Jan P. Meier‐KolthoffpersName, J. Sarda CarbassepersName, Rosa L Peinado-OlartepersName, Markus GökerpersName (2022date). “TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes.” Nucleic Acids Researchtitle·venue.
Object of study — A REGISTER OF WHICH NAMES HAVE LEGAL STANDING, PAIRED WITH A SERVICE THAT DECIDES CLASSIFICATIONterm FROM A GENOME - the List of Prokaryotic names with Standing in Nomenclatureterm·var and the Type (Strain) Genome Server, run as one interconnected pair at the DSMZ
Research question — how to keep a nomenclatureterm register and a genome-based classifier in step when names are proposed faster than they are validated and 99% of the organisms have no valid name at all
Contribution — an expanded LPSNterm that now lists names WITHOUT standing and marks them as such, an API and CSV export for both platforms, and TYGSterm improvements for choosing the closest type strains
phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | a code under which a name either is or is not validly published, applied to a domain where the naming rate is rising, the geography of naming is shifting and the type material itself is under debate — “Classification in turn needs an internationally accepted system of nomenclature to unambiguously assign names to taxa ( 3 ). The cornerstone of the ICNP is the status of taxon names as being validly published; other names have no claim to recognition under this code” | |
| claim-type | method — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | |
| method — evidence | — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | |
| object of study — evidence | — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | |
| research question — evidence | — “The global prokaryotic diversity is estimated to encompass 0.8–1.6 million species ( 1 ) of which currently only about 1% ( 2 ) have a name that is validly published under the International Code of Nomenclature of Prokaryotes (ICNP) ( 3 ). Even though these estimates are likely to fluctuate, microbial life still remains largely unknown and unconnected to the only system of nomenclature accepted by the majority of microbiologists, the ICNP.” | |
| contribution — evidence | — “An even more fundamental advantage of including not validly published names is that it adds clarity. If a name is shown on LPSN and explicitly marked as not being validly published, this leaves no doubt with regard to its status, as opposed to just not showing the name at all.” | |
| mechanism | A NAME EITHER HAS LEGAL STANDING OR IT HAS NONE, AND 99% OF THE ORGANISMS HAVE NONE: `The global prokaryotic diversity is estimated to encompass 0.8-1.6 MILLION SPECIES of which currently ONLY ABOUT 1% have a name that is VALIDLY PUBLISHED under the ICNP` - and `The cornerstone of the ICNP is the status of taxon names as being validly published; other names have no claim to recognition under this code.` The corpus holds committees that vote and codes that classify; this is a code that confers a STATUS, and the status is binary — “The global prokaryotic diversity is estimated to encompass 0.8–1.6 million species ( 1 ) of which currently only about 1% ( 2 ) have a name that is validly published under the International Code of Nomenclature of Prokaryotes (ICNP) ( 3 ). Even though these estimates are likely to fluctuate, microbial life still remains largely unknown and unconnected to the only system of nomenclature accepted by the majority of microbiologists, the ICNP.” | mechanisms[0] |
| mechanism | AND THE REGISTER NOW LISTS THE NAMES THAT HAVE NO STANDING, BECAUSE ABSENCE IS AMBIGUOUS: `An even more fundamental advantage of including not validly published names is that it adds clarity. If a name is shown on LPSN and explicitly marked as not being validly published, this leaves no doubt with regard to its status, as opposed to just not showing the name at all.` A working solution to `an empty state is not an instance` - the difference between a name that failed and a name nobody entered, made visible on the page — “An even more fundamental advantage of including not validly published names is that it adds clarity. If a name is shown on LPSN and explicitly marked as not being validly published, this leaves no doubt with regard to its status, as opposed to just not showing the name at all.” | mechanisms[1] |
| mechanism | AND THEY CAMPAIGN ON IT: `The storage of not validly published names in LPSN allows for conducting campaigns to increase the rate of validation. As of July 2021, ALMOST 900 E-MAILS WERE SENT to corresponding authors to inform them about names proposed by them that as yet have no claim to recognition under the ICNP, COVERING >1500 NAMES.` A register that writes to the authors of the rows it holds — “The storage of not validly published names in LPSN allows for conducting campaigns to increase the rate of validation. As of July 2021, almost 900 e-mails were sent to corresponding authors to inform them about names proposed by them that as yet have no claim to recognition under the ICNP ( 3 ), covering >1500 names.” | mechanisms[2] |
| mechanism | AND STANDING CAN BE LOST RETROSPECTIVELY, AND MANY AUTHORS DO NOT KNOW IT EXISTS: `many names with an effective publication outside IJSEM are validated at a later date anyway ... Conversely, names supposed to be validly published may later on be recognized as not having met the necessary requirements. Moreover, not all taxonomist are aware of the need for validation.` The status moves in both directions and is not self-announcing — “For instance, many names with an effective publication outside IJSEM are validated at a later date anyway ( 3 ), hence their earlier consideration facilitates data analysis. Conversely, names supposed to be validly published may later on be recognized as not having met the necessary requirements ( 32 ). Moreover, not all taxonomist are aware of the need for validation” | mechanisms[3] |
| mechanism | AND THE COUNTERFACTUAL IS PUBLISHED BESIDE THE NAME: 'comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists.' A field saying when a verdict would change, in the wild - the row states what would have to be true for its own verdict to change — “Comments on taxonomic terminology were added to LPSN for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists ( 35 ).” | mechanisms[4] |
| mechanism | AND THE NAME IS ANCHORED TO A PHYSICAL SPECIMEN, PERMANENTLY: `The nomenclatural type is the entity with which A taxon name is permanently associated. In the cases of prokaryotic species and subspecies, the nomenclatural type is the type strain. Cultures of type strains thus firmly connect taxon names and genome sequences.` Our anchors point at a span of text; theirs point at a living culture in a collection — “The nomenclatural type is the entity with which a taxon name is permanently associated ( 3 ). In the cases of prokaryotic species and subspecies, the nomenclatural type is the type strain. Cultures of type strains thus firmly connect taxon names and genome sequences. Quality-checked ( 17 ) genome and proteome sequences of verified type strains are the starting point of TYGS analyses.” | mechanisms[5] |
| mechanism | AND AN ATTEMPT TO LET A GENOME BE THE ANCHOR FAILED: `While A recent attempt to modify the ICNP to allow for using genome sequences as nomenclatural type was unsuccessful, alternative solutions to the perceived underlying problem are currently actively debated.` The question of WHAT MAY SERVE AS THE ANCHOR OF A NAME, put to a vote and rejected - and the consequence is that a species with no cultivable strain cannot be named at all — “While a recent attempt to modify the ICNP to allow for using genome sequences as nomenclatural type was unsuccessful ( 39 ), alternative solutions to the perceived underlying problem are currently actively debated ( 40 ).” | mechanisms[6] |
| mechanism | AND THE INCLUSION CRITERION IS A RULE OF THE CODE RATHER THAN AN EDITORIAL JUDGEMENT: `a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names ... The inclusion criterion is the presence of an effective publication as defined by the ICNP.` Anonymous submission with a code-defined gate: who proposes is unrestricted, what qualifies is not — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | mechanisms[7] |
| mechanism | AND ONE GROUP IS GOVERNED BY TWO CODES AT ONCE: the register adds `names of Cyanobacteria validly published under the ICN (International Code of Nomenclature for algae, fungi and plants), in anticipation of the recent changes to the ICNP` - so a name's standing depends on which code you ask, and the register has to hold both answers — “A major change regarding the selection of taxon names for inclusion in LPSN is the addition of names that are not validly published ( Candidatus names and other names), as well as of names of Cyanobacteria validly published under the ICN (International Code of Nomenclature for algae, fungi and plants), in anticipation of the recent changes to the ICNP ( 29 ).” | mechanisms[8] |
| mechanism | AND THE RIVAL INDEX IS INCONSISTENT WITH ITSELF ACROSS IMPLEMENTATIONS: `the dDDH approach was shown to OUTPERFORM the `AVERAGE NUCLEOTIDE IDENTITY` (ANI) approach ... More recently, `ANI` was found to yield results that are inconsistent across its various implementations due to a lack of standardization.` One named measure, several programs, different numbers - a species boundary that depends on which implementation you ran — “As noted earlier, the dDDH approach was shown to outperform ( 18 , 19 ) the ‘average nucleotide identity’ (ANI) approach, which is also frequently used in scientific studies as an alternative OGRI index ( 5 ). More recently, ‘ANI’ was found to yield results that are inconsistent across its various implementations due to a lack of standardization ( 38 ).” | mechanisms[9] |
| mechanism | AND A NEIGHBOURING RESOURCE'S BREADTH IS ITS HAZARD: `other platforms such as EzBioCloud may provide access to A BROADER SELECTION OF `REFERENCE GENOMES`, including non-type strains, these are to the best of our knowledge frequently confused or misinterpreted as type strains and may thus lead to taxonomic misinterpretations.` A category error made possible by a database that does not mark the distinction the code turns on — “Even though other platforms such as EzBioCloud ( 37 ) may provide access to a broader selection of ‘reference genomes’, including non-type strains, these are to the best of our knowledge frequently confused or misinterpreted as type strains and may thus lead to taxonomic misinterpretations.” | mechanisms[10] |
| mechanism | AND THE MACHINE-READABLE EXPORT IS SCOPED BY A SUPERSEDED SPREADSHEET: `The LPSN CSV file needed to be downwards compatible with that Excel file as far as possible, hence it was and is intended to contain only the names of genera, species and subspecies validly published under the ICNP.` So the download excludes exactly the not-validly-published names the website added for clarity - a reader sees the absence marked and a program does not, and the reason is a format from a service that no longer exists — “The LPSN CSV (comma-separated values) file became available for download once LPSN was established at DSMZ ( 2 ). An Excel file was previously offered by the PNU (Prokaryotic Nomenclature Up-to-date) service of DSMZ, which was superseded by the new LPSN. The LPSN CSV file needed to be downwards compatible with that Excel file as far as possible, hence it was and is intended to contain only the names of genera, species and subspecies validly published under the ICNP.” | mechanisms[11] |
| extends | the 2020 relaunch of LPSN at the DSMZ and the original TYGS paper, both by overlapping authors - this is the joint update of the two — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | claim_relations[0] |
| critiques | the average nucleotide identity (ANI) index, which 'was found to yield results that are inconsistent across its various implementations due to a lack of standardization' — “As noted earlier, the dDDH approach was shown to outperform ( 18 , 19 ) the ‘average nucleotide identity’ (ANI) approach, which is also frequently used in scientific studies as an alternative OGRI index ( 5 ). More recently, ‘ANI’ was found to yield results that are inconsistent across its various implementations due to a lack of standardization ( 38 ).” | claim_relations[1] |
| critiques | databases offering 'reference genomes' including non-type strains, which are 'frequently confused or misinterpreted as type strains' — “Even though other platforms such as EzBioCloud ( 37 ) may provide access to a broader selection of ‘reference genomes’, including non-type strains, these are to the best of our knowledge frequently confused or misinterpreted as type strains and may thus lead to taxonomic misinterpretations.” | claim_relations[2] |
| sense | `validly published` - the ICNP status a name either has or has not; names without it `have no claim to recognition under this code`, and the status can be granted late or withdrawn on review — “Classification in turn needs an internationally accepted system of nomenclature to unambiguously assign names to taxa ( 3 ). The cornerstone of the ICNP is the status of taxon names as being validly published; other names have no claim to recognition under this code” | senses[0] |
| sense | `effective publication` - the weaker condition that gets a name INTO the register without standing; it is `The inclusion criterion` for LPSN, not for the code — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | senses[1] |
| sense | `nomenclatural type` - `the entity with which a taxon name is permanently associated`; for prokaryotes a living type STRAIN, and an attempt to admit a genome sequence instead was rejected — “The nomenclatural type is the entity with which a taxon name is permanently associated ( 3 ). In the cases of prokaryotic species and subspecies, the nomenclatural type is the type strain. Cultures of type strains thus firmly connect taxon names and genome sequences. Quality-checked ( 17 ) genome and proteome sequences of verified type strains are the starting point of TYGS analyses.” | senses[2] |
| sense | `correct name` - LPSN's current judgement, published alongside `the conditions under which a name would be regarded as the correct name if it is not currently so regarded` — “Comments on taxonomic terminology were added to LPSN for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists ( 35 ).” | senses[3] |
| control | showing names that are NOT validly published and marking them as such, rather than omitting them — held — “The storage of not validly published names in LPSN allows for conducting campaigns to increase the rate of validation. As of July 2021, almost 900 e-mails were sent to corresponding authors to inform them about names proposed by them that as yet have no claim to recognition under the ICNP ( 3 ), covering >1500 names.” — rules out the ambiguity between a name that failed the code and a name nobody entered — “An even more fundamental advantage of including not validly published names is that it adds clarity. If a name is shown on LPSN and explicitly marked as not being validly published, this leaves no doubt with regard to its status, as opposed to just not showing the name at all.” | controls[0] |
| control | restricting the classification evidence to genomes of VERIFIED TYPE STRAINS rather than reference genomes — held — “Even though other platforms such as EzBioCloud ( 37 ) may provide access to a broader selection of ‘reference genomes’, including non-type strains, these are to the best of our knowledge frequently confused or misinterpreted as type strains and may thus lead to taxonomic misinterpretations.” — rules out a non-type genome standing in for the nomenclatural type and carrying a name it has no claim to — “The nomenclatural type is the entity with which a taxon name is permanently associated ( 3 ). In the cases of prokaryotic species and subspecies, the nomenclatural type is the type strain. Cultures of type strains thus firmly connect taxon names and genome sequences. Quality-checked ( 17 ) genome and proteome sequences of verified type strains are the starting point of TYGS analyses.” | controls[1] |
| control | keeping the CSV export downwards compatible with the superseded PNU Excel file — partial — “An even more fundamental advantage of including not validly published names is that it adds clarity. If a name is shown on LPSN and explicitly marked as not being validly published, this leaves no doubt with regard to its status, as opposed to just not showing the name at all.” — rules out breaking existing pipelines - at the cost of excluding from the export exactly the not-validly-published names the website added for clarity — “The LPSN CSV (comma-separated values) file became available for download once LPSN was established at DSMZ ( 2 ). An Excel file was previously offered by the PNU (Prokaryotic Nomenclature Up-to-date) service of DSMZ, which was superseded by the new LPSN. The LPSN CSV file needed to be downwards compatible with that Excel file as far as possible, hence it was and is intended to contain only the names of genera, species and subspecies validly published under the ICNP.” | controls[2] |
| weight | the 2020 relaunch of LPSN at the DSMZ and the original TYGS paper, both by overlapping authors - this is the joint update of the two — 0.95 — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | claim_relations[0] |
| weight | the average nucleotide identity (ANI) index, which 'was found to yield results that are inconsistent across its various implementations due to a lack of standardization' — 0.9 — “As noted earlier, the dDDH approach was shown to outperform ( 18 , 19 ) the ‘average nucleotide identity’ (ANI) approach, which is also frequently used in scientific studies as an alternative OGRI index ( 5 ). More recently, ‘ANI’ was found to yield results that are inconsistent across its various implementations due to a lack of standardization ( 38 ).” | claim_relations[1] |
| weight | databases offering 'reference genomes' including non-type strains, which are 'frequently confused or misinterpreted as type strains' — 0.85 — “Even though other platforms such as EzBioCloud ( 37 ) may provide access to a broader selection of ‘reference genomes’, including non-type strains, these are to the best of our knowledge frequently confused or misinterpreted as type strains and may thus lead to taxonomic misinterpretations.” | claim_relations[2] |
| note | LPSN —is-a→ an expert-curated authoritative resource for prokaryotic nomenclature — 'The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature.' The word 'authoritative' is doing work: the register does not merely record which names have standing, it is where the field looks to find out - and the same institution runs the classifier that supplies the evidence — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | concept_edges[0] |
| relation | LPSN —is-a→ an expert-curated authoritative resource for prokaryotic nomenclature — LPSN is presented as the authoritative register for prokaryotic names - expert curation is part of the claim, not an implementation detail — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature” | concept_edges[0] |
| weight | LPSN —is-a→ an expert-curated authoritative resource for prokaryotic nomenclature — 0.95 — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | concept_edges[0] |
| note | TYGS —is-a→ a high-throughput platform for accurate genome-based taxonomy — 'The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy.' The pairing is the point: one platform decides what a thing IS and the other decides what it may be CALLED, and the paper's argument is that neither works well without the other — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | concept_edges[1] |
| relation | TYGS —is-a→ a high-throughput platform for accurate genome-based taxonomy — TYGS is the classification side of the pair - genomes in, phylogenies and species boundaries out — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” — “The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy” | concept_edges[1] |
| weight | TYGS —is-a→ a high-throughput platform for accurate genome-based taxonomy — 0.95 — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | concept_edges[1] |
| note | The inclusion criterion —operationalised-as→ the presence of an effective publication — 'a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names ... The inclusion criterion is the presence of an effective publication as defined by the ICNP.' Who proposes is unrestricted; what qualifies is not. And note the two-tier design: effective publication gets a name INTO the register, valid publication gives it STANDING, and the register shows both states — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | concept_edges[2] |
| relation | The inclusion criterion —operationalised-as→ the presence of an effective publication — what enters the register is decided by a condition of the ICNP, not by an editor - so anonymous submissions are accepted and the gate is the code — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” — “The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | concept_edges[2] |
| weight | The inclusion criterion —operationalised-as→ the presence of an effective publication — 0.95 — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | concept_edges[2] |
| note | nomenclature —distinct-from→ classification — 'The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists.' The change in question is publishing, beside a name, 'the conditions under which a name would be regarded as the correct name if it is not currently so regarded' - a row that states what would have to be true for its own verdict to change — “Comments on taxonomic terminology were added to LPSN for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists ( 35 ).” | concept_edges[3] |
| relation | nomenclature —distinct-from→ classification — what a taxon may be called and where a taxon sits are separate questions, and the register publishes comments specifically to keep them apart — “Comments on taxonomic terminology were added to LPSN for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists ( 35 ).” — “The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists” | concept_edges[3] |
| weight | nomenclature —distinct-from→ classification — 0.95 — “Comments on taxonomic terminology were added to LPSN for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists ( 35 ).” | concept_edges[3] |
| effect direction | the availability of genome sequences of type strains —causes→ emendations — increases — “The number of validly published names per country and year reflects the well-known shift of taxonomic activity to East Asian nations ( 28 ). The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains ( 8–11 ). More importantly, the overall number of names that become validly published per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered.” — “emendations also shows an increasing trend, caused by the availability of genome sequences of type strains” | concept_edges[4] |
| note | the availability of genome sequences of type strains —causes→ emendations — 'The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains.' A new instrument reaching back into names already settled - the same shape as bishop2017's discontinuity worry and staab2017's index terms, except here the corrections are counted per year and rising — “The number of validly published names per country and year reflects the well-known shift of taxonomic activity to East Asian nations ( 28 ). The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains ( 8–11 ). More importantly, the overall number of names that become validly published per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered.” | concept_edges[4] |
| relation | the availability of genome sequences of type strains —causes→ emendations — genome sequences of type strains are driving a rising rate of formal corrections to already-valid names — “The number of validly published names per country and year reflects the well-known shift of taxonomic activity to East Asian nations ( 28 ). The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains ( 8–11 ). More importantly, the overall number of names that become validly published per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered.” — “The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains ( 8–11 ).” | concept_edges[4] |
| weight | the availability of genome sequences of type strains —causes→ emendations — 0.95 — “The number of validly published names per country and year reflects the well-known shift of taxonomic activity to East Asian nations ( 28 ). The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains ( 8–11 ). More importantly, the overall number of names that become validly published per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered.” | concept_edges[4] |
| outcome | control — held — “An even more fundamental advantage of including not validly published names is that it adds clarity. If a name is shown on LPSN and explicitly marked as not being validly published, this leaves no doubt with regard to its status, as opposed to just not showing the name at all.” — “The storage of not validly published names in LPSN allows for conducting campaigns to increase the rate of validation. As of July 2021, almost 900 e-mails were sent to corresponding authors to inform them about names proposed by them that as yet have no claim to recognition under the ICNP ( 3 ), covering >1500 names.” | controls[0] |
| outcome | control — held — “The nomenclatural type is the entity with which a taxon name is permanently associated ( 3 ). In the cases of prokaryotic species and subspecies, the nomenclatural type is the type strain. Cultures of type strains thus firmly connect taxon names and genome sequences. Quality-checked ( 17 ) genome and proteome sequences of verified type strains are the starting point of TYGS analyses.” — “Even though other platforms such as EzBioCloud ( 37 ) may provide access to a broader selection of ‘reference genomes’, including non-type strains, these are to the best of our knowledge frequently confused or misinterpreted as type strains and may thus lead to taxonomic misinterpretations.” | controls[1] |
| outcome | control — partial — “The LPSN CSV (comma-separated values) file became available for download once LPSN was established at DSMZ ( 2 ). An Excel file was previously offered by the PNU (Prokaryotic Nomenclature Up-to-date) service of DSMZ, which was superseded by the new LPSN. The LPSN CSV file needed to be downwards compatible with that Excel file as far as possible, hence it was and is intended to contain only the names of genera, species and subspecies validly published under the ICNP.” — “An even more fundamental advantage of including not validly published names is that it adds clarity. If a name is shown on LPSN and explicitly marked as not being validly published, this leaves no doubt with regard to its status, as opposed to just not showing the name at all.” | controls[2] |
| limitation | THE COVERAGE OF NAMES WITHOUT STANDING CANNOT BE COMPLETE, AND THEY SAY WHY: `Because they are not centrally collected in a journal such as IJSEM, the coverage of names by LPSN that have an effective publication but are not validly published under the code cannot be expected to be complete. LPSN attempts to focus on names that are in use, i.e. are found in the literature or in other databases.` The invalid half of the register is a convenience sample of what people actually write — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | limitations[0] |
| limitation | AND THE GROWTH IS IN THE DATA, NOT IN THE UNDERSTANDING: `the overall number of names that become validly published per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered` - against 1% of estimated species named at all, so the rate rises while the fraction barely moves — “The number of validly published names per country and year reflects the well-known shift of taxonomic activity to East Asian nations ( 28 ). The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains ( 8–11 ). More importantly, the overall number of names that become validly published per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered.” | limitations[1] |
| limitation | AND THE SCALE IS SMALL AGAINST THE DOMAIN: `the LPSN database provides ... >26K NAMES of any category and >21K SPECIES NAMES validly published under the ICNP ... the TYGS database contains >15K TYPE-STRAIN GENOMES.` Twenty-one thousand named species against an estimated 0.8-1.6 million — “As of July 2021, the LPSN database (Figure 1 ) provides a large variety of expert-curated nomenclatural data, including >26k names of any category and >21k species names validly published under the ICNP ( 3 ). At the time of writing, the TYGS database (Figure 1 ) contains >15k type-strain genomes and was used by >3.7k different users worldwide for conducting >27k distinct analyses (Figure 2 ) involving 15M + genome comparisons.” | limitations[2] |
| limitation | AND THE TWO PLATFORMS ARE ONE INSTITUTION'S: both LPSN and TYGS are run at the Leibniz Institute DSMZ by the same four authors, and the paper's own recommendation is to migrate users off the earlier GGDC tool onto TYGS. The register of what counts as a name and the service that supplies the evidence for classification share a roof — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | limitations[3] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | — “The global prokaryotic diversity is estimated to encompass 0.8–1.6 million species ( 1 ) of which currently only about 1% ( 2 ) have a name that is validly published under the International Code of Nomenclature of Prokaryotes (ICNP) ( 3 ). Even though these estimates are likely to fluctuate, microbial life still remains largely unknown and unconnected to the only system of nomenclature accepted by the majority of microbiologists, the ICNP.” | content_tags.findings[0] |
| finding | — “An even more fundamental advantage of including not validly published names is that it adds clarity. If a name is shown on LPSN and explicitly marked as not being validly published, this leaves no doubt with regard to its status, as opposed to just not showing the name at all.” | content_tags.findings[1] |
| finding | — “Comments on taxonomic terminology were added to LPSN for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists ( 35 ).” | content_tags.findings[2] |
| finding | — “While a recent attempt to modify the ICNP to allow for using genome sequences as nomenclatural type was unsuccessful ( 39 ), alternative solutions to the perceived underlying problem are currently actively debated ( 40 ).” | content_tags.findings[3] |
| finding | — “As noted earlier, the dDDH approach was shown to outperform ( 18 , 19 ) the ‘average nucleotide identity’ (ANI) approach, which is also frequently used in scientific studies as an alternative OGRI index ( 5 ). More recently, ‘ANI’ was found to yield results that are inconsistent across its various implementations due to a lack of standardization ( 38 ).” | content_tags.findings[4] |
| finding | — “The LPSN CSV (comma-separated values) file became available for download once LPSN was established at DSMZ ( 2 ). An Excel file was previously offered by the PNU (Prokaryotic Nomenclature Up-to-date) service of DSMZ, which was superseded by the new LPSN. The LPSN CSV file needed to be downwards compatible with that Excel file as far as possible, hence it was and is intended to contain only the names of genera, species and subspecies validly published under the ICNP.” | content_tags.findings[5] |
| finding | — “The storage of not validly published names in LPSN allows for conducting campaigns to increase the rate of validation. As of July 2021, almost 900 e-mails were sent to corresponding authors to inform them about names proposed by them that as yet have no claim to recognition under the ICNP ( 3 ), covering >1500 names.” | content_tags.findings[6] |
| quantity | about 1% of an estimated 0.8-1.6 million species — — “The global prokaryotic diversity is estimated to encompass 0.8–1.6 million species ( 1 ) of which currently only about 1% ( 2 ) have a name that is validly published under the International Code of Nomenclature of Prokaryotes (ICNP) ( 3 ). Even though these estimates are likely to fluctuate, microbial life still remains largely unknown and unconnected to the only system of nomenclature accepted by the majority of microbiologists, the ICNP.” | content_tags.quantities[0] |
| quantity | >26,000 names of any category and >21,000 validly published species names in LPSN; >15,000 type-strain genomes in TYGS — — “As of July 2021, the LPSN database (Figure 1 ) provides a large variety of expert-curated nomenclatural data, including >26k names of any category and >21k species names validly published under the ICNP ( 3 ). At the time of writing, the TYGS database (Figure 1 ) contains >15k type-strain genomes and was used by >3.7k different users worldwide for conducting >27k distinct analyses (Figure 2 ) involving 15M + genome comparisons.” | content_tags.quantities[1] |
| quantity | almost 900 emails covering more than 1,500 names — — “The storage of not validly published names in LPSN allows for conducting campaigns to increase the rate of validation. As of July 2021, almost 900 e-mails were sent to corresponding authors to inform them about names proposed by them that as yet have no claim to recognition under the ICNP ( 3 ), covering >1500 names.” | content_tags.quantities[2] |
| variable | standing in nomenclature — “For instance, many names with an effective publication outside IJSEM are validated at a later date anyway ( 3 ), hence their earlier consideration facilitates data analysis. Conversely, names supposed to be validly published may later on be recognized as not having met the necessary requirements ( 32 ). Moreover, not all taxonomist are aware of the need for validation” | content_tags.variables[0] |
| definition | validly published — “Classification in turn needs an internationally accepted system of nomenclature to unambiguously assign names to taxa ( 3 ). The cornerstone of the ICNP is the status of taxon names as being validly published; other names have no claim to recognition under this code” | content_tags.definitions[0] |
| definition | nomenclatural type — “The nomenclatural type is the entity with which a taxon name is permanently associated ( 3 ). In the cases of prokaryotic species and subspecies, the nomenclatural type is the type strain. Cultures of type strains thus firmly connect taxon names and genome sequences. Quality-checked ( 17 ) genome and proteome sequences of verified type strains are the starting point of TYGS analyses.” | content_tags.definitions[1] |
| concept | LPSN — not defined in this paper's own words; the List of Prokaryotic names with Standing in Nomenclature, the register of which names have status under the code — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | concepts[0] |
| concept | an expert-curated authoritative resource for prokaryotic nomenclature — not defined in this paper's own words; what LPSN is declared to be, in the abstract — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | concepts[1] |
| concept | TYGS — not defined in this paper's own words; the Type (Strain) Genome Server, which supplies the classification evidence — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | concepts[2] |
| concept | a high-throughput platform for accurate genome-based taxonomy — not defined in this paper's own words; what TYGS is declared to be — “The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de . The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de .” | concepts[3] |
| concept | The inclusion criterion — not defined in this paper's own words; the rule deciding what enters the register at all, as against what has standing — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | concepts[4] |
| concept | the presence of an effective publication — not defined in this paper's own words; the code-defined condition that criterion resolves to — “To improve the coverage, a web form for submission was added to LPSN that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterion is the presence of an effective publication as defined by the ICNP ( 3 ).” | concepts[5] |
| concept | nomenclature — not defined in this paper's own words; the rules for assigning and validating names — “Comments on taxonomic terminology were added to LPSN for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists ( 35 ).” | concepts[6] |
| concept | classification — not defined in this paper's own words; the placement of organisms into taxa, which the names then label — “Comments on taxonomic terminology were added to LPSN for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSN. The latter change is supposed to improve the understanding of the difference between nomenclature and classification, which may puzzle many microbiologists ( 35 ).” | concepts[7] |
| concept | emendations — not defined in this paper's own words; formal corrections to a validly published name's circumscription — “The number of validly published names per country and year reflects the well-known shift of taxonomic activity to East Asian nations ( 28 ). The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains ( 8–11 ). More importantly, the overall number of names that become validly published per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered.” | concepts[8] |
| concept | the availability of genome sequences of type strains — not defined in this paper's own words; the new evidence base that is driving those corrections — “The number of validly published names per country and year reflects the well-known shift of taxonomic activity to East Asian nations ( 28 ). The relative and absolute number of emendations also shows an increasing trend, caused by the availability of genome sequences of type strains ( 8–11 ). More importantly, the overall number of names that become validly published per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered.” | concepts[9] |
| a species boundary that depends on which program computed it | — “As noted earlier, the dDDH approach was shown to outperform ( 18 , 19 ) the ‘average nucleotide identity’ (ANI) approach, which is also frequently used in scientific studies as an alternative OGRI index ( 5 ). More recently, ‘ANI’ was found to yield results that are inconsistent across its various implementations due to a lack of standardization ( 38 ).” | content_tags.statistics[0] |
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4 nar Nucleic Acids Research Nucleic Acids Res Oxford University Press PMC8728197 8728197 8728197 34634793 10.1093/nar/gkab902 TYGSterm and LPSNterm: a database tandem for fast and reliable genome-based classificationterm and nomenclatureterm of prokaryotes Meier-KolthoffpersName Jan P 1 ✉ CarbassepersName Joaquim Sardà 2 Peinado-OlartepersName Rosa L 3 GökerpersName Markus 4 1 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany 2 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany 3 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany 4 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany ✉ To whom correspondence should be addressed. Tel: +49 531 2616 424; Email: jan.meier-kolthoffpersName@dsmz.de 11 10 2021 50 D1 D801 D801–D807 5 1 2022 © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/ ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Microbial systematics is heavily influenced by genome-based methods and challenged by an ever increasing number of taxon names and associated sequences in public data repositories. This poses a challenge for database systems, particularly since it is obviously advantageous if such data are based on a globally recognized approach to manage names, such as the International Code of Nomenclatureterm of Prokaryotes. The amount of data can only be handled if accurate and reliable high-throughput platforms are available that are able to both comply with this demand and to keep track of all changes in an efficient and flexible way. The List of Prokaryotic names with Standing in Nomenclatureterm·var (LPSNterm) is an expert-curated authoritative resource for prokaryotic nomenclatureterm and is available at https://lpsnterm.dsmz.de . The Type (Strain) Genome Server (TYGSterm) is a high-throughput platform for accurate genome-based taxonomyterm and is available at https://tygsterm.dsmz.de . We here present important updates of these two previously introduced, heavily interconnected platforms for taxonomic nomenclatureterm and classificationterm, including new high-level facilities providing access to bioinformatic algorithms, a considerable expansion of the database content, and new ways to easily access the data.
status released display-pdf yes is-olf no is-manuscript no is-preprint no is-journal-matter no is-scanned no is-retracted no Accepted 2021 Sep 22; Revised 2021 Sep 18; Received 2021 Aug 20; Collection date 2022 Jan 7.
INTRODUCTION The global prokaryotic diversity is estimated to encompass 0.8–1.6 million species ( 1 ) of which currently only about 1% ( 2 ) have a name that is validly publishedterm·def under the International Code of Nomenclatureterm of Prokaryotes (ICNP) ( 3 ). Even though these estimates are likely to fluctuate, microbial life still remains largely unknown and unconnected to the only system of nomenclatureterm accepted by the majority of microbiologists, the ICNP. But a continuous and systematic understanding of this large genetic and enzymatic reservoir is necessary to further elucidate the biological mechanisms affecting important topics such as the global geochemical cycles, public health and biotechnology.
For more than a century, microbial taxonomy is dedicated to the characterization, classificationterm and nomenclatureterm of microbial life. The data acquired through characterization ( 4 ), which presently significantly relies on genome-based approaches ( 5 ), are used to establish the classificationterm of microbes. Classificationterm in turn needs an internationally accepted system of nomenclatureterm to unambiguously assign names to taxa ( 3 ). The cornerstone of the ICNP is the status of taxon names as being validly publishedterm·def; other names have no claim to recognition under this code ( 3 ).
Due to the fast-paced changes in prokaryotic nomenclatureterm and the continued influx of newly proposed names, expert-curated and at least partially automated database systems are needed to keep track of these processes. One of the most influential and authoritative resources in this regard is the List of Prokaryotic names with Standing in Nomenclatureterm·var (LPSNterm), which was first introduced more than two decades ago as a manually curated database ( 6 ) and maintained over the years ( 7 ). Since 2020 LPSNterm is located at https://lpsnterm.dsmz.de at the Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures ( 2 ). The move from the previous platform to the DSMZ was accompanied by the establishment of a database infrastructure, of automated data import routines and of a database-driven web interface ( 2 ). Pages for individual taxon names were equipped with information on etymology, type-strain deposits, 16S rRNA gene sequences in FASTA format, INSDC 16S rRNA gene accession numbers, taxonomic and nomenclatural status and many notes ( 2 ).
Taxonomic classificationterm is currently strongly influenced by genome-scale data and related methods ( 8–15 ). The ever-increasing growth of genome data ( 16 ) demands technical solutions for efficient, reproducible and standardized taxonomic analyses. Comparisons with the genome sequences of type strains are mandatory when classifying novel strains ( 4 ). Hence, a reliable mapping between type strains, genome sequences and taxon names has to be established.
To address these requirements, the Type (Strain) Genome Server (TYGSterm) was previously introduced as a large database of curated type-strain genomes combined with selected metadata and facilities for conducting truly genome-based taxonomic analyses in a high-throughput setup ( 17 ). Queries to the TYGSterm database, located at https://tygsterm.dsmz.de , are made with one to several uploaded genome sequences. The results include genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries for both user-provided sequences and automatically determined closest type genome sequences. Metadata for these are provided to facilitate the taxonomic exploration of the outcome, including nomenclatureterm, synonymy and associated taxonomic literature ( 17 ).
In this study we present the current state of the heavily used TYGSterm and LPSNterm databases, including updates and improvements which were added since the last publications ( 2 , 17 ). The establishment of LPSNterm at the DSMZ allows for strongly interconnecting the two databases ( 2 , 17 ) to further increase their usability, a topic that is also addressed below.
TYGSterm AND LPSNterm IN 2021 The databases As of July 2021, the LPSNterm database (Figure 1 ) provides a large variety of expert-curated nomenclatural data, including >26k names of any category and >21k species names validly publishedterm·def under the ICNP ( 3 ). At the time of writing, the TYGSterm database (Figure 1 ) contains >15k type-strain genomes and was used by >3.7k different users worldwide for conducting >27k distinct analyses (Figure 2 ) involving 15M + genome comparisons.
Figure 1. Left, dependencies of the TYGSterm and LPSNterm platforms and relationships to the legacy GGDC platform and to the DSMZ gene phylogeny server. Right, description of the most relevant (partially shared) contents of the TYGSterm and LPSNterm databases.
Figure 2. ( A ) statistics on the cumulative, non-linear growth of TYGSterm type-strain genome sequences per month. ( B ) non-cumulative number of TYGSterm job submissions per month since its establishment in 2019. Job submissions are grouped according to the top-level domain of the e-mail address included in each job submission. The top-level domain was matched to the country of origin wherever possible.
The content of the TYGSterm and LPSNterm databases was introduced in previous publications ( 2 , 17 ) and is here only briefly recapitulated (Figure 1 ). The depicted database content reflects the focus of the two databases, which accordingly share many kinds of data.
The authority of a taxon name reflects its original publication and thus links nomenclatureterm and scientific literature. Synonymy of names is another key component of taxonomic information to which LPSNterm allows comprehensive access. The nomenclatural typeterm·def is the entity with which a taxon name is permanently associated ( 3 ). In the cases of prokaryotic species and subspecies, the nomenclatural typeterm·def is the type strain. Cultures of type strains thus firmly connect taxon names and genome sequences.
Quality-checked ( 17 ) genome and proteome sequences of verified type strains are the starting point of TYGSterm analyses. Accurate intergenomic GBDP (Genome BLAST Distance Phylogeny) ( 18 ) distances and digital DNA:DNA hybridization (dDDH) values are calculated and stored in the TYGSterm database. Most of them are inferred well in advance of user requests to considerably accelerate the processing of these requests. The distances are used for phylogenetic inference and also form the basis for the dDDH method, one of the most widely used overall genome relatedness indices (OGRI) for in silico species delineation ( 18 , 19 ). Genome-scale and proteome-scale phylogenies, 16S rRNA gene trees and type-based clusterings at the species and subspecies levels are the data entries that represent the final step of the comprehensive genome-based taxonomic analyses available in the TYGSterm.
Analyses on the DSMZ single-gene phylogeny server (Figure 1 ) can be triggered by the TYGSterm as well as via LPSNterm. The server calculates pairwise similarities ( 20 ), multiple sequence alignments ( 21 ) and phylogenetic trees under the maximum-likelihood ( 22 ) and maximum parsimony ( 23 ) criteria from single-gene data sets as introduced previously ( 24 ). The DSMZ single-gene phylogeny server is also contacted by the TYGSterm on user request to infer single-gene phylogenies from a comprehensive set of 16S rRNA gene sequences that may include closely related but not yet genome-sequenced type strains.
New kinds of TYGSterm data and new TYGSterm facilities The initial release of the TYGSterm determined a set of type strains most closely related to a respective user sequence by using only 16S rRNA gene sequence distances ( 17 ). As not all user sequences contain an extractable 16S rRNA gene, the most closely related type-strain genomes are now also determined using intergenomic Mash distances ( 25 ), a fast initial approximation of intergenomic relatedness. The set of type-strain genomes having the smallest MASH distances among the entire TYGSterm database is combined with those having the smallest 16S rRNA gene distances. This approach also ensures that the most closely related type strains are chosen if the user genome sequence belongs to a group of organisms for which the 16S rRNA gene sequence does not properly resolve the phylogenetic relationships. However, the usage of 16S rRNA gene sequences remains highly relevant for detecting closely related type strains that have not yet been genome-sequenced.
Mash distances are now also used to split job submissions that contain query genomes that are only remotely related. If otherwise such an analysis would result in the selection of distinct sets of closest type strain genomes and trigger taxonomically useless calculations. Subdivided submissions, if any, are accordingly indicated on the job confirmation page. This feature further improves the genome-based taxonomic analyses by determining efficient type strain selection in a variety of data situations.
For very diverse datasets of strains, the average branch support even of a genome-scale phylogeny and even for a strain selection restricted as described above, might be too low when based on nucleotide sequences. We thus added the option to conduct an additional GBDP analysis using amino-acid sequences under the recommended settings ( 26 ), which automatically becomes available on the TYGSterm result page in case of insufficient support.
It should be noted that the Genome-to-Genome Distance Calculator (GGDC) preceded the TYGSterm and is still one of the most popular online tools for the calculation of dDDH values for in silico (sub-)species delineation ( 18 , 19 ). Although the current GGDC version, 3.0, also incorporates several new features and optimizations from the previous years, the database-driven TYGSterm offers many more facilities, overall. Although GGDC and TYGSterm are equally reliable regarding species delineation, GGDC users are strongly advised to switch to the TYGSterm. In rare cases, the GGDC 3.0 can still be useful for specialized analyses but since a larger file upload cap can usually be requested via the TYGSterm feedback form, the TYGSterm is certainly the more comprehensive platform since its initial release.
The series of publicly available pre-calculated TYGSterm result sets that can be accessed from the ‘Examples’ menu item on the TYGSterm main page demonstrates the new facilities listed above. All TYGSterm results are now also available within a compact, publication-ready PDF report.
Each TYGSterm result usually includes links to external sites such as Bac Dive ( 27 ) and GenBank to provide further information on each used type strain. As a result of the move of LPSNterm to DSMZ, the preferred names of each type strain listed on the respective TYGSterm result page now link to the specific LPSNterm page of that species. Links to the Bac Dive database now point to the specific strain page whenever possible.
Expansion of the scope The growth of the number of genome sequences in the TYGSterm database is shown in Figure 2 while the growth of the number of taxon names in the LPSNterm database is shown in Figure 3 . As for names validly publishedterm·def under the ICNP ( 3 ), the increase of names in LPSNterm and accordingly of type-strain genome sequences in the TYGSterm simply mirrors the increase of the rate of valid published names per year. The number of validly publishedterm·def names per country and year reflects the well-known shift of taxonomic activity to East Asian nations ( 28 ). The relative and absolute number of emendationsterm also shows an increasing trend, caused by the availability of genome sequences of type strainsterm ( 8–11 ). More importantly, the overall number of names that become validly publishedterm·def per year shows an ever-increasing trend. One of the challenges of nomenclature-related databases is apparently the sheer increase of the volume of the data to be considered.
Figure 3. ( A ) Number of new prokaryotic names included in LPSNterm grouped by year and taxonomic category and nomenclatural status (shades of blue, validly publishedterm·def under the ICNP; shades of red, not validly publishedterm·def). Left, all names; right, names currently regarded as correct name ( 3 ) in LPSNterm. ( B ) Number of new prokaryotic names validly publishedterm·def under the ICNP and number of emendationsterm of such names included in LPSNterm, grouped by year and country of origin of the taxonomic study. Left, number of validly publishedterm·def names; right, number of emendationsterm of such names. The country of origin of each study represents the country of origin of the author indicated as corresponding author including an e-mail address.
A major change regarding the selection of taxon names for inclusion in LPSNterm is the addition of names that are not validly publishedterm·def ( Candidatus names and other names), as well as of names of Cyanobacteria validly publishedterm·def under the ICN (International Code of Nomenclatureterm for algae, fungi and plants), in anticipation of the recent changes to the ICNP ( 29 ). Whereas they do not have standing in nomenclatureterm·var, the addition of names to LPSNterm that have an effective publication but are not validly publishedterm·def had started at an early stage ( 6 ), although the names were not linked to the hierarchical classificationterm.
An improved integration of not validly publishedterm·def names in LPSNterm reflects the inclusion of additional categories regulated under the rules of the ICNP ( 30 ) and the publication of lists of Candidatus names in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) ( 31 ). This integration also has other advantages. For instance, many names with an effective publication outside IJSEM are validated at a later date anyway ( 3 ), hence their earlier consideration facilitates data analysis. Conversely, names supposed to be validly publishedterm·def may later on be recognized as not having met the necessary requirements ( 32 ). Moreover, not all taxonomist are aware of the need for validation ( 33 ). The storage of not validly publishedterm·def names in LPSNterm allows for conducting campaigns to increase the rate of validation. As of July 2021, almost 900 e-mails were sent to corresponding authors to inform them about names proposed by them that as yet have no claim to recognition under the ICNP ( 3 ), covering >1500 names.
An even more fundamental advantage of including not validly publishedterm·def names is that it adds clarity. If a name is shown on LPSNterm and explicitly marked as not being validly publishedterm·def, this leaves no doubt with regard to its status, as opposed to just not showing the name at all. Because they are not centrally collected in a journal such as IJSEM, the coverage of names by LPSNterm that have an effective publication but are not validly publishedterm·def under the code cannot be expected to be complete. LPSNterm attempts to focus on names that are in use, i.e. are found in the literature or in other databases. To improve the coverage, a web form for submission was added to LPSNterm that allows for anonymous suggestions of taxon names. Synonymy relationships between taxon names and assignments of child taxa to parent taxa (i.e, genera to families, families to orders etc.) can also be suggested. The inclusion criterionterm is the presence of an effective publicationterm as defined by the ICNP ( 3 ).
New kinds of information on LPSNterm Apart from the constant addition of taxon names and associated information and the regular update of information provided by third parties, such as the risk-group assignments for species and subspecies ( 34 ), a variety of LPSNterm facilities and pages were established since the relaunch of the entire site at DSMZ ( 2 ). All of these pages are accessible through the LPSNterm navigation page.
Greatly expanded and regularly updated pages on Frequently Asked Questions, nomenclatureterm, etymology, and taxonomy and systematics provide access to the relevant literature. A variety of pages provide more specific etymological information on bacterial names. The LPSNterm glossary now contains more entries and more cross references; key terms related to the rules of nomenclatureterm ( 3 ) have been augmented to explain critical issues. Special pages on Requests for an Opinion and Judicial Opinions ( 32 ) are also intended to increase nomenclatural literacy.
The LPSNterm page on culture collections, which is augmented in parallel to the registering of type-strain deposits in LPSNterm, lists hundreds of biological resource centres. In addition to links and postal addresses the page now also contains country codes and WDCM (World Data Centre for Microorganisms) numbers to further ease the access to information on collections.
Comments on taxonomic terminology were added to LPSNterm for single taxon names where appropriate, as well as comments about the conditions under which a name would be regarded as the correct name if it is not currently so regarded by LPSNterm. The latter change is supposed to improve the understanding of the difference between nomenclatureterm and classificationterm, which may puzzle many microbiologists ( 35 ). LPSNterm now also includes a scoring based on genomic distances calculated by the TYGSterm ( 26 ). These comments highlight groups that may need a taxonomic revision.
Improved access to the data The LPSNterm CSV (comma-separated values) file became available for download once LPSNterm was established at DSMZ ( 2 ). An Excel file was previously offered by the PNU (Prokaryotic Nomenclatureterm Up-to-date) service of DSMZ, which was superseded by the new LPSNterm. The LPSNterm CSV file needed to be downwards compatible with that Excel file as far as possible, hence it was and is intended to contain only the names of genera, species and subspecies validly publishedterm·def under the ICNP.
LPSNterm was augmented with an API (Application Programming Interface) to provide greater flexibility. The LPSNterm API is designed to be expandable in the future without creating backwards incompatibility. The LPSNterm API has a REST (Representational State Transfer) interface that allows for two kinds of searches and yields JSON (JavaScript Object Notation). Code examples and clients in two programming languages are provided inline.
Users are advised to register for the LPSNterm mailing list because forthcoming changes to CSV download file or API are announced on this list in order to avoid severe incompatibilities with previous formats. The LPSNterm record numbers as used in the CSV files and in the API are also visible on each page to ease comparisons.
The TYGSterm platform was similarly augmented with a REST API to allow users to download tabular results in the open interchange format JSON, phylogenetic results in either PhyloXML ( 36 ) or Newick format and scientific citations in BibTex format. Details on the API are available online and users are asked to follow the instructions on the TYGSterm API page on how and when to use the API.
CONCLUSION This update of the TYGSterm and LPSNterm platforms again underlines the need for an expert-curated nomenclatural database and for a database of verified type strain genomes, their metadata and subsequent facilities for taxonomic analysis, as well as an improved access to the data. Even though other platforms such as EzBioCloud ( 37 ) may provide access to a broader selection of ‘reference genomes’, including non-type strains, these are to the best of our knowledge frequently confused or misinterpreted as type strains and may thus lead to taxonomic misinterpretations. TYGSterm and LPSNterm, a synergistic pair of database-driven platforms, not only cover the core fields of (genome-based) taxonomy but also provide guidance especially for non-experts in a field in which one may have difficulties in choosing between a plethora of tools and data entries.
The calculation and storage of intergenomic distances and dDDH values provides for a high level of standardization within the TYGSterm database, with dDDH being one of the most widely used overall genome relatedness indices (OGRI) for in silico species delineation ( 18 , 19 ). As noted earlier, the dDDH approach was shown to outperform ( 18 , 19 ) the ‘average nucleotide identity’ (ANI) approach, which is also frequently used in scientific studies as an alternative OGRI index ( 5 ). More recently, ‘ANI’ was found to yield results that are inconsistent across its various implementations due to a lack of standardization ( 38 ).
While a recent attempt to modify the ICNP to allow for using genome sequences as nomenclatural typeterm·def was unsuccessful ( 39 ), alternative solutions to the perceived underlying problem are currently actively debated ( 40 ). Independent of the outcome of these discussions, the expansion of the LPSNterm infrastructure demonstrates that it is already capable of dealing with taxon names that have a status under distinct codes of nomenclatureterm. As expected for these two highly interconnected platforms, the broadening of the scope of names included in LPSNterm automatically also broadens the scope of genome sequences found in the TYGSterm.
DATA AVAILABILITY The provided TYGSterm data can be freely downloaded in various formats (e.g. CSV, XLS, JSON, PDF, SVG, PNG, PhyloXML, Newick and BibTeX) without restrictions, except that the origin of the data has to be properly cited ( 17 ) when used in other works. Information obtained from LPSNterm should also be properly cited ( 2 ). Registration is necessary to access the LPSNterm download files and the LPSNterm API but registration is free and easy to accomplish.
ACKNOWLEDGEMENTS The work of our colleagues Lorenz C. Reimer and Julia Koblitz on the Bac Dive API, API clients and mailing list also helped establishing the according facilities for LPSNterm, which is gratefully acknowledged. We cordially thank the DSMZ student assistants Patrick Bergmann, Adelina Gllareva and Sanja Haake for their help in maintaining the LPSNterm database. The LPSNterm acknowledgements page lists the users who sent us LPSN-related information, feature requests or error reports, which is gratefully acknowledged. We would also like to thank the two anonymous reviewers for their helpful comments.
Author contributions : J.P.M.K. and M.G. conceived, designed and implemented the TYGSterm. J.P.M.K. also designed and implemented the novel TYGSterm features. M.G. conceived LPSNterm and its new features, implemented the database back-end, and curated parts of the LPSNterm database. J.S.C. implemented the front-end of the LPSNterm API and the associated facilities. R.P.O. curated parts of the LPSNterm database. J.P.M.K. drafted the manuscript. J.P.M.K. and M.G. finalized the manuscript. All authors have read and approved the final version of the manuscript.
Contributor Information Jan P Meier-KolthoffpersName, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Joaquim Sardà CarbassepersName, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Rosa L Peinado-OlartepersName, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Markus GökerpersName, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
FUNDING Deutsche Forschungsgemeinschaft [Sonderforschungsbereich TRR 51 to J.P.M.K.]. Funding for open access charge: Deutsche Forschungsgemeinschaft [Sonderforschungsbereich TRR 51 to J.P.M.K.].
Conflict of interest statement . None declared.