International Code of Nomenclature of Prokaryotes

国际原核生物命名法
  • 文章类型: Journal Article
    国际原核生物系统学委员会通过《国际原核生物命名法》管理原核生物命名规则,确保国际系统和进化微生物学杂志的出版,并致力于代表有关原核命名法的微生物学学科的利益。国际原核生物系统学委员会(ICSP)的职能和运作机制在其章程中进行了定义,最后一次修订是在2019年。作为2020-2023年和2023-2026年ICSP执行委员会和司法委员会的成员,我们在这里提出了一些进一步的修订,以帮助提高法规的清晰度和功能。
    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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  • 文章类型: Journal Article
    在1990年代中期,“Candidatus”类别是为尚未培养的原核生物的推定分类群建立的。“Candidatus”的状态未正式包含在《国际原核生物命名法》的规则中。因此,\'Candidatus\'名称在命名法中没有代表。自2020年以来,已发布了“Candidatus”名称(不包括门)的精选注释列表。到2021年4月,已经发布了大约2700个“Candidatus”类群的名称。国际原核生物系统学委员会最近拒绝了允许基因序列数据作为命名类型的提议。现在正在开发一种命名未培养微生物的替代代码(“SeqCode”),用于命名大多数尚未培养的原核生物。在作者看来,不需要这样的代码,作为现有的系统,还对“候选人”名称进行命名质量控制,满足需求。诸如GAN之类的计算机程序可以从拉丁语和希腊语单词元素的简短列表中生成大量正确形成的名称,而Protologger则可以直接从基因组序列中生成描述,这在将来对于从宏基因组和单细胞基因组数据中自动命名和描述大量“Candidatus”分类群的重要性。然而,鼓励尽可能形成有趣和有意义的名字。
    In the mid-1990s, the category \'Candidatus\' was established for putative taxa of as yet uncultivated prokaryotes. The status of \'Candidatus\' is not formally included in the rules of the International Code of Nomenclature of Prokaryotes. Thus, \'Candidatus\' names do not have standing in the nomenclature. Curated annotated lists of \'Candidatus\' names (not including phyla) have been published since 2020. By April 2021, about 2700 names of \'Candidatus\' taxa had been published. The International Committee on Systematics of Prokaryotes recently rejected proposals to allow gene sequence data as nomenclatural types. An alternative code for naming uncultivated microorganisms (the \'SeqCode\') is now being developed for naming the majority of prokaryotes that are as yet uncultivated. In the opinion of the author, there is no need for such a code, as the existing system, with nomenclature quality control also for \'Candidatus\' names, fulfills the needs. Computer programs such as GAN which generates large numbers of correctly formed names from the short lists of Latin and Greek word elements and Protologger that produce descriptions directly from genome sequences will become important in the future for automated naming and description of large numbers of \'Candidatus\' taxa from metagenomic and single cell genome data. However, the formation of interesting and meaningful names is encouraged whenever possible.
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  • 文章类型: Journal Article
    The International Committee on Systematics of Prokaryotes has held an electronic discussion on proposals to amend the International Code of Nomenclature of Prokaryotes in order to allow the use of gene sequence data as type. The scientific discussion is reported. Subsequently members of the International Committee on Systematics of Prokaryotes voted on these proposals, which were rejected.
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  • 文章类型: Journal Article
    In their paper entitled \"Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa\" (BMC Genomics (2018) 19:931), Fitzgerald et al. proposed a neotype strain for F. prausnitzii (strain A2-165 = DSM 17677 = JCM 31915) and assigned strain ATCC 27768 = NCIMB 13872 to a newly established taxon, Faecalibacterium moorei nom. Nov. These proposals contravene the Rules of the International Code of Nomenclature of Prokaryotes (ICNP). Neotype strains can only be established following a formal proposal in the International Journal of Systematic and Evolutionary Microbiology in accordance with Rule 18c and Appendix 7 of the ICNP. A proposed neotype becomes an established neotype after 2 years, provided that no objections were submitted to the Judicial Commisson of the International Committee on Systematics of Prokaryotes within the first year following publication of the request. F. moorei as proposed by Fitzgerald et al. is a later homotypic synonym of F. prausnitzii. It cannot be a \'nom. nov.\' (nomen novum): based on Rule 34a of the ICNP: this term is only used when an author transfers a species to another genus or a subspecies to another species as a new combination, but the original specific epithet cannot be used as \'comb. nov.\' (combinatio nova) as a result of homonymy. Moreover, ATCC 27768 and NCIMB 13872 cannot be proposed as the type strain of F. moorei as these remain permanently associated with the type strain of F. prausnitzii unless the Judicial Commission of the ICSP will decide otherwise.
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  • 文章类型: Journal Article
    Studies on Pseudomonas nautica Baumann et al. 1972 (Approved Lists 1980) and Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 have shown that they should be treated as heterotypic synonyms. As a consequence, they have been treated as belonging to a single species, Marinobacter hydrocarbonoclasticus Gauthier et al. 1992. This interpretation of the International Code of Nomenclature of Bacteria/Prokaryotes is, however, based on a fundamental flaw in the interpretation of the wording of Rule 15 as documented in the 1975 and 1990 revisions where the wording has been partially corrected in the 2008 revision. A key aspect of the incorrect interpretation is that the nomenclatural type of a taxon, in this case Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 (the nomenclatural type of the Marinobacter Gauthier et al. 1992) must be used instead of recognising the priority of the epithet in Pseudomonas nautica Baumann et al. 1972 (Approved Lists 1980), with the creation of a new combination Marinobacter nauticus (Baumann et al. 1972). It is now clear that there is no justification for that interpretation and it is necessary to create a new combination, Marinobacter nauticus (Baumann et al. 1972) in the situation where Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 and Pseudomonas nautica Baumann et al. 1972 (Approved Lists 1980) are treated as heterotypic synonyms. Additional studies have shown that Marinobacter aquaeolei Nguyen et al. 1993 and Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 should also be treated as heterotypic synonyms.
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