Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214

Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214 | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214 Mark J Pallen This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4235597/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Here, an established approach to the generation of well-formed arbitrary Latinate names at a scale has been adopted and adapted to name tens of thousands of new, but unnamed taxa within GTDB Release r214.1. New Latinate Candidatus names have been created and assigned to two new archaeal and twelve new bacterial phyla; six new archaeal and 48 new bacterial classes; 13 new archaeal and 158 new bacterial orders; 60 new archaeal and 597 new bacterial families; 271 new archaeal and 3,869 new bacterial genera; and 1,097 new archaeal and 18,126 new bacterial species. New Candidatus names for bacterial phyla include Ca. Afuciota, Ca. Axiviota, Ca. Bobupiota, C a. Fitepiota, Ca. Hubebiota, Ca. Ibociota, Ca. Inuciota, Ca. Luxamiota, Ca. Megaciota, Ca. Nasexiota, Ca . Oviciota , Ca. Ucifiota, and Ca . Uvuciota, while new names for archaeal phyla include Ca. Acigarchota and Ca. Omefarchota. These efforts show that the creation of arbitrary names for prokaryotic taxa remains sustainable, despite the relentless progress of discovery. General Microbiology Bacterial nomenclature archaeal nomenclature genome taxonomy shotgun metagenomics Candidatus names Introduction In a recent publication, my collaborators and I described how bacterial nomenclature cannot keep up with the need for new names for the many thousands of prokaryotic taxa discovered each year [ 1 ]. Instead, users of the widely used comprehensive sequence-based Genome Taxonomy Database (GTDB) [ 2 ] have been forced to use confusing and hard-to-remember alphanumeric placeholder labels. To address this problem, over 65,000 Candidatus names were created for unnamed prokaryotic taxa in GTDB release r207, which dates from April 2022. However, microbiology remains a victim of its own success, in that GTDB release r214.1, which dates from September 2023, contains an additional > 17,000 species with placeholder labels, plus many additional high-level placeholder taxa, including fifteen new unnamed phyla [ https://data.gtdb.ecogenomic.org/releases/release214/214.1/ ]. To provide new well-formed Latinate names for these newly discovered taxa, previously used approaches have been adapted to provide the microbiology community with a fresh set of new names at a scale sufficient to cope with the demand. Methods The workflow from the previous publication has been updated. New scripts and files are available from Zenodo The new workflow can be run using two shell scripts r214_renamer_1.sh and r214_renamer_2.sh once the required scripts and programmes are in place. GDTB taxonomy and metadata files were downloaded from the r214 release archive. A python script replace_names.py was used—with a name replacement table (Table S1) created from outputs from the previous paper—to replace ~ 77,000 placeholders in the taxonomy files with the arbitrary names or epithets published in the previous paper. The Python script anomaly_finder.py was then used to find new anomalous taxa, where a placeholder string for a higher-level taxon has not been derived from a placeholder associated with a type genus or where placeholders have been used when a Latinate name is available for a genus within the taxon. Anomalous phylogenies were analysed in Excel and used to create anomaly replacement tables for Archaea and Bacteria (Table S2), which were used with the replace_names.py script to replace anomalous placeholders with appropriate alternatives, which were marked with an exclamation mark. As in the previous publication [ 1 ], a set of > 4 million excluded terms was assembled from Latin stems compiled by Whitaker, a fresh download of headwords from the English Wiktionary and a fresh download of names already in use in taxonomy, using the script input_terms_clean.py to extract the terms from the input files. The Python script name_creator_r214.py was used to create a new set of arbitrary genus and species names that excluded these restricted terms and arbitrary names used in the previous publication. In the previous work [ 1 ], the stems for arbitrary genus names were required to be two character changes apart from all other stems. However, when reapplied to new archaeal genera, this approach failed to generate enough archaeal genus names. Therefore, this requirement was relaxed to create a comprehensive set of stems with the form “consonant-vowel-consonant-vowel-consonant”—to which were added the endings specified in the previous paper, restricting use of the endings -osa and -ana to species names. As names are assigned randomly across the GTDB phylogeny, the potential for confusion stemming from closely related taxa having similar names remains very low. The script placeholder_extractor.py was used to extract remaining placeholders from the edited GDTB r214 taxonomy files and to randomly assign arbitrary names to them. This process included addition of appropriate suffixes for high-level taxa and tagging of new names with an exclamation mark so that they could identified by later scripts. This resulted in the creation of name replacement tables for Archaea and Bacteria (Table S3). The script was run repeatedly for each domain until it generated sufficiently distinctive and agreeable new phylum names, after which the associated replacement tables were selected for downstream use. The script replace_names.py was then used to replace r214-specific placeholders in the taxonomy files for Archaea and Bacteria with new arbitrary names. The resulting renamed placeholder-free taxonomies were then pasted into the r214 metadata files (after sorting original and modified files by accession number) to create renamed placeholder-free metadata files for Archaea and Bacteria. The script protologue.maker.py was used to generate protologues for newly named taxa after comparing the original and renamed metadata files for Archaea and Bacteria. Results Ten new archaeal anomalous placeholders and 177 new bacterial anomalous placeholders from the R214 taxonomies were replaced with consistently used placeholders or well-formed Latin names built from genus designations after scrutiny of anomalous phylogenies (Table S2). In most cases, the anomalies were the result of reclassification of taxa, but in some cases they reflected typographical errors, e.g. where a genus and family are recorded as g__G023898745 and f__G023898745, but the associated order is recorded as o__G02398745. For the phylum we called Efretiota in our previous paper (GTDB placeholder p__FCPU426), during the transition from r207 to r214k, the type genus Efretia (GTDB placeholder g__ JAAXVQ01) was moved into a new phylum with the new GTDB placeholder p__JAAXVQ01. The Candidatus phylum name Efretiota was therefore transferred to the new phylum, while the original phylum was renamed after one of the three remaining genera in the phylum, Luxamia (GTDB placeholder g__PALSA-1180), which had already been used to create the names for a family, order and class. Once anomalous names had been corrected, 1,720 new alphanumeric placeholder names or epithets were retrieved from the archaeal taxonomy file and 26,679 from the bacterial taxonomy file and used to build name-replacement tables (Table S3). These new names incorporate the choices made by GTDB for type genomes for species, replacing alphanumeric designations wherever they occur in the taxonomic hierarchy. The name-replacement tables were used to replace placeholders in the GTDB taxonomy and metadata files, assigning new well-formed arbitrary Latinate Candidatus names to two new archaeal and twelve new bacterial phyla; six new archaeal and 48 new bacterial classes; 13 new archaeal and 158 new bacterial orders; 60 new archaeal and 597 new bacterial families; 271 new archaeal and 3,869 new bacterial genera; and 1,097 new archaeal and 18,126 new bacterial species (Table S3). As before, renamed GTDB taxonomy files (Table S4) were created along with protologues for all new Candidatus taxa. However, the resulting sets of taxonomic descriptions was too large to be presented in the body of this manuscript and are instead available as RTF files on Zenodo. Given that new phylum names are likely to see the heaviest use, protologues for newly named phyla and associated type genera and species are presented in Table 1. Discussion The astonishing progress of prokaryotic taxonomic discovery continues at a relentless pace, as evidenced by the fact that the latest release of GTDB contains nearly 30% more species than the previous release [ https://gtdb.ecogenomic.org/stats/r214 ]. This highlights the continuing need for creating and assigning new taxonomic names at scale. Recent attempts to create procedures for publishing names-with-standing for uncultured prokaryotes [ 3 , 4 ] ignore the far more pressing issue of how to create enough well-formed names to cope with the deluge of discovery. Failure to meet this challenge effectively means abandoning Linnaean nomenclature for around 80% of known prokaryotic taxa. It is worth contrasting the 17,000 or more new species described in the latest GTDB release with the relatively slow process of naming new species under the ICNP, when 2,364 validly published and 597 Candidatus species names were added to LPSN in 2023 [ https://lpsn.dsmz.de/advanced_search ]. More worrying still, > 300 taxonomic names have been validly published exclusively under the SeqCode, [ https://disc-genomics.uibk.ac.at/seqcode/names?status=SeqCode ], even though this initiative was set up with the goal of naming uncultured prokaryotes. In 2021, with colleagues, I described an approach for automated creation of descriptive names en masse [ 5 ]. When applied to taxa from the chicken gut [ 6 ], this led to the publication of hundreds of new Candidatus names, which have been propagated into online databases including LPSN, NCBI and GTDB. However, it soon became clear that this approach was not suitable for clearing the backlog of the tens of thousands of new names required, as this would entail exhaustive reconstruction and comparisons of phenotypes and genome metadata to create descriptive names that are accurate and precise. But even then, the resulting name space is unlikely to contain enough descriptive name that are short enough to be usable. As a result, we published over 65,000 arbitrary Candidatus names to fill the gap [ 1 ]. Here, I show that this approach remains sustainable, despite the relentless progress of discovery. Our arbitrary Candidatus names have begun to be cited in research publications [ 7 – 12 ], but, curiously, the names cannot be validly published under the SeqCode, as the SeqCode rules explicitly exclude use of arbitrary components in the creation of names, despite over a century and a half of precedents for such practice [ 13 ] and recent adoption of arbitrary artificial suffixes in the quest to replace descriptive names for prokaryotic phyla and kingdoms with those built from type genera [14,15]. If the SeqCode community prefers not to use our arbitrary names, they should at least rise to the challenge of creating tens of thousands of new names that do meet their own arbitrary rules. The new set of arbitrary names I have published here, along with the previous set, are now available for use by the scientific community. They provide distinctive and user-friendly alternatives to unwieldy alphanumeric placeholders. However, given the lack of standing associated with Candidatus names, any of them could be replaced by alternative names, should the need arise. The names are likely to be used in earnest only once studies begin on the taxa they are associated with, which will depend on how many such taxa attract research attention. At the very least, the new arbitrary phylum names are likely to provide handy signposts to new functional and phylogenetic diversity. The challenge for the future is to ensure that each new release of GTDB is met with a new set of arbitrary names in a timely fashion, so that the legacy of Linnaeus can be kept alive at the exciting frontier of prokaryotic discovery. Declarations Author statements Authors and contributors Conceptualization, MJP; Data curation, Methodology: MJP; Writing: MJP. Conflicts of interest The author declares that there are no conflicts of interest. Funding information MJP is supported by the Medical Research Council CLIMB-BIG-DATA grant MR/T030062/1. References Pallen MJ, Rodriguez-R LM, Alikhan NF. Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database. Int J Syst Evol Microbiol . 2022;72(9):10.1099/ijsem.0.005482. doi:10.1099/ijsem.0.005482 Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 doi: 10.1093/nar/gkab776 Hedlund BP, Chuvochina M, Hugenholtz P, et al. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat Microbiol . 2022;7(10):1702-1708. doi:10.1038/s41564-022-01214-9 Arahal D, Bisgaard M, Christensen H, et al. The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol . 2024;74(1):10.1099/ijsem.0.006188. doi:10.1099/ijsem.0.006188 Pallen MJ, Telatin A, Oren A. The Next Million Names for Archaea and Bacteria. Trends Microbiol . 2021;29(4):289-298. doi:10.1016/j.tim.2020.10.009 Gilroy R, Ravi A, Getino M, et al. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ . 2021;9:e10941. Published 2021 Apr 6. doi:10.7717/peerj.10941 Kaminsky RA, Reid PM, Altermann E, et al. Rumen Lachnospiraceae isolate NK3A20 exhibits metabolic flexibility in response to substrate and coculture with a methanogen. Appl Environ Microbiol . 2023;89(10):e0063423. doi:10.1128/aem.00634-23 Venkatachalam S, Jabir T, Vipindas PV, Krishnan KP. Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems. Appl Microbiol Biotechnol . 2024;108(1):128. doi:10.1007/s00253-023-12991-6 Vila-Costa M, Lundin D, Fernández-Pinos MC, Iriarte J, Irigoien X, Piña B, Dachs J. Responses to organic pollutants in the tropical Pacific and subtropical Atlantic Oceans by pelagic marine bacteria. Frontiers in Environmental Science. 2023;11:1110169. Bowman JP. Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al . 2000 into Telluria Bowman et al . 1993, Mokoshia gen. nov. and Zemynaea gen. nov. Int J Syst Evol Microbiol . 2023;73(8):10.1099/ijsem.0.005991. doi:10.1099/ijsem.0.005991 Bottom of Form Gilroy R, Adam ME, Kumar B, Pallen MJ. An initial genomic blueprint of the healthy human oesophageal microbiome. Access Microbiol . 2023;5(6):acmi000558.v3. Published 2023 Jun 26. doi:10.1099/acmi.0.000558.v3 de Candolle A. Lois de la Nomenclature Botanique . Masson; 1867 Whitman WB, Oren A, Chuvochina M, et al. Proposal of the suffix -ota to denote phyla. Addendum to 'Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes'. Int J Syst Evol Microbiol . 2018;68(3):967-969. doi:10.1099/ijsem.0.002593 Göker M, Oren A. Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol . 2023;73(2):10.1099/ijsem.0.005650. doi:10.1099/ijsem.0.005650 Table Table 1 is available in the Supplementary Files section Supplementary Files Supplementary Files are not available with this version Additional Declarations The authors declare no competing interests. Supplementary Files Table1.docx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4235597","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":288764888,"identity":"ffa019f5-9685-4b82-86d0-c9feab7fdc1c","order_by":0,"name":"Mark J Pallen","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABFklEQVRIiWNgGAWjYHACZhAhw8fAwPgAyGBsgIlLENDCwwZkGJCshU2CKC267WcfGzDusONhY+89VvG2zU52e/vpBIYfNQyJMxuwazE7k26cwHgmmYeN51zazbltycZzzuRuYOw5xpA4G4ctZgfSmA8wtjHzsEnkmN3mbWNOnMGQu4GBt4EhcR4uLeefgbTU87DJvzEr5m2rT5zB/3YD4198Wm6kMScwth0G2sJjxszbdjhxhkTuBmaQLTgdduMZs0HimeNAv+QYS845d9x4hsTbDYdljkkY4/T++TRmiY87quX42c8YfnhTVi07gz9348M3NTayMw7gsAYEEmHm8UDpA3gjEgTg0ceDT9UoGAWjYBSMWAAALwZVJMomFa0AAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0003-1807-3657","institution":"Quadram Institute Bioscience","correspondingAuthor":true,"prefix":"","firstName":"Mark","middleName":"J","lastName":"Pallen","suffix":""}],"badges":[],"createdAt":"2024-04-08 10:18:16","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-4235597/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4235597/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":54383543,"identity":"319e63a2-d22d-4166-93b7-e7f23543e64e","added_by":"auto","created_at":"2024-04-09 16:34:07","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":142574,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4235597/v1/01974c56-d52a-494b-bd93-897840ca7ba4.pdf"},{"id":54383315,"identity":"51a304f9-a59c-4257-a72b-370769b6ceb0","added_by":"auto","created_at":"2024-04-09 16:26:07","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":29073,"visible":true,"origin":"","legend":"","description":"","filename":"Table1.docx","url":"https://assets-eu.researchsquare.com/files/rs-4235597/v1/b88458c9b1948bfc7d429e2b.docx"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eUpdating the unnamed: over 20,000 new \u003cem\u003eCandidatus\u003c/em\u003e names for unnamed taxa in GTDB release r214\u003c/p\u003e","fulltext":[{"header":"Introduction","content":"\u003cp\u003eIn a recent publication, my collaborators and I described how bacterial nomenclature cannot keep up with the need for new names for the many thousands of prokaryotic taxa discovered each year [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. Instead, users of the widely used comprehensive sequence-based Genome Taxonomy Database (GTDB) [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e] have been forced to use confusing and hard-to-remember alphanumeric placeholder labels. To address this problem, over 65,000 \u003cem\u003eCandidatus\u003c/em\u003e names were created for unnamed prokaryotic taxa in GTDB release r207, which dates from April 2022. However, microbiology remains a victim of its own success, in that GTDB release r214.1, which dates from September 2023, contains an additional\u0026thinsp;\u0026gt;\u0026thinsp;17,000 species with placeholder labels, plus many additional high-level placeholder taxa, including fifteen new unnamed phyla [\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://data.gtdb.ecogenomic.org/releases/release214/214.1/\u003c/span\u003e\u003cspan address=\"https://data.gtdb.ecogenomic.org/releases/release214/214.1/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e]. To provide new well-formed Latinate names for these newly discovered taxa, previously used approaches have been adapted to provide the microbiology community with a fresh set of new names at a scale sufficient to cope with the demand.\u003c/p\u003e"},{"header":"Methods","content":"\u003cp\u003eThe workflow from the previous publication has been updated. New scripts and files are available from Zenodo The new workflow can be run using two shell scripts \u003cem\u003er214_renamer_1.sh\u003c/em\u003e and \u003cem\u003er214_renamer_2.sh\u003c/em\u003e once the required scripts and programmes are in place.\u003c/p\u003e \u003cp\u003eGDTB taxonomy and metadata files were downloaded from the r214 release archive. A python script \u003cem\u003ereplace_names.py\u003c/em\u003e was used\u0026mdash;with a name replacement table (Table S1) created from outputs from the previous paper\u0026mdash;to replace\u0026thinsp;~\u0026thinsp;77,000 placeholders in the taxonomy files with the arbitrary names or epithets published in the previous paper. The Python script \u003cem\u003eanomaly_finder.py\u003c/em\u003e was then used to find new anomalous taxa, where a placeholder string for a higher-level taxon has not been derived from a placeholder associated with a type genus or where placeholders have been used when a Latinate name is available for a genus within the taxon. Anomalous phylogenies were analysed in Excel and used to create anomaly replacement tables for Archaea and Bacteria (Table S2), which were used with the \u003cem\u003ereplace_names.py\u003c/em\u003e script to replace anomalous placeholders with appropriate alternatives, which were marked with an exclamation mark.\u003c/p\u003e \u003cp\u003eAs in the previous publication [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e], a set of \u0026gt;\u0026thinsp;4\u0026nbsp;million excluded terms was assembled from Latin stems compiled by Whitaker, a fresh download of headwords from the English Wiktionary and a fresh download of names already in use in taxonomy, using the script \u003cem\u003einput_terms_clean.py\u003c/em\u003e to extract the terms from the input files. The Python script \u003cem\u003ename_creator_r214.py\u003c/em\u003e was used to create a new set of arbitrary genus and species names that excluded these restricted terms and arbitrary names used in the previous publication. In the previous work [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e], the stems for arbitrary genus names were required to be two character changes apart from all other stems. However, when reapplied to new archaeal genera, this approach failed to generate enough archaeal genus names. Therefore, this requirement was relaxed to create a comprehensive set of stems with the form \u0026ldquo;consonant-vowel-consonant-vowel-consonant\u0026rdquo;\u0026mdash;to which were added the endings specified in the previous paper, restricting use of the endings \u003cem\u003e-osa\u003c/em\u003e and \u003cem\u003e-ana\u003c/em\u003e to species names. As names are assigned randomly across the GTDB phylogeny, the potential for confusion stemming from closely related taxa having similar names remains very low.\u003c/p\u003e \u003cp\u003eThe script \u003cem\u003eplaceholder_extractor.py\u003c/em\u003e was used to extract remaining placeholders from the edited GDTB r214 taxonomy files and to randomly assign arbitrary names to them. This process included addition of appropriate suffixes for high-level taxa and tagging of new names with an exclamation mark so that they could identified by later scripts. This resulted in the creation of name replacement tables for Archaea and Bacteria (Table S3). The script was run repeatedly for each domain until it generated sufficiently distinctive and agreeable new phylum names, after which the associated replacement tables were selected for downstream use. The script \u003cem\u003ereplace_names.py\u003c/em\u003e was then used to replace r214-specific placeholders in the taxonomy files for Archaea and Bacteria with new arbitrary names. The resulting renamed placeholder-free taxonomies were then pasted into the r214 metadata files (after sorting original and modified files by accession number) to create renamed placeholder-free metadata files for Archaea and Bacteria. The script \u003cem\u003eprotologue.maker.py\u003c/em\u003e was used to generate protologues for newly named taxa after comparing the original and renamed metadata files for Archaea and Bacteria.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003eTen new archaeal anomalous placeholders and 177 new bacterial anomalous placeholders from the R214 taxonomies were replaced with consistently used placeholders or well-formed Latin names built from genus designations after scrutiny of anomalous phylogenies (Table S2). In most cases, the anomalies were the result of reclassification of taxa, but in some cases they reflected typographical errors, e.g. where a genus and family are recorded as g__G023898745 and f__G023898745, but the associated order is recorded as o__G02398745.\u003c/p\u003e \u003cp\u003eFor the phylum we called \u003cem\u003eEfretiota\u003c/em\u003e in our previous paper (GTDB placeholder p__FCPU426), during the transition from r207 to r214k, the type genus Efretia (GTDB placeholder g__ JAAXVQ01) was moved into a new phylum with the new GTDB placeholder p__JAAXVQ01. The \u003cem\u003eCandidatus\u003c/em\u003e phylum name \u003cem\u003eEfretiota\u003c/em\u003e was therefore transferred to the new phylum, while the original phylum was renamed after one of the three remaining genera in the phylum, \u003cem\u003eLuxamia\u003c/em\u003e (GTDB placeholder g__PALSA-1180), which had already been used to create the names for a family, order and class.\u003c/p\u003e \u003cp\u003eOnce anomalous names had been corrected, 1,720 new alphanumeric placeholder names or epithets were retrieved from the archaeal taxonomy file and 26,679 from the bacterial taxonomy file and used to build name-replacement tables (Table S3). These new names incorporate the choices made by GTDB for type genomes for species, replacing alphanumeric designations wherever they occur in the taxonomic hierarchy.\u003c/p\u003e \u003cp\u003eThe name-replacement tables were used to replace placeholders in the GTDB taxonomy and metadata files, assigning new well-formed arbitrary Latinate \u003cem\u003eCandidatus\u003c/em\u003e names to two new archaeal and twelve new bacterial phyla; six new archaeal and 48 new bacterial classes; 13 new archaeal and 158 new bacterial orders; 60 new archaeal and 597 new bacterial families; 271 new archaeal and 3,869 new bacterial genera; and 1,097 new archaeal and 18,126 new bacterial species (Table S3). As before, renamed GTDB taxonomy files (Table S4) were created along with protologues for all new \u003cem\u003eCandidatus\u003c/em\u003e taxa. However, the resulting sets of taxonomic descriptions was too large to be presented in the body of this manuscript and are instead available as RTF files on Zenodo. Given that new phylum names are likely to see the heaviest use, protologues for newly named phyla and associated type genera and species are presented in Table\u0026nbsp;1.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eThe astonishing progress of prokaryotic taxonomic discovery continues at a relentless pace, as evidenced by the fact that the latest release of GTDB contains nearly 30% more species than the previous release [\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://gtdb.ecogenomic.org/stats/r214\u003c/span\u003e\u003cspan address=\"https://gtdb.ecogenomic.org/stats/r214\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e]. This highlights the continuing need for creating and assigning new taxonomic names at scale. Recent attempts to create procedures for publishing names-with-standing for uncultured prokaryotes [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e] ignore the far more pressing issue of how to create enough well-formed names to cope with the deluge of discovery. Failure to meet this challenge effectively means abandoning Linnaean nomenclature for around 80% of known prokaryotic taxa.\u003c/p\u003e \u003cp\u003eIt is worth contrasting the 17,000 or more new species described in the latest GTDB release with the relatively slow process of naming new species under the ICNP, when 2,364 validly published and 597 \u003cem\u003eCandidatus\u003c/em\u003e species names were added to LPSN in 2023 [\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://lpsn.dsmz.de/advanced_search\u003c/span\u003e\u003cspan address=\"https://lpsn.dsmz.de/advanced_search\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e]. More worrying still, \u0026gt;\u0026thinsp;300 taxonomic names have been validly published exclusively under the SeqCode, [\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://disc-genomics.uibk.ac.at/seqcode/names?status=SeqCode\u003c/span\u003e\u003cspan address=\"https://disc-genomics.uibk.ac.at/seqcode/names?status=SeqCode\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e], even though this initiative was set up with the goal of naming uncultured prokaryotes.\u003c/p\u003e \u003cp\u003eIn 2021, with colleagues, I described an approach for automated creation of descriptive names \u003cem\u003een masse\u003c/em\u003e [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. When applied to taxa from the chicken gut [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e], this led to the publication of hundreds of new \u003cem\u003eCandidatus\u003c/em\u003e names, which have been propagated into online databases including LPSN, NCBI and GTDB. However, it soon became clear that this approach was not suitable for clearing the backlog of the tens of thousands of new names required, as this would entail exhaustive reconstruction and comparisons of phenotypes and genome metadata to create descriptive names that are accurate and precise. But even then, the resulting name space is unlikely to contain enough descriptive name that are short enough to be usable. As a result, we published over 65,000 arbitrary \u003cem\u003eCandidatus\u003c/em\u003e names to fill the gap [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. Here, I show that this approach remains sustainable, despite the relentless progress of discovery.\u003c/p\u003e \u003cp\u003eOur arbitrary \u003cem\u003eCandidatus\u003c/em\u003e names have begun to be cited in research publications [\u003cspan additionalcitationids=\"CR8 CR9 CR10 CR11\" citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e], but, curiously, the names cannot be validly published under the SeqCode, as the SeqCode rules explicitly exclude use of arbitrary components in the creation of names, despite over a century and a half of precedents for such practice [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e] and recent adoption of arbitrary artificial suffixes in the quest to replace descriptive names for prokaryotic phyla and kingdoms with those built from type genera [14,15]. If the SeqCode community prefers not to use our arbitrary names, they should at least rise to the challenge of creating tens of thousands of new names that do meet their own arbitrary rules.\u003c/p\u003e \u003cp\u003eThe new set of arbitrary names I have published here, along with the previous set, are now available for use by the scientific community. They provide distinctive and user-friendly alternatives to unwieldy alphanumeric placeholders. However, given the lack of standing associated with \u003cem\u003eCandidatus\u003c/em\u003e names, any of them could be replaced by alternative names, should the need arise. The names are likely to be used in earnest only once studies begin on the taxa they are associated with, which will depend on how many such taxa attract research attention. At the very least, the new arbitrary phylum names are likely to provide handy signposts to new functional and phylogenetic diversity. The challenge for the future is to ensure that each new release of GTDB is met with a new set of arbitrary names in a timely fashion, so that the legacy of Linnaeus can be kept alive at the exciting frontier of prokaryotic discovery.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003eAuthor statements\u003c/p\u003e\n\u003cp\u003eAuthors and contributors\u003c/p\u003e\n\u003cp\u003eConceptualization, MJP; Data curation, Methodology: MJP; Writing: MJP.\u003c/p\u003e\n\u003cp\u003eConflicts of interest\u003c/p\u003e\n\u003cp\u003eThe author declares that there are no conflicts of interest.\u003c/p\u003e\n\u003cp\u003eFunding information\u003c/p\u003e\n\u003cp\u003eMJP is supported by the Medical Research Council CLIMB-BIG-DATA grant MR/T030062/1.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003ePallen MJ, Rodriguez-R LM, Alikhan NF. Naming the unnamed: over 65,000 \u003cem\u003eCandidatus\u003c/em\u003e names for unnamed \u003cem\u003eArchaea\u003c/em\u003e and \u003cem\u003eBacteria\u003c/em\u003e in the Genome Taxonomy Database. \u003cem\u003eInt J Syst Evol Microbiol\u003c/em\u003e. 2022;72(9):10.1099/ijsem.0.005482. doi:10.1099/ijsem.0.005482\u003c/li\u003e\n \u003cli\u003eParks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785\u0026ndash;D794 doi: 10.1093/nar/gkab776\u003c/li\u003e\n \u003cli\u003eHedlund BP, Chuvochina M, Hugenholtz P, et al. SeqCode: a nomenclatural code for prokaryotes described from sequence data.\u0026nbsp;\u003cem\u003eNat Microbiol\u003c/em\u003e. 2022;7(10):1702-1708. doi:10.1038/s41564-022-01214-9\u003c/li\u003e\n \u003cli\u003eArahal D, Bisgaard M, Christensen H, et al. The best of both worlds: a proposal for further integration of\u0026nbsp;\u003cem\u003eCandidatus\u003c/em\u003e names into the International Code of Nomenclature of Prokaryotes.\u0026nbsp;\u003cem\u003eInt J Syst Evol Microbiol\u003c/em\u003e. 2024;74(1):10.1099/ijsem.0.006188. doi:10.1099/ijsem.0.006188\u003c/li\u003e\n \u003cli\u003ePallen MJ, Telatin A, Oren A. The Next Million Names for Archaea and Bacteria.\u0026nbsp;\u003cem\u003eTrends Microbiol\u003c/em\u003e. 2021;29(4):289-298. doi:10.1016/j.tim.2020.10.009\u003c/li\u003e\n \u003cli\u003eGilroy R, Ravi A, Getino M, et al.\u0026nbsp;Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.\u0026nbsp;\u003cem\u003ePeerJ\u003c/em\u003e. 2021;9:e10941. Published 2021 Apr 6. doi:10.7717/peerj.10941\u003c/li\u003e\n \u003cli\u003eKaminsky RA, Reid PM, Altermann E, et al. Rumen\u0026nbsp;\u003cem\u003eLachnospiraceae\u003c/em\u003e isolate NK3A20 exhibits metabolic flexibility in response to substrate and coculture with a methanogen.\u0026nbsp;\u003cem\u003eAppl Environ Microbiol\u003c/em\u003e. 2023;89(10):e0063423. doi:10.1128/aem.00634-23\u003c/li\u003e\n \u003cli\u003eVenkatachalam S, Jabir T, Vipindas PV, Krishnan KP.\u0026nbsp;Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems.\u0026nbsp;\u003cem\u003eAppl Microbiol Biotechnol\u003c/em\u003e. 2024;108(1):128. doi:10.1007/s00253-023-12991-6\u003c/li\u003e\n \u003cli\u003eVila-Costa M, Lundin D, Fern\u0026aacute;ndez-Pinos MC, Iriarte J, Irigoien X, Pi\u0026ntilde;a B, Dachs J. Responses to organic pollutants in the tropical Pacific and subtropical Atlantic Oceans by pelagic marine bacteria. \u003cem\u003eFrontiers in Environmental\u003c/em\u003e Science. 2023;11:1110169.\u003c/li\u003e\n \u003cli\u003eBowman JP. Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of \u003cem\u003eMassilia\u003c/em\u003e La Scola \u003cem\u003eet al\u003c/em\u003e. 2000 into \u003cem\u003eTelluria\u003c/em\u003e Bowman \u003cem\u003eet al\u003c/em\u003e. 1993, \u003cem\u003eMokoshia\u003c/em\u003e gen. nov. and \u003cem\u003eZemynaea\u003c/em\u003e gen. nov. \u003cem\u003eInt J Syst Evol Microbiol\u003c/em\u003e. 2023;73(8):10.1099/ijsem.0.005991. doi:10.1099/ijsem.0.005991\u003c/li\u003e\n \u003cli\u003eBottom of Form\u003c/li\u003e\n \u003cli\u003eGilroy R, Adam ME, Kumar B, Pallen MJ. An initial genomic blueprint of the healthy human oesophageal microbiome. \u003cem\u003eAccess Microbiol\u003c/em\u003e. 2023;5(6):acmi000558.v3. Published 2023 Jun 26. doi:10.1099/acmi.0.000558.v3\u003c/li\u003e\n \u003cli\u003ede Candolle A. \u003cem\u003eLois de la Nomenclature Botanique\u003c/em\u003e.\u0026nbsp;Masson; 1867\u003c/li\u003e\n \u003cli\u003eWhitman WB, Oren A, Chuvochina M, et al. Proposal of the suffix -ota to denote phyla. Addendum to \u0026apos;Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes\u0026apos;. \u003cem\u003eInt J Syst Evol Microbiol\u003c/em\u003e. 2018;68(3):967-969. doi:10.1099/ijsem.0.002593\u003c/li\u003e\n \u003cli\u003eG\u0026ouml;ker M, Oren A. Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes. \u003cem\u003eInt J Syst Evol Microbiol\u003c/em\u003e. 2023;73(2):10.1099/ijsem.0.005650. doi:10.1099/ijsem.0.005650\u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Table ","content":"\u003cp\u003eTable 1 is available in the Supplementary Files section\u003c/p\u003e"},{"header":"Supplementary Files","content":"\u003cp\u003eSupplementary Files are not available with this version\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Bacterial nomenclature, archaeal nomenclature, genome taxonomy, shotgun metagenomics, Candidatus names","lastPublishedDoi":"10.21203/rs.3.rs-4235597/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4235597/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eHere, an established approach to the generation of well-formed arbitrary Latinate names at a scale has been adopted and adapted to name tens of thousands of new, but unnamed taxa within GTDB Release r214.1. New Latinate \u003cem\u003eCandidatus\u003c/em\u003e names have been created and assigned to two new archaeal and twelve new bacterial phyla; six new archaeal and 48 new bacterial classes; 13 new archaeal and 158 new bacterial orders; 60 new archaeal and 597 new bacterial families; 271 new archaeal and 3,869 new bacterial genera; and 1,097 new archaeal and 18,126 new bacterial species. New \u003cem\u003eCandidatus \u003c/em\u003enames for bacterial phyla include \u003cem\u003eCa.\u003c/em\u003e Afuciota, \u003cem\u003eCa.\u003c/em\u003eAxiviota, \u003cem\u003eCa.\u003c/em\u003e Bobupiota, C\u003cem\u003ea.\u003c/em\u003e Fitepiota, \u003cem\u003eCa.\u003c/em\u003e Hubebiota, \u003cem\u003eCa.\u003c/em\u003eIbociota, \u003cem\u003eCa.\u003c/em\u003e Inuciota, \u003cem\u003eCa.\u003c/em\u003e Luxamiota, \u003cem\u003eCa.\u003c/em\u003e Megaciota, \u003cem\u003eCa.\u003c/em\u003eNasexiota, \u003cem\u003eCa\u003c/em\u003e. Oviciota\u003cem\u003e, Ca.\u003c/em\u003e Ucifiota, and \u003cem\u003eCa\u003c/em\u003e. Uvuciota, while new names for archaeal phyla include \u003cem\u003eCa.\u003c/em\u003e Acigarchota and \u003cem\u003eCa.\u003c/em\u003eOmefarchota. These efforts show that the creation of arbitrary names for prokaryotic taxa remains sustainable, despite the relentless progress of discovery.\u003c/p\u003e","manuscriptTitle":"Updating the unnamed: over 20,000 new Candidatus names for unnamed taxa in GTDB release r214","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-04-09 16:26:02","doi":"10.21203/rs.3.rs-4235597/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"e2efbe1f-d7d2-418c-8e53-f06ea7cf293c","owner":[],"postedDate":"April 9th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":30400581,"name":"General Microbiology"}],"tags":[],"updatedAt":"2024-04-09T16:26:02+00:00","versionOfRecord":[],"versionCreatedAt":"2024-04-09 16:26:02","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4235597","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4235597","identity":"rs-4235597","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}