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Oren A. On validly published names, correct names, and changes in the nomenclature of phyla and genera of prokaryotes: a guide for the perplexed. NPJ Biofilms Microbiomes 2024; 10:20. [PMID: 38467688 PMCID: PMC10928132 DOI: 10.1038/s41522-024-00494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.
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2
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Arahal D, Bisgaard M, Christensen H, Clermont D, Dijkshoorn L, Duim B, Emler S, Figge M, Göker M, Moore ERB, Nemec A, Nørskov-Lauritsen N, Nübel U, On SLW, Vandamme P, Ventosa A. 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. [PMID: 38180015 DOI: 10.1099/ijsem.0.006188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.
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Affiliation(s)
- David Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | | | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, CRBIP, CIP-Collection of Institut Pasteur, F-75015 Paris, France
| | - Lenie Dijkshoorn
- Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, Leiden / Torensteelaan 68, 3281 MA Numansdorp, Netherlands
| | - Birgitta Duim
- Department Biomolecular Health Sciences, Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CS Utrecht, Netherlands
| | - Stefan Emler
- SmartGene Services SARL, EPFL Innovation Park, PSE-C, CH-1015 Lausanne, Switzerland
| | - Marian Figge
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8 3584 CT, Utrecht, Netherlands
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Edward R B Moore
- Department of Infectious Disease and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-402 34 Gothenburg, Sweden
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Srobarova 48, 100 00 Prague 10, Czech Republic
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, V Úvalu 84, 150 06 Prague 5, Czechia
| | | | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Faculty of Agricultural Science, Lincoln University, Lincoln 7647, Christchurch, New Zealand
| | - Peter Vandamme
- BCCM/LMG, Laboratorium voor Microbiologie, Universiteit Gent (UGent) K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
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3
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Whitman WB, Hedlund BP, Palmer M, Sutcliffe I, Chuvochina M. Request for public discussion and ballot to amend SeqCode rules on priority of Candidatus names and correction of typographic and orthographic errors. ISME COMMUNICATIONS 2023; 3:96. [PMID: 37709936 PMCID: PMC10502122 DOI: 10.1038/s43705-023-00303-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Affiliation(s)
| | - Brian P Hedlund
- School of Life Sciences and Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Iain Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
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4
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Nilsson RH, Ryberg M, Wurzbacher C, Tedersoo L, Anslan S, Põlme S, Spirin V, Mikryukov V, Svantesson S, Hartmann M, Lennartsdotter C, Belford P, Khomich M, Retter A, Corcoll N, Gómez Martinez D, Jansson T, Ghobad-Nejhad M, Vu D, Sanchez-Garcia M, Kristiansson E, Abarenkov K. How, not if, is the question mycologists should be asking about DNA-based typification. MycoKeys 2023; 96:143-157. [PMID: 37214179 PMCID: PMC10194844 DOI: 10.3897/mycokeys.96.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/28/2023] [Indexed: 05/24/2023] Open
Abstract
Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
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Affiliation(s)
- R. Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
- College of Science, King Saud University, 1145 Riyadh, Saudi Arabia
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Sergei Põlme
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Viacheslav Spirin
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Sten Svantesson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Martin Hartmann
- Botany Unit (Mycology), Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
| | - Charlotte Lennartsdotter
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Pauline Belford
- Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Maryia Khomich
- Interaction Design and Software Engineering, Chalmers University of Technology, Lindholmsplatsen 1, 417 56 Göteborg, Sweden
| | - Alice Retter
- Department of Clinical Science, University of Bergen, Box 7804, 5020 Bergen, Norway
| | - Natàlia Corcoll
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Daniela Gómez Martinez
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Tobias Jansson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Masoomeh Ghobad-Nejhad
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Duong Vu
- Department of Biotechnology, Iranian Research Organization for Science and Technology, PO Box 3353-5111, Tehran 3353136846, Iran
| | | | - Erik Kristiansson
- Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Kessy Abarenkov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
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5
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Oren A. Naming new taxa of prokaryotes in the 21st century. Can J Microbiol 2023; 69:151-157. [PMID: 36852830 DOI: 10.1139/cjm-2022-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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6
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Kannan S, Sharma S, Ciufo S, Clark K, Turner S, Kitts PA, Schoch CL, DiCuccio M, Kimchi A. Collection and curation of prokaryotic genome assemblies from type strains at NCBI. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748495 DOI: 10.1099/ijsem.0.005707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains. The average nucleotide identity (ANI)-based quality control processes introduced at NCBI to verify the genomes from type strains and improve related sequence records are detailed here. Using the curated genomes from type strains as reference, the taxonomy of over 1.1 million GenBank genomes were verified and the taxonomy of over 7000 new submissions before acceptance to GenBank and over 1800 existing genomes in GenBank were reclassified.
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Affiliation(s)
- Sivakumar Kannan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Shobha Sharma
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Seán Turner
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Paul A Kitts
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Michael DiCuccio
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Avi Kimchi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
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7
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Göker M, Moore ERB, Oren A, Trujillo ME. Status of the SeqCode in the International Journal of Systematic and Evolutionary Microbiology. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748408 DOI: 10.1099/ijsem.0.005754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The recent publication of an alternative nomenclatural code that targets prokaryotes, the Code of Nomenclature of Prokaryotes Described from DNA Sequence Data (SeqCode), raises questions about how to treat names 'validly published' under that code in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Here, it is reiterated that the IJSEM must function in accordance with the International Code of Nomenclature of Prokaryotes (ICNP). It is also reiterated that the ICNP covers all prokaryotes and that it accordingly assigns a nomenclatural status to all names of prokaryotic taxa. This implies that the ICNP also assigns a status to names that are only 'validly published' under the SeqCode. It follows that the IJSEM must treat such names as not validly published, since 'validly published under the SeqCode' is not a nomenclatural status, under the ICNP. Such names should be marked accordingly as Candidatus names or printed in quotation marks. The same measures would need to be taken by other journals which intend to adhere to the ICNP.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Edward R B Moore
- Department of Infectious Disease and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-402 34 Gothenburg, Sweden
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
| | - Martha E Trujillo
- University of Salamanca, Dpto de Microbiología y Genética, Campus Unamuno, 37007 Salamanca, Spain
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8
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Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst Appl Microbiol 2022; 45:126305. [PMID: 36049255 PMCID: PMC9489671 DOI: 10.1016/j.syapm.2022.126305] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022]
Abstract
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.
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Affiliation(s)
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innrain 15 / 01-05, Innsbruck 6020, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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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. [PMID: 36125864 DOI: 10.1099/ijsem.0.005482] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.
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Affiliation(s)
- Mark J Pallen
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK.,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Luis M Rodriguez-R
- Department of Microbiology, University of Innsbruck, Innsbruck, Tyrol, Austria.,Digital Science Center, University of Innsbruck, Innsbruck, Tyrol, Austria
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10
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It’s time for a new type of type to facilitate naming the microbial world. New Microbes New Infect 2022; 47:100991. [PMID: 35800027 PMCID: PMC9253472 DOI: 10.1016/j.nmni.2022.100991] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/09/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Since January 1, 2001, the only acceptable nomenclatural type for species under the International Code of Nomenclature of Prokaryotes (ICNP) has been pure cultures. Here, we argue that this requirement is discordant with the more inclusive nature of nomenclatural types accepted under other codes of nomenclature and posit that the unique rigidity of the ICNP has failed to serve the broad research community and has stifled progress. This case is based on the axiom that many archaea and bacteria are interdependent in nature and therefore difficult, if not impossible, to grow, preserve, and distribute as pure cultures. As such, a large proportion of Earth's biodiversity cannot be named under the current system, which limits our ability to communicate about microbial diversity within and beyond the microbiology research community. Genome sequence data are now encouraged for valid publication of new taxa in microbial systematics journals, and metagenome-assembled genomes and single cell-amplified genomes are being generated rapidly from every biome on Earth. Thus, genome sequences are available for both cultivated and uncultivated microorganisms and can readily serve as a new category of nomenclatural type, allowing for a unified nomenclature for all archaea and bacteria, whether or not they are available as pure cultures. Ideally this would be under a single code of nomenclature but, as we review here, the newly established SeqCode will operate in parallel with the ICNP as a first step toward this goal.
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11
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ICSP response to 'Science depends on nomenclature, but nomenclature is not science'. Nat Rev Microbiol 2022; 20:249-250. [PMID: 35181770 DOI: 10.1038/s41579-022-00706-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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