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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 74, part 1 of the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38695346 DOI: 10.1099/ijsem.0.006271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
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2
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Proposal of Shuttleworthella gen. nov. and Nostocoides gen. nov. as replacement names for the illegitimate prokaryotic generic names Shuttleworthia and Tetrasphaera, respectively. Int J Syst Evol Microbiol 2024; 74. [PMID: 38573081 DOI: 10.1099/ijsem.0.006318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
The prokaryotic generic name Shuttleworthia Downes et al. 2002 is illegitimate because it is a later homonym of the plant genus Shuttleworthia Meisner 1840 and the mollusk genus Shuttleworthia Baker 1941 (Principle 2 and Rule 51b(5) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Shuttleworthella, with type species Shuttleworthella satelles comb. nov. The prokaryotic generic name Tetrasphaera Maszenan et al. 2000 is illegitimate because it is a later homonym of Tetrasphaera Popofsky 1913 (Protozoa, Radiolaria) and of Tetrasphaera Górka 1965 (a fossil dinoflagellate) (Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Nostocoides, with type species Nostocoides japonicum comb. nov.
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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
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Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74:006229. [PMID: 38546332 PMCID: PMC10995726 DOI: 10.1099/ijsem.0.006229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Indexed: 04/07/2024] Open
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 11 of the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38437003 DOI: 10.1099/ijsem.0.006213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
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6
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Proposed minimal standards for description of new taxa of the class Halobacteria. Int J Syst Evol Microbiol 2024; 74:006290. [PMID: 38456846 PMCID: PMC10999741 DOI: 10.1099/ijsem.0.006290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/24/2024] [Indexed: 03/09/2024] Open
Abstract
Halophilic archaea of the class Halobacteria are the most salt-requiring prokaryotes within the domain Archaea. In 1997, minimal standards for the description of new taxa in the order Halobacteriales were proposed. From then on, the taxonomy of the class Halobacteria provides an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods were implemented. The last decades have witnessed a rapid expansion of the number of described taxa within the class Halobacteria coinciding with the era of genome sequencing development. The current members of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria propose these revisions to the recommended minimal standards and encourage the use of advanced technologies in the taxonomic description of members of the Halobacteria. Most previously required and some recommended minimal standards for the description of new taxa in the class Halobacteria were retained in the present revision, but changes have been proposed in line with the new methodologies. In addition to the 16S rRNA gene, the rpoB' gene is an important molecular marker for the identification of members of the Halobacteria. Phylogenomic analysis based on concatenated conserved, single-copy marker genes is required to infer the taxonomic status of new taxa. The overall genome relatedness indexes have proven to be determinative in the classification of the taxa within the class Halobacteria. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values should be calculated for rigorous comparison among close relatives.
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 12 of the IJSEM. Int J Syst Evol Microbiol 2024; 74:006243. [PMID: 38546333 PMCID: PMC10995960 DOI: 10.1099/ijsem.0.006243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Indexed: 04/07/2024] Open
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Proposals to revise the Statutes of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 2024; 74:006291. [PMID: 38441551 PMCID: PMC10999737 DOI: 10.1099/ijsem.0.006291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
The International Committee on Systematics of Prokaryotes serves to administer the rules of prokaryotic nomenclature via the International Code of Nomenclature of Prokaryotes, ensures the publication of the International Journal of Systematic and Evolutionary Microbiology, and works to represent the interests of the microbiological disciplines regarding prokaryotic nomenclature. The functions and mechanisms of operation of the International Committee on Systematics of Prokaryotes (ICSP) are defined in its Statutes, which were last revised in 2019. As members of the 2020-2023 and the 2023-2026 ICSP Executive Board and the Judicial Commission, we propose here some further revisions to help improve the clarity and functionality of the Statutes.
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Minutes of the open plenary meetings of the International Committee on Systematics of Prokaryotes, 11 October 2022 and 14 December 2023. Int J Syst Evol Microbiol 2024; 74. [PMID: 38411503 DOI: 10.1099/ijsem.0.006274] [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: 02/28/2024] Open
Abstract
Open virtual plenary meetings of the International Committee on Systematics of Prokaryotes (ICSP) were held on 11 October 2022 and on 14 December 2023. To comply with Articles 4(d) and 5(d)(1) of the statutes of the ICSP, the minutes of these meetings are published here.
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Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38299482 DOI: 10.1099/ijsem.0.006173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
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11
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Reclassification of Allomuricauda and Muricauda species as members of the genus Flagellimonas Bae et al. 2007 and emended description of the genus Flagellimonas. Int J Syst Evol Microbiol 2024; 74. [PMID: 38421264 DOI: 10.1099/ijsem.0.006286] [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: 03/02/2024] Open
Abstract
The recently proposed genus Allomuricauda Deshmukh and Oren 2023 is illegitimate because it includes the type species of the genera Flagellimonas Bae et al. 2007 and Spongiibacterium Yoon and Oh 2012, contravening Rule 51b(1) of the International Code of Nomenclature of Prokaryotes. As Flagellimonas Bae et al. 2007 is the earlier described genus, we here reclassify 36 species earlier described as belonging to the illegitimate genus Muricauda as species of Flagellimonas. We also present an emended description of the genus Flagellimonas.
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 10 of the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38299470 DOI: 10.1099/ijsem.0.006172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
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13
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Notification of changes in taxonomic opinion previously published outside the IJSEM. List of Changes in Taxonomic Opinion no. 39. Int J Syst Evol Microbiol 2024; 74. [PMID: 38299467 DOI: 10.1099/ijsem.0.006145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
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14
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Is the bacterial genus name Rhodococcus Zopf 1891 illegitimate? Request for an Opinion. Int J Syst Evol Microbiol 2024; 74. [PMID: 38265282 DOI: 10.1099/ijsem.0.006251] [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: 01/25/2024] Open
Abstract
In 2014, it was reported that the bacterial genus name Rhodococcus Zopf 1891 was illegitimate due to the priority of the cyanobacterial genus name Rhodococcus Hansgirg 1884. Since that time, the consequences of this conclusion have been largely ignored, whilst changes have been made to relevant Rules of the International Code of Nomenclature of Prokaryotes, including significant changes to the way in which the Code treats the names of members of Cyanobacteriota. Given the complexity of the nomenclatural issues, we request the opinion of the Judicial Commission of the International Committee on Systematics of Prokaryotes as to whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate.
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Emendation of Appendix 9 of the International Code of Nomenclature of Prokaryotes to provide guidelines for naming genera after geographical locations. Int J Syst Evol Microbiol 2024; 74. [PMID: 38289226 DOI: 10.1099/ijsem.0.006252] [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: 02/01/2024] Open
Abstract
Following a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes with guidelines for the naming of genera after geographical locations, I here report the outcome of the ballot on this proposal by the members of the International Committee on Systematics of Prokaryotes and present the guidelines to be incorporated in Appendix 9.
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Valid publication of names of two domains and seven kingdoms of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38252124 DOI: 10.1099/ijsem.0.006242] [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: 01/23/2024] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 8 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 38038642 DOI: 10.1099/ijsem.0.006094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
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Validation List no. 214. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 38038645 DOI: 10.1099/ijsem.0.006080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
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19
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The gender gap in names of prokaryotes honouring persons. Int J Syst Evol Microbiol 2023; 73. [PMID: 37909279 DOI: 10.1099/ijsem.0.006115] [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: 11/03/2023] Open
Abstract
The aim of this study is to analyse prokaryotic names which honour persons, eponyms, from a gender perspective. Data were retrieved from the List of Prokaryotic names with Standing in Nomenclature. Excluding new combinations, the etymologies of 23 315 unique names at the rank of genus, species and subspecies were analysed. A total of 2018 (8.7 %) names honour persons (eponyms), for which the development of the female share over time was further investigated. Women started to be honoured very recently (1947) compared to men (1823). Moreover, only 14.8 % of all prokaryotic eponyms refer to females. This ratio has hardly improved since 1947, although the number of women whose contributions to microbiology could have been recognized has increased over time. In contrast, about 50 % of prokaryotic names derived from mythological characters refer to females. To reduce this gender gap, we encourage authors proposing new taxon names to honour female scientists who can serve as role models for new generations.
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 9 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37937952 DOI: 10.1099/ijsem.0.006158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
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21
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Emendation of Principle 8, Rules 5b, 8, 15, 33a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes to include the categories of kingdom and domain. Int J Syst Evol Microbiol 2023; 73. [PMID: 37909283 DOI: 10.1099/ijsem.0.006123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Following an electronic discussion on proposals to emend Principle 8, Rules 5b, 8, 15, 33a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes (ICNP), I here report the outcome of the ballot on these proposals by the members of the International Committee on Systematics of Prokaryotes. These emendations enact the addition of the categories of kingdom and domain to the ICNP.
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 6 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787066 DOI: 10.1099/ijsem.0.006009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
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23
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Proposal of Allopseudospirillum gen. nov. as a replacement name for the illegitimate prokaryotic generic name Pseudospirillum Satomi et al. 2002. Int J Syst Evol Microbiol 2023; 73. [PMID: 37882658 DOI: 10.1099/ijsem.0.006129] [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: 10/27/2023] Open
Abstract
The prokaryotic generic name Pseudospirillum Satomi et al. 2002 is illegitimate because it is a later homonym of Pseudospirillum Alexeieff 1917, a genus of uncertain affiliation, possibly belonging to the Mesomycetozoa (Principle 2 and Rule 51b(5) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Allopseudospirillum, with type species Allopseudospirillum japonicum.
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Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787078 DOI: 10.1099/ijsem.0.005997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
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25
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 7 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37906095 DOI: 10.1099/ijsem.0.006041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
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Proposal of Allomuricauda gen. nov. and Allofranklinella gen. nov. as replacement names for the illegitimate prokaryotic generic names Muricauda and Franklinella, respectively. Int J Syst Evol Microbiol 2023; 73. [PMID: 37747448 DOI: 10.1099/ijsem.0.006023] [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: 09/26/2023] Open
Abstract
The prokaryotic generic names Muricauda Bruns et al. 2001 and Franklinella Bernard et al. 2022 are illegitimate because they are later homonyms of the genus names Muricauda Small 1903 (synonym of Arisaema; Tracheophyta - Liliopsida - Araceae) and Franklinella Stewart and Hendrix 1945 (a Devonian ostracod genus) and Franklinella Lenz 1973 (a Devonian brachiopod genus), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic names Allomuricauda and Allofranklinella, with type species Allomuricauda ruestringensis and Allofrankinella schreckenbergeri, respectively.
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Emendation of Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2023; 73. [PMID: 37695654 DOI: 10.1099/ijsem.0.006070] [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: 09/12/2023] Open
Abstract
Following an electronic discussion on proposals to emend Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes, I here report the outcome of the ballot on these proposals by the members of the International Committee on Systematics of Prokaryotes.
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Proposal of Thalassovita gen. nov. and Alloyangia gen. nov. as replacement names for the illegitimate prokaryotic generic names Thalassobius and Yangia, respectively. Int J Syst Evol Microbiol 2023; 73. [PMID: 37695726 DOI: 10.1099/ijsem.0.006025] [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: 09/13/2023] Open
Abstract
The prokaryotic generic names Thalassobius Arahal et al. 2005 and Yangia Dai et al. 2006 are illegitimate because they are later homonyms of the genus names Thalassobius Solier 1849 (Coleoptera) and Yangia Zheng 1997 (fossil Rodentia), respectively Principle two and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes]. We therefore propose the replacement generic names Thalassovita and Alloyangia, with type species Thalassovita gelatinovora and Alloyangia pacifica, respectively.
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Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) now includes the phylum category. For the purpose of the valid publication of their names under the ICNP, we consider here four phyla. Slightly modified descriptions of 'Abditibacteriota' Tahon et al. 2018 and 'Desulfobacterota' Waite et al. 2020 are provided to meet the requirements of the ICNP for phylum names. Methanobacteriota is proposed as a substitute for 'Euryarchaeota' Garrity and Holt 2021, while Nanobdellota is proposed to replace 'Nanoarchaeota' Huber et al. 2002, based on the genus Nanobdella Kato et al. 2022.
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Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37526968 DOI: 10.1099/ijsem.0.005931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023] Open
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31
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 4 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37526974 DOI: 10.1099/ijsem.0.005937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023] Open
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32
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Notification of changes in taxonomic opinion previously published outside the IJSEM. List of Changes in Taxonomic Opinion no. 38. Int J Syst Evol Microbiol 2023; 73. [PMID: 37526965 DOI: 10.1099/ijsem.0.005923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023] Open
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 5 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37651177 DOI: 10.1099/ijsem.0.005996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 3 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37399063 DOI: 10.1099/ijsem.0.005910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
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Corrigendum: Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov., and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola, and Sala, respectively. Int J Syst Evol Microbiol 2023; 73. [PMID: 37436804 DOI: 10.1099/ijsem.0.005954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023] Open
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Coraliomargarita parva sp. nov., isolated from mangrove sediment and genome-based analysis of the class Opitutae revealed five novel families: Coraliomargaritaceae fam. nov., Pelagicoccaceae fam. nov., Cerasicoccaeae fam. nov., Oceanipulchritudinaceae fam. nov., and Alterococcaeae fam. nov. Front Microbiol 2023; 14:1202141. [PMID: 37362914 PMCID: PMC10288369 DOI: 10.3389/fmicb.2023.1202141] [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: 04/07/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Members of the class Opitutae are widely distributed in various environments such as rice paddy soil, freshwater lakes, seawater, marine sediment, and invertebrate digestive tracts. The class currently consists of two orders, Opitutales and Puniceicoccales, represented by the families Opitutaceae and Puniceicoccaceae, respectively, which are primarily delineated on the basis of 16S rRNA gene sequences and limited phenotypic characterizations of a few type strains. The scarcity of 16S rRNA gene and genome sequences generated from the type strains of the class Opitutae constrained our understanding of the ecological distribution and adequate resolution of its taxonomy. Here, an Opitutae strain designated WMMB3T, isolated from a mangrove sediment, was subjected to taxonomic characterization. The 16S rRNA gene of strain WMMB3T shared high sequence similarities with Coraliomargarita akajimensis DSM 45221T and C. sinensis WN38T of 96.1 and 95.9%, respectively. Phylogenetic analysis suggested that strain WMMB3T formed a monophyletic branch affiliated to the genus Coraliomargarita. The average nucleotide identity (ANI) values, digital DNA-DNA hybridization (dDDH) values and average amino acid identity (AAI) values of strain WMMB3T compared between Coraliomargarita members were 71.8-72.5, 20.7, and 68.2-68.7%, respectively, indicating that strain WMMB3T represented a novel species of Coraliomargarita. The genome of strain WMMB3T was 4.5 Mbp with a DNA G + C content of 56.0%. The respiratory quinone was menaquinone-7. The major fatty acids were iso-C14:0, and C18:1ω9c. Based on genomic, phenotypic, and chemotaxonomic characterizations, strain WMMB3T represents a novel species, and Coraliomargarita parva sp. nov. is proposed. Additionally, the phylogenomic analysis of more than 500 genomes of the class Opitutae, encompassing a majority of uncultivated bacteria and a few type strains, was performed using the Genome Taxonomic Database toolkit (GTDB-Tk) to present adequate resolution of the taxonomy. Combined with 16S rRNA gene sequence phylogeny and genomic relatedness, five novel families retrieved mainly from marine habitats were proposed: Coraliomargaritaceae fam. nov., Pelagicoccaceae fam. nov., Cerasicoccaeae fam. nov., Oceanipulchritudinaceae fam. nov., and Alterococcaeae fam. nov. AAI values of 58-60% could be considered as the boundary to delineate families of the class Opitutae. This study provided a new taxonomic framework of the class Opitutae based on the genomic data.
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Naming genera after geographical locations. Proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2023; 73. [PMID: 37163413 DOI: 10.1099/ijsem.0.005873] [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: 05/12/2023] Open
Abstract
Appendix 9, Section E of the International Code of Nomenclature of Prokaryotes provides guidelines on how to form adjectival specific and subspecific epithets that reflect the geographical location where the organism was found or studied. It does not mention ways of naming genera after geographical locations. We here propose emendation of Appendix 9 with the recommendations on how to form such names. Comments on the implementation of the current wording of Appendix 9, Section E are also made.
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Validation List no. 211. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37255409 DOI: 10.1099/ijsem.0.005845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
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39
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International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision). Int J Syst Evol Microbiol 2023; 73. [PMID: 37219928 DOI: 10.1099/ijsem.0.005585] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
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40
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Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov. and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola and Sala, respectively. Int J Syst Evol Microbiol 2023; 73. [PMID: 37200073 DOI: 10.1099/ijsem.0.005901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
The prokaryotic generic names Eoetvoesia Felföldi et al. 2014, Paludicola Li et al. 2017, Rivicola Sheu et al. 2014 and Sala Song et al. 2023 are illegitimate because they are later homonyms of the genus names Eoetvoesia Schulzer et al. 1866 (Ascomycota), Paludicola Wagler 1830 (Amphibia) and Paludicola Hodgson 1837 (Aves), Rivicola Fitzinger 1833 (Mollusca) and Sala Walker 1867 (Hemiptera) and the subgenus name Sala Ross 1937 (Hymenoptera), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic names Eoetvoesiella, Paludihabitans, Rivihabitans and Salella, with type species Eoetvoesiella caeni, Paludihabitans psychrotolerans, Rivihabitans pingtungensis and Sallella cibi, respectively.
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 2 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37255410 DOI: 10.1099/ijsem.0.005862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
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Proposal of Christiangramia gen. nov., Neomelitea gen. nov. and Nicoliella gen. nov. as replacement names for the illegitimate prokaryotic generic names Gramella Nedashkovskaya et al. 2005, Melitea Urios et al. 2008 and Nicolia Oliphant et al. 2022, respectively. Int J Syst Evol Microbiol 2023; 73. [PMID: 37040175 DOI: 10.1099/ijsem.0.005806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
The prokaryotic generic names Gramella Nedashkovskaya et al. 2005, Melitea Urios et al. 2008 and Nicolia Oliphant et al. 2022 are illegitimate because they are later homonyms of the names Gramella Kozur 1971, a genus of fossil ostracods, Melitea Péron and Lesueur 1810 (Scyphozoa, Cnidaria), Melitea Lamouroux 1812 (Anthozoa, Cnidaria), Nicolia Unger 1842, an extinct plant genus, and Nicolia Gibson-Smith and Gibson-Smith 1979 (Bivalvia, Mollusca), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). For Gramella, we therefore propose the replacement generic name Christiangramia with type species Christiangramia echinicola comb. nov. and we propose the reclassification of 18 other species of Gramella in the genus Christiangramia as new combinations. In addition, we propose the replacement generic names Neomelitea with type species Neomelitea salexigens comb. nov. and Nicoliella with type species Nicoliella spurrieriana comb. nov.
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 1 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37115012 DOI: 10.1099/ijsem.0.005835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
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Validation List no. 210. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37000643 DOI: 10.1099/ijsem.0.005812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 72, part 12 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37009845 DOI: 10.1099/ijsem.0.005799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
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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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Notification of changes in taxonomic opinion previously published outside the IJSEM. List of Changes in Taxonomic Opinion no. 37. Int J Syst Evol Microbiol 2023; 73. [PMID: 36724106 DOI: 10.1099/ijsem.0.005696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Paracrocinitomix mangrovi gen. nov., sp. nov., isolated from a mangrove sediment: proposal of two new families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov., and emended description of the family Schleiferiaceae. Antonie Van Leeuwenhoek 2023; 116:171-184. [PMID: 36346556 DOI: 10.1007/s10482-022-01790-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
A Gram-stain-negative and short rod-shaped bacterial strain designated GM2-3-6-6T was obtained from a mangrove sediment. Cells were light yellow-pigmented, catalase-positive and oxidase-positive. Carotenoid pigment was produced. Phylogeny of the 16S rRNA gene showed that strain GM2-3-6-6T was affiliated to the family Crocinitomicaceae, sharing maximum sequence similarities with Crocinitomix algicola 0182T, C. catalasitica IFO 15977T, and Putridiphycobacter roseus SM1701T of 93.8%, 93.6%, and 92.5%, respectively. The average nucleotide identity values, digital DNA-DNA hybridization estimates and average amino acid identity values between strain GM2-3-6-6T and the three close relatives were 68.6-68.8%, 18.5-19.2%, and 59.0-62.3%, respectively. The complete circular genome of strain GM2-3-6-6T was 4,365,762 bp in length with a DNA G + C content of 35.0%. The respiratory quinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, two unidentified phospholipids, one unidentified aminoglycolipid, one unidentified aminolipid and four other unidentified lipids. The major fatty acids were iso-C15:0, iso-C15:1 G, summed feature 3 (C16:1ω7c and/or C16:1ω6c), and iso-C17:0 3-OH. Based on genomic, phenotypic, and chemotaxonomic characterizations, strain GM2-3-6-6T represents a novel species of a novel genus, for which the name Paracrocinitomix mangrovi gen. nov., sp. nov. is proposed. The type strain is GM2-3-6-6T (= MCCC 1K04831T = KCTC 82931T). Additionally, phylogenomic analysis of the type strains of the family Schleiferiaceae and family Cryomorphaceae related members including uncultivated bacteria, was performed using the Genome Taxonomic Database toolkit (GTDB-Tk). Based on 16S rRNA gene phylogeny and genomic features, two novel families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov. are proposed. An emended description of the family Schleiferiaceae is also proposed.
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 72, part 11 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 36856171 DOI: 10.1099/ijsem.0.005762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
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