZ.
A concrete reader scenario
Suppose a lab identifies an isolate as "Bacillus examplensis" from an older paper. Before publishing, check LPSN: if the name has standing, cite it as is; if it does not, you may need to use the current valid name or note the earlier name as a synonym. This is routine in microbial systematics and prevents propagating invalid names.
Decision criterion
Use a name with standing when you need the nomenclaturally correct label. Use a name without standing only when discussing the history of a proposal, and say so explicitly.
How does LPSN differ from other nomenclature databases like NCBI Taxonomy?
LPSN is a nomenclature-focused register, while NCBI Taxonomy is a sequence-oriented classification system. That distinction determines which one you should open first.
What each resource is actually for
LPSN LPSN centers on the valid publication of prokaryotic names — whether a name has standing in nomenclature, who proposed it, its etymology, and its correct spelling under the rules of the International Code of Nomenclature of Prokaryotes. Its browse tree runs by rank (domain through species), with collections, etymology and statistics alongside.
NCBI Taxonomy NCBI Taxonomy exists to organize sequence records. It assigns every GenBank/RefSeq entry to a taxon so that genomes, rRNA genes and amplicon reads can be grouped and compared. It is broader — all cellular life plus viruses — and updates quickly as sequences arrive.
Practical differences
| Question you are asking | Better starting point |
|---|---|
| Is this name validly published? | LPSN |
| Who proposed this species, and when? | LPSN |
| What does the epithet mean? | LPSN |
| Which genome or sequence records map to this taxon? | NCBI Taxonomy |
| I need a taxid for a pipeline or database join | NCBI Taxonomy |
| The name in my paper may be a synonym or misspelling | LPSN, then verify against the sequence record |
The trade-off is curation philosophy. LPSN is authoritative but deliberately narrow: it covers prokaryotes and reflects nomenclatural rules, so a name that is widely used in journals may still be flagged as not validly published. NCBI Taxonomy is permissive and practical — it accepts informal labels such as "uncultured bacterium" and "sp." clusters that have no standing in nomenclature at all — which makes it indispensable for sequence work but unreliable as a source on name validity.
A concrete scenario
Suppose a reviewer questions the species name in your manuscript. Check LPSN first for valid publication and correct spelling, then pull the NCBI Taxonomy record for the same organism to confirm which sequence accessions and type-strain genome data you should cite. If the two disagree, treat the nomenclature question as LPSN's to answer and the sequence-identity question as NCBI's.
Related resources worth knowing
For a medical or clinical audience, LPSN's recommended-names list is designed for situations where established usage conflicts with strict nomenclature. For type-strain genomes and genome-based classification, the same DSMZ group runs TYGS TYGS, which complements LPSN's nomenclatural data.
Can I download or access LPSN data programmatically via an API?
Yes. LPSN is accessible programmatically through an API, and there is also a dedicated downloads section. Both are listed in the site's main navigation, so you don't need to scrape the browse pages.
What "programmatic access" means here
- API: intended for querying nomenclatural records (names, ranks, taxonomy, etymology and related metadata) from your own scripts or pipelines.
- Downloads: bulk files for offline work, useful when you need the whole dataset rather than repeated queries.
The practical difference matters:
| Need | Better fit |
|---|---|
| Look up a few names, check a record, integrate into a pipeline | API |
| Build a local database, run large-scale analyses, avoid rate limits | Downloads |
| Reproducible analysis with a fixed snapshot | Downloads |
| Always-current answers | API |
Practical scenario
Suppose you are curating a culture collection or a metagenomics pipeline and need to validate thousands of prokaryotic names against current nomenclature. Querying the API name-by-name works but couples your run to network availability and response times. Pulling a download once, loading it into a local table, and refreshing periodically is usually faster and reproducible — then use the API only for spot checks or records added since your last snapshot.
Before you build
Check the FAQ and the citation guidance, since LPSN asks that you cite specific publications depending on which parts you use — the API has its own citation, separate from the recommended medical names list. Attribution requirements are normal for a resource supported by ICSP and recognized as a Global Core Biodata Resource and ELIXIR Core Data Resource, so plan for them in your documentation.
For complementary nomenclature and taxonomy resources, see DSMZ and NCBI.
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