期刊：nature microbiology (30.964/Q1)
SeqCode: a nomenclatural code for prokaryotes described from sequence data
SeqCode：根据序列数据描述的原核生物的命名代码
Abstract
Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.
大多数原核生物没有纯培养物，因此没有资格按照《国际原核生物命名法》（ICNP）的规则和建议进行命名。这里我们总结了SeqCode的发展，这是一个命名法的代码，根据这个代码，基因组序列可以作为命名法的类型。该代码使基于分离的基因组、宏基因组组装的基因组或单扩增的基因组序列的原核生物名称得以有效公布。在其他方面，它与ICNP在名称的形成和优先权的规则方面相似。它通过SeqCode注册处（https://seqco.de/）运作，这是一个注册门户，通过它，名称和命名类型被注册、验证并与元数据相联系。我们描述了目前在SeqCode中可用来注册和验证名称的两种途径，包括Candidatus名称，并提供了两种途径的例子。我们提供了关于DNA序列的最低标准的建议。因此，SeqCode为所有原核生物的命名提供了一个可重复的和客观的框架，而不考虑可培养性，并促进了微生物学科间的交流。
It is widely recognized that the requirement of the International Code of Nomenclature of Prokaryotes (ICNP) for deposition of axenic and viable cultures as nomenclatural types has hindered the development of a nomenclature for uncultured and fastidious cultured prokaryotes (archaea and bacteria) and thus effective communication of microbial diversity 1–3. As-yet-uncultivated taxa account for ~85% of the phylogenetic diversity of prokaryotes 4 and named prokaryotes account for <0.2% of total species 5. By excluding the uncultured majority, a substantial portion of the tree of life is relegated to poorly ordered, ambiguous and often synonymous names or alphanumeric codes. Most of these alphanumeric codes are of limited mnemonic value because each letter or number contributes to a limited memory or digit span 6, whereas a taxonomic name can be remembered as a single word, especially if it is meaningful or familiar.
人们普遍认为，《国际原核生物命名法》（ICNP）要求将轴突培养物和活体培养物作为命名类型存放，这阻碍了未培养和快速培养的原核生物（古细菌和细菌）命名法的发展，从而阻碍了微生物多样性1-3的有效交流。尚未培养的分类群占原核生物系统发育多样性的~85%4，而命名的原核生物占总物种的<0.2%5。由于排除了未培养的大多数，生命之树的很大一部分就被归入了秩序不佳、含糊不清且经常是同义的名称或字母数字代码。大多数这些字母数字代码的记忆价值有限，因为每个字母或数字都有助于有限的记忆或数字跨度6，而分类学名称可以作为一个词来记忆，特别是如果它是有意义的或熟悉的。
To address this problem, Konstantinidis et al. 1 and subsequently Murray et al. 2 proposed two paths, which were endorsed by 121 authors and signatories from 22 countries and six continents 2. Initial ‘plan A’ was based on proposals that DNA sequences could serve as nomenclatural types and be incorporated into the existing ICNP infrastructure 7. However, the International Committee on Systematics of Prokaryotes (ICSP) rejected that proposal 8, thus triggering ‘plan B’, which called for a new code of nomenclature 2.
为了解决这个问题，Konstantinidis等人1和随后的Murray等人2提出了两条路径，得到了来自22个国家和六大洲的121位作者和签名者的赞同2。最初的 "计划A "是基于DNA序列可以作为命名类型并被纳入现有的ICNP基础设施的建议7。然而，国际原核生物系统学委员会（ICSP）拒绝了这一建议8，从而引发了 "B计划"，要求制定新的命名法则2。
Results
Recognizing the importance of further community engagement in the implementation of ‘plan B’, an ad hoc SeqCode Organizing Committee held a series of online workshops (https://www.isme-microbes.org/reports-sponsored-events) that garnered over 848 registrants from a broad range of microbiology disciplines, from 42 countries and 6 continents, as described in the Methods. Over 90% of participants reported that they would use a new code that accepts DNA sequences as types (https://www.isme-microbes.org/sites/default/files/reports/Path_forward_Naming_Uncultivated.pdf). Given strong participation and near-unanimous support, the SeqCode Organizing Committee deliberated carefully and acted on a variety of community recommendations as described in the Methods. The result was the writing of the SeqCode (formally The Code of Nomenclature of Prokaryotes Described from Sequence Data; Supplementary Information) and progress on systems to implement it. These actions initiated a process with the goal of SeqCode implementation through community support and action (Table 1), with this publication serving as a crucial but early step.
认识到在实施 "B计划 "中进一步的社区参与的重要性，一个特设的SeqCode组织委员会举行了一系列的在线研讨会（https://www.isme-microbes.org/reports-sponsored-events），获得了来自42个国家和6大洲广泛的微生物学学科的848名注册者，如方法中所述。超过90%的参与者表示他们会使用一个接受DNA序列作为类型的新代码（https://www.isme-microbes.org/sites/default/files/reports/Path_forward_Naming_Uncultivated.pdf）。鉴于强烈的参与和近乎一致的支持，SeqCode组织委员会仔细审议并对方法中描述的各种社区建议采取了行动。结果是编写了SeqCode（正式名称为The Code of Nomenclature of Prokaryotes Described from Sequence Data; Supplementary Information），并在系统上取得了进展，以实施它。这些行动启动了一个进程，目标是通过社区的支持和行动来实施SeqCode（表1），该出版物是一个关键但早期的步骤。
The SeqCode uses genome sequence data as common currency for typification of both cultivated and uncultivated microorganisms and follows rules similar to those of the ICNP for priority 9. In essence, the rules of both codes state that the earliest validly published name for a taxon in a particular position is the correct name (has priority), observing historical precedent and stabilizing nomenclature. The SeqCode also recognizes the priority of names validly published under the rules of the ICNP provided they do not violate the priority of names published under the SeqCode, thus minimizing divergence between the systems.
SeqCode使用基因组序列数据作为培养的和未培养的微生物的类型化的共同货币，并遵循与ICNP类似的优先级9的规则。从本质上讲，这两种编码的规则都指出，在某一特定位置的分类群的最早有效公布的名称是正确的名称（具有优先权），遵守历史先例并稳定命名法。SeqCode也承认根据ICNP的规则有效公布的名称的优先权，只要它们不违反根据SeqCode公布的名称的优先权，从而最大限度地减少系统之间的分歧。
Name validation through the SeqCode Registry.
Taxonomic names validated under the SeqCode will be captured in the SeqCode Registry, a registration web portal through which names and nomenclatural types are registered, validated and linked to metadata. The SeqCode Registry supports three main objectives: (1) the registration and evaluation of names to be proposed in accordance with the SeqCode; (2) the automated identification of Candidatus names currently used in the literature so that many of them may be normalized and standardized through validation under the SeqCode; and (3) the maintenance of a standardized, publicly available list of names validated under the SeqCode, along with key links and machine-readable metadata. While still under development, a draft version is currently available at https://seqco.de/. All of its public data are accessible and reusable through the Creative Commons Attribution 4.0 License, except where otherwise noted, and the underlying code is released as open source under the terms of the Massachusetts Institute of Technology License. When completed, the SeqCode Registry will provide user-friendly, graphical interface access to its resources as well as computer-readable entries in JavaScript Object Notation format for easy integration by third-party services. Examples of the system’s use are provided below and in the Supplementary Information for the registration of names under different publication circumstances.
根据SeqCode验证的分类学名称将被记录在SeqCode注册处，这是一个注册网络门户，通过它，名称和命名学类型被注册、验证并与元数据链接。SeqCode注册处支持三个主要目标：（1）注册和评估根据SeqCode提出的名称；（2）自动识别目前在文献中使用的暂定种名称，以便通过SeqCode的验证使其中的许多名称规范化和标准化；以及（3）维护一个标准化的、可公开使用的根据SeqCode验证的名称清单，以及关键链接和机器可读元数据。虽然仍在开发中，但目前在https://seqco.de/，有一个草案版本。它的所有公共数据都可以通过知识共享署名4.0许可进行访问和重用，除非另有说明，底层代码根据麻省理工学院许可条款作为开放源代码发布。当完成后，SeqCode登记处将提供用户友好的图形界面访问其资源，以及计算机可读的JavaScript Object Notation格式的条目，以便于第三方服务的整合。下面和补充资料中提供了该系统的使用实例，用于在不同的出版情况下的名称注册。
Currently, two different mechanisms to register and validate names are available through the SeqCode Registry (Fig. 1); a third mechanism may be possible in the future. In the best-case scenario, data will be entered and reviewed before publication through a preregistration process that takes place before initial submission or resubmission of a manuscript (Fig. 1, left or blue arrows, path 1). This route allows the SeqCode Registry to perform automated checks and provide curator input, both of which serve as resources to guide the user community. By providing these prechecks, path 1 serves two important roles as follows. (1) Automated checks and curator input during preregistration can prevent mistakes such as synonymy or problems with Latinization before names are published and thus prevent confusion resulting from name changes after publication. This process is thus somewhat similar to manual nomenclatural checks during peer review at the International Journal of Systematic and Evolutionary Microbiology (IJSEM). However, by automating the process as much as possible, the aim is to maximize speed and scalability and minimize human error. Similarly, data quality checks guide the user community by ensuring that genomic data serving as nomenclatural types are of sufficient quality. Currently genome quality and completeness data are entered by the user and checked against requirements and recommendations, although in the future these checks will be automated. (2) SeqCode identifier Uniform Resource Locators (URLs) generated during preregistration can be included in manuscripts that are submitted as the effective publication (the publication in which new names are proposed). These URLs allow peer reviewers and editors to access the preregistered names to ensure they have passed SeqCode checks. This process should improve and simplify peer review of new names and associated genomes because approval by the SeqCode Registry at the preregistration phase can provide confidence that the names are free of problems such as synonymy and poor Latinization and that the sequence data serving as the nomenclatural type are of sufficient quality. It should also be noted that minor orthographic variants of names that are validated under the SeqCode can be proposed by anyone at any time within the SeqCode Registry without publishing errata, which is also aimed at minimizing workload and confusion. Decisions on these orthographic variants will be refereed by curators. Under path 1, the completion of the registration process and thus date of priority of a name, is the date on which the Digital Object Identifier (DOI) is entered in the SeqCode Registry. This would normally be done by authors but, if SeqCode identifier URLs are used in the effective publication, then the DOI will be automatically captured by the SeqCode Registry once the manuscript is published, completing the registration process.
目前，通过SeqCode注册中心有两种不同的机制来注册和验证名称（图1）；未来可能会有第三种机制。在最好的情况下，数据将在发表前通过预注册程序进行输入和审查，该程序在首次提交或再次提交稿件前进行（图1，左边或蓝色箭头，路径1）。这条路径允许SeqCode注册处进行自动检查并提供馆长的意见，这两者都是指导用户社区的资源。通过提供这些预检查，路径1起到以下两个重要作用。(1) 预注册期间的自动检查和馆长输入可以在名称公布前防止同义词或拉丁化问题等错误，从而防止名称公布后的变化造成的混乱。因此，这个过程有点类似于《国际系统和进化微生物学杂志》（IJSEM）同行评审期间的人工名词检查。然而，通过尽可能地将这一过程自动化，目的是最大限度地提高速度和可扩展性，并尽量减少人为错误。同样，数据质量检查通过确保作为命名法类型的基因组数据具有足够的质量来指导用户群体。目前，基因组质量和完整性数据由用户输入，并根据要求和建议进行检查，尽管将来这些检查将是自动的。(2) 预注册期间产生的SeqCode标识符统一资源定位器（URLs）可以包含在作为有效出版物（提出新名称的出版物）提交的稿件中。这些URLs允许同行评审员和编辑访问预注册的名称，以确保它们通过SeqCode检查。这个过程应该改善和简化同行对新名称和相关基因组的审查，因为SeqCode注册处在预注册阶段的批准可以提供信心，即这些名称没有同义词和不良拉丁化等问题，作为命名类型的序列数据具有足够的质量。还应该注意的是，在SeqCode下验证的名称的小的正字法变体可以由任何人在SeqCode注册处的任何时候提出，而不需要公布勘误表，这也是为了尽量减少工作量和混淆。关于这些正字变体的决定将由策展人进行裁判。在路径1下，注册程序的完成以及名称的优先权日期是数字对象标识符（DOI）被输入SeqCode注册表的日期。这通常是由作者完成的，但是，如果SeqCode标识符URLs被用于有效的出版，那么一旦稿件出版，DOI将被SeqCode注册处自动捕获，完成注册过程。
The second mechanism (middle or orange arrows, path 2) allows registration and validation of names that are already published, including Candidatus names. The name and metadata are entered into the Registry and screened by the same automated checks implemented under path 1. Then, SeqCode curators review the names and acceptance of the entry completes registration and marks the date of priority of the name. At that point, the name is valid and the Candidatus designation can be removed. We note that path 2 is less desirable than path 1 because problems with nomenclature or genome quality would not be flagged and corrected before publication of the names. As such, names published in the literature may ultimately be emended or invalid under the SeqCode; however, as described above, the SeqCode and Registry are deliberately designed to be as flexible as possible to best serve the community. This is possible because the SeqCode Registry is simultaneously the registration and validation system and the official and up-to-date listing of names validated under the SeqCode. The third mechanism (right or pink arrows, path 3) would involve simultaneous peer review and Registry curator review as an integrated path to the validation of proposed names, similar to the integrated review system of the IJSEM, which serves names proposed under the ICNP.
第二个机制（中间或橙色箭头，路径2）允许注册和验证已经公布的名称，包括候选名称。名称和元数据被输入到注册中心，并由路径1下实施的相同的自动检查进行筛选。 然后，SeqCode馆长对名称进行审查，接受条目就完成了注册并标记了名称的优先日期。在这一点上，该名称是有效的，候选者的称号可以被移除。我们注意到，路径2不如路径1，因为命名法或基因组质量的问题在名称公布前不会被标记和纠正。因此，根据SeqCode，在文献中发表的名称最终可能被修改或无效；然而，如上所述，SeqCode和注册中心被有意设计为尽可能灵活，以最好地服务于社区。这是有可能的，因为SeqCode注册处同时是注册和验证系统以及根据SeqCode验证的官方和最新的名称列表。第三种机制（右边或粉红色箭头，路径3）将涉及到同时进行的同行评审和注册处的馆长评审，作为验证所提议的名称的综合路径，类似于IJSEM的综合评审系统，它为ICNP下提议的名称服务。
Application of the SeqCode before publication through path 1.
A concrete example of how this process might work is described below for Wolframiiraptor gerlachensis and related taxa and in the Supplementary Information. Briefly, several authors of the SeqCode (M.P., A.-L.R. and B.H.) recently completed a combined cultivation/ metagenomics study of a previously undescribed group of Archaea in the Genome Taxonomy Database (GTDB) family designated as NZ13-MGT within the phylum Thermoproteota 10, also previously discussed in the literature as ‘Aigarchaeota’ groups 4, 5 and 7 (refs. 11,12). The study initially focused on anaerobic enrichment cultures from sediments of Great Boiling Spring, Nevada, United States, containing a single member of the taxon, which was shown to require tungsten for growth on corn stover or a sugar mix under fermentative conditions. Fluorescence in situ hybridization combined with nanometre-scale secondary ion mass spectrometry was then used to confirm xylose as the preferred substrate. The taxon was represented by a single high-quality metagenome-assembled genome (MAG), although that MAG formed a >99.5% average nucleotide identity (ANI) cluster with MAGs of lower quality from separate samples of the same enrichment culture and sediments from which the enrichment culture was derived. To expand the study, 77 additional high-quality MAGs assigned to the GTDB family NZ13-MGT by GTDB-Tk 13 were assembled from metagenomes from other terrestrial and marine hydrothermal systems.
下面就Wolframiiraptor gerlachensis和相关类群以及补充资料中描述了这一过程可能工作的一个具体例子。简而言之，SeqCode的几位作者（M.P.、A.-L.R.和B.H.）最近完成了对基因组分类数据库（GTDB）家族中以前未描述的一组古细菌的联合培养/元基因组学研究，指定为热保护动物门10中的NZ13-MGT，以前在文献中也讨论为'Aigarchaeota' 4、5和7群（参考文献11,12）。该研究最初侧重于来自美国内华达州大沸泉沉积物的厌氧富集培养物，其中含有该类群的一个成员，该类群在发酵条件下需要钨在玉米秸秆或混合糖上生长。荧光原位杂交结合纳米级二次离子质谱法被用来确认木糖是首选底物。该分类群由一个高质量的元基因组组装基因组（MAG）代表，尽管该MAG与来自同一富集培养物和富集培养物所来自的沉积物的质量较低的MAG形成了一个>99.5%的平均核苷酸一致性（ANI）集群。为了扩大研究范围，从其他陆地和海洋热液系统的元基因组中组装了另外77个由GTDB-Tk 13分配给GTDB家族NZ13-MGT的高质量MAGs。
It is recommended in Table 2 that species or subspecies named under the SeqCode include more than one genome. This parallels the general recommendation under the ICNP to characterize multiple strains for proposals of new taxonomic names and is especially important for MAGs and single-amplified genomes (SAGs) because of challenges associated with accurately binning metagenomic data and the low completeness of most SAGs. Here, FastANI 14 was used to dereplicate the 78 high-quality MAGs into 11 >95% ANI clusters (species clusters14,15), and phylogenetic analyses of concatenated marker gene sets confirmed that each ANI cluster was monophyletic. In total, 9 of the species clusters were represented by 2–16 high-quality MAGs (after Bowers et al. 16) from metagenomes from different sampling dates and/or geothermal springs. Comparison of the multiple MAGs per species cluster allowed assessment of: (1) monophyly of each species by using a multiple marker gene set; (2) the true presence of multiple copies of normally single-copy, conserved marker genes and true absence of conserved marker genes used to assess genome completeness and contamination; (3) the existence of homologues of genes encoding important functions (in this case, tungstate transporters, tungstoenzymes and genes related to energy conservation); (4) shared gene content in general; and (5) similar genome content and size for the genomes within a species. These comparisons strengthened conclusions about the proposed mode of energy conservation, evolution of the organisms and their enzyme systems and allowed identification and rejection of problematic MAGs. We note that the MAGs from several GTDB species representatives were detected and analysed phylogenetically but most were not of sufficient quality to name under the SeqCode (Table 3).
表2中建议在SeqCode下命名的物种或亚种包括一个以上的基因组。这与ICNP的一般建议相类似，即为新的分类学名称的建议提供多个菌株的特征，这对MAG和单扩增基因组（SAGs）特别重要，因为与精确的元基因组数据相关的挑战和大多数SAGs的低完整度。在这里，FastANI 14被用来将78个高质量的MAG去复制成11个>95%的ANI集群（物种集群14,15），对连接的标记基因集进行系统发育分析，证实每个ANI集群是单系的。总的来说，9个物种集群由2-16个高质量的MAGs代表（根据Bowers等人的研究16），这些MAGs来自不同采样日期和/或地热泉的元基因组。对每个物种集群的多个MAGs进行比较，可以评估。(1)通过使用多个标记基因组来评估每个物种的单系性；(2)通常单拷贝的、保守的标记基因的真实存在，以及用于评估基因组完整性和污染的保守标记基因的真实缺乏。(3）存在编码重要功能的基因的同源物（在这种情况下，钨酸盐运输器、钨酶和与能量保存有关的基因）；（4）总体上共享基因内容；以及（5）一个物种内的基因组内容和大小相似。这些比较加强了关于拟议的能量保存模式、生物体的进化及其酶系统的结论，并允许识别和拒绝有问题的MAG。我们注意到，来自几个GTDB物种代表的MAGs被检测到并进行了系统发育分析，但大多数质量不够好，无法根据SeqCode命名（表3）。
In the end, type sequences meeting the data quality standards for the SeqCode (Table 3) were available for 11 species clusters, leading to proposals for 11 species names as well as their parent taxa under the SeqCode. Names were formed under the rules of Latin following general recommendations of Appendix 9 of the ICNP and other guidance 17 and were checked by the nomenclature expert A. Oren. In the future, they would be checked by curators within the SeqCode Registry. The process for preregistration is described in detail in the Supplementary Information section entitled ‘SeqCode preregistration’. Following preregistration, the effective publication 10 was submitted for peer review. The effective publication includes the following for each taxonomic name: (1) clear designation of the nomenclatural type; (2) designation of the taxonomic rank; and (3) etymology of the new name (Table 2). The nomenclature proposals were presented within protologues, examples of which for two taxonomic ranks are shown below. While protologues are not required under the SeqCode, they are useful for taxonomic descriptions because they compile the critical information in one place. Tables may also be used, examples of which are in the Supplementary Information. We note here that the SeqCode Registry produces protologues once preregistration is complete. Those protologues are useful for the scientific community as they can be linked via URLs within the effective publication, modified to serve as protologues in publications or accessed any time online within the Registry.
最后，有11个物种群的类型序列符合SeqCode的数据质量标准（表3），从而提出了11个物种名称以及它们在SeqCode下的母类群。名称是按照ICNP附录9的一般建议和其他指南17的拉丁语规则形成的，并由命名专家A. Oren检查。在未来，它们将由SeqCode注册处的馆员检查。预注册的过程在题为 "SeqCode预注册 "的补充信息部分有详细描述。在预注册之后，有效出版物10被提交给同行评审。有效出版物包括每个分类名的以下内容：（1）明确指定命名类型；（2）指定分类等级；（3）新名称的词源（表2）。命名建议是在原始资料中提出的，下面是两个分类等级的例子。虽然在SeqCode中不要求原生质谱，但它们对于分类学描述是有用的，因为它们将关键信息汇编在一个地方。表格也可以使用，其例子在补充资料中。我们在此注意到，一旦预注册完成，SeqCode注册处就会产生原始资料。这些图谱对科学界是有用的，因为它们可以通过有效出版物中的URL链接，修改后作为出版物中的图谱，或在注册中心内随时在线访问。
In the effective publication10, names are proposed for the previously undescribed family Wolframiiraptoraceae, which is the parent taxon for the previously undescribed genus Wolframiiraptor. This family name replaces the GTDB designation NZ13-MGT and is described in the Supplementary Information. The protologue below describes the previously undescribed genus Wolframiiraptor. Note that for a genus, the nomenclatural type is a species, as in the ICNP. Notes explaining the elements of the protologue as they pertain to the principles, rules and recommendations of the SeqCode are shown in brackets.
在有效出版物10中，为以前未描述的Wolframiiraptoraceae科提出了名称，该科是以前未描述的Wolframiiraptor属的母类群。这个科的名称取代了GTDB的命名NZ13-MGT，并在补充资料中进行了描述。下面的原始资料描述了以前未曾描述过的Wolframiiraptor属。请注意，对于一个属来说，命名类型是一个种，就像ICNP中一样。解释原生动物的元素的说明，因为它们与SeqCode的原则、规则和建议有关，在括号中显示。
Wolframiiraptor (Wolf.ra.mi.i.rap’tor N.L. neut. N. wolframium, tungsten; L. masc. n. raptor, snatcher or thief; N.L. masc. n. Wolframiiraptor, snatcher of tungsten). (This text designates the taxonomic rank (genus) and the etymology under SeqCode rules 26.4 and 26.5.)
Members of this genus have been identified from geothermal springs in the Great Basin and Yellowstone National Park, United States, and the Rehai Geothermal Field and the town of Dientan, Tengchong, China. Average amino acid identity (AAI) values among genomes representing separate species within the genus range between 81% and 90%. On the basis of ancestral state reconstruction analysis, likely losses of the genes encoding cytochrome c oxidase subunits, the aerobic carbon monoxide dehydrogenase large subunit and sulfide:quinone oxidoreductase (Sqr), indicate that members of this genus are probably strict anaerobes and are incapable of sulfide oxidation. Genomes of this genus encode a tupA subunit of the tungstate (Tup) ABC transporter and contain multiple genes encoding tungsten-dependent oxidoreductases, including three putative aldehyde:ferredoxin oxidoreductase (AOR)-like, one formaldehyde:ferredoxin oxidoreductase (FOR-like) and one glyceraldehyde-3-phosphate:ferredoxin oxidoreductase (GAPOR)-like proteins. This taxon is supported as a genus-level group by phylogenomics, AAI and relative evolutionary divergence. (This text includes a description of the taxon, following recommendation 26. Such text is recommended but not required under the SeqCode.)
该属的成员已从美国大盆地和黄石国家公园的地热泉以及中国腾冲的热海地热田和滇滩镇被鉴定出来。代表该属内独立物种的基因组之间的平均氨基酸一致性（AAI）值在81%和90%之间。在祖先状态重建分析的基础上，编码细胞色素c氧化酶亚单位、好氧一氧化碳脱氢酶大亚单位和硫化物：醌氧化还原酶（Sqr）的基因可能损失，表明该属成员可能是严格厌氧菌，不能进行硫化物氧化。该属的基因组编码钨酸盐（Tup）ABC转运器的tupA亚单位，并含有多个编码钨依赖性氧化还原酶的基因，包括三个推定的醛：递质氧化还原酶（AOR）-like，一个甲醛：递质氧化还原酶（FOR-like）和一个甘油醛-3-磷酸：递质氧化还原酶（GAPOR）-like蛋白。该分类群被系统发育组学、AAI和相对进化分歧支持为属级群。(该文本包括对该分类群的描述，遵循建议26。这样的文字是推荐的，但在SeqCode中不是必须的）。
The nomenclatural type of the genus is Wolframiraptor gerlachensisTs. (This text designates the nomenclatural type under rule 26.3. Note that the nomenclatural type for rank of genus is a species, typically the first legitimate species in the genus. These dates are clearly shown in the SeqCode Registry. Rule 26.3 embodies principle 5 and serves to unambiguously identify the taxon. See rule 16 and rule 22. Note that genus names do not need to have a standard suffix like family, order and above but they should avoid suffixes used for other taxonomic ranks to prevent confusion. See rule 15. Under chapter 4, the superscript Ts can be added when this species is a nomenclatural type and the type of the species is a DNA sequence.)
该属的命名类型为Wolframiraptor gerlachensisTs。(该文本指定了规则26.3下的命名类型。请注意，属的等级的命名类型是一个物种，通常是该属的第一个合法物种。这些日期在SeqCode注册表中明确显示。规则26.3体现了原则5，并起到了毫不含糊地识别分类群的作用。参见规则16和规则22。请注意，属名不需要像科、目及以上的标准后缀，但应避免使用其他分类学等级的后缀，以防止混淆。见第15条规则。在第4章下，当该物种为命名学类型，且该物种的类型为DNA序列时，可添加上标Ts)。
The protologue below describes the previously undescribed species W. gerlachensis. Note that for a species, the nomenclatural type is a DNA sequence, typically a genome assembly (Table 3).
下面的原始文献描述了以前未描述的物种W. gerlachensis。请注意，对于一个物种来说，命名类型是一个DNA序列，通常是一个基因组组合（表3）。
W. gerlachensisTs (ger.lach.en’sis N.L. masc. adj. gerlachensis, of Gerlach, the town where Great Boiling Spring is located in Nevada and where the samples containing this organism were obtained.) (This text designates the taxonomic rank (species) and the etymology under rules 26.4 and 26.5. Under chapter 4, the superscript Ts can be added to denote that this species is the type for the genus and its type is a DNA sequence.)
W. gerlachensisTs (ger.lach.en'sis N.L. masc. adj. gerlachensis, of Gerlach, the town where Great Boiling Spring is located in Nevada and where the sample containing this organism were obtained. ) (此文本指定了分类学等级（物种）和规则26.4和26.5下的词源。在第4章中，可以加上上标Ts，表示该物种是该属的类型，其类型是一个DNA序列）。
A MAG representing this species was recovered from metagenomic sequencing of a stable enrichment culture, established from an in situ corn stover enrichment from Great Boiling Spring, Nevada, United States. Enrichment and maintenance of this species within the mixed-culture community was optimal at an incubation temperature of 80 °C with lignocellulose or a mix of sugars as carbon sources under fermentative conditions, at circumneutral pH. This species was dependent on tungsten for growth; without tungsten added to the growth medium, the species was lost after several culture transfers. Additionally, transcripts for several tungstoenzymes conserved within the genus were present at high abundance during growth on corn stover, suggesting direct involvement of tungstoenzymes in fermentation of complex carbohydrates. Cells of this organism showed significant isotope enrichment when grown on isotopically labelled xylose-amended medium, with limited isotope enrichment during growth on medium amended with isotopically labelled amino acids, glucose, ribose or starch, indicating preferential assimilation of xylose. The type genome sequence of this species is 1,277,965 base pairs, consists of 27 contigs and has a G+C content of 52%. Completeness is estimated at 98.06% with 0.49% contamination, as estimated with CheckM. ANI comparisons between this genome and those of closely related species were below 86%, supporting the delineation of this taxon as unique and distinct from other species in the genus. (This text includes a description of the taxon, following recommendation 26. Such text is recommended but not required under the SeqCode.)
代表该物种的MAG是从稳定的富集培养物的元基因组测序中恢复的，该富集培养物来自美国内华达州大沸泉的原地玉米秸秆富集物。该物种在混合培养物群落中的富集和维持是最理想的，培养温度为80℃，在发酵条件下以木质纤维素或混合糖类为碳源，pH值为中性。该物种依赖于钨的生长；如果不在生长培养基中添加钨，该物种在几次培养转移后就会消失。此外，在玉米秸秆上生长期间，该属内保守的几种钨酶的转录本含量很高，这表明钨酶直接参与复杂碳水化合物的发酵。该生物体的细胞在同位素标记的木糖混合培养基上生长时表现出明显的同位素富集，而在同位素标记的氨基酸、葡萄糖、核糖或淀粉混合培养基上生长时同位素富集有限，表明优先吸收木糖。该物种的类型基因组序列为1,277,965个碱基对，由27个片段组成，G+C含量为52%。根据CheckM的估计，完整度为98.06%，污染度为0.49%。该基因组与密切相关物种的基因组之间的ANI比较低于86%，支持将该分类群划分为独特的、有别于该属其他物种的分类。(该文本包括对该分类群的描述，遵循建议26。这样的文字是推荐的，但在SeqCode中不是必须的）。
The genome Wger_A8Ts, available under the GenBank assembly accession number (GCA_021323375.2Ts), is the designated nomenclatural type for the species and was recovered from an enrichment culture, established from an in situ enrichment from Great Boiling Spring, Nevada, United States. (This text designates the nomenclatural type under rule 26.3. Note that the nomenclatural type for rank of species or subspecies is a DNA sequence, typically a genomic assembly. Rule 26.3 embodies principle 5 and serves to unambiguously identify the taxon. Metadata for this sequence is included in the GenBank entry. Under chapter 4, the superscript Ts can be added to denote that this genomic assembly is the nomenclatural type of the species.)
基因组Wger_A8Ts，可在GenBank汇编加入号（GCA_021323375.2Ts）下获得，是该物种的指定命名类型，从美国内华达州大沸泉的原位富集培养中获得。(该文本指定了规则26.3下的命名类型。请注意，物种或亚种等级的命名类型是一个DNA序列，通常是一个基因组组合。规则26.3体现了原则5，用于明确地识别分类群。该序列的元数据包含在GenBank条目中。在第4章下，可以加上上标Ts，表示这个基因组组合是该物种的命名类型）。
Application of the SeqCode through path 2 for already published names, including Candidatus names.
The SeqCode also enables registration of previously published names, such as Candidatus names that conform to its rules. Candidatus is a provisional status lacking priority and standing in nomenclature and is relegated to the non-legislative appendix 11 of the ICNP. It was developed for organisms for which ‘more than a mere nucleic acid sequence is available’ 18. Since its inception, visualization of the taxon in a natural sample has been recommended 18,19 but this is rarely implemented. It has been argued that Candidatus names should be granted priority under the ICNP 20; however, this proposal was also rejected by the ICSP8. As a result, many Candidatus names may prove to be ephemeral. Validation of these names under the SeqCode will give them priority and the Candidatus designation can be dropped (Fig. 1, path 2). These names are of special importance because a catalogue of over 1,000 Candidatus names has been compiled21 and recently 917 Candidatus names were published as part of a study of the chicken fecal microbiome 22. The SeqCode was deliberately developed with very few requirements in the effective publication to allow these and other names to be validated (Table 2). In fact, any Candidatus name in the literature can be validated under path 2 as long as the taxa are named in the effective publication and a genome meets data quality standards required of the nomenclatural type (see Supplementary Information for an example). This is possible because critical data, including designation of the nomenclatural type, can be captured in the SeqCode Registry during validation. We plan to initiate this effort, which will be done in collaboration with the community. However, the authors of Candidatus taxa themselves are welcome to validate names that are already effectively published and meet the sequence quality standards. Because the SeqCode Registry is already operational, this could begin immediately. The basic procedure to validate large numbers of Candidatus names is: (1) assess genome sequences assigned to each Candidatus taxon for data quality; (2) where a sequence is of sufficient quality to serve as a type, contact authors to check autofilled templates generated by the SeqCode Registry and complete missing data fields; (3) complete validation in the SeqCode Registry; and (4) publish a paper with collaborators from the community announcing validation of the names. This project would result in validation of Candidatus names, centralize names and metadata for these taxa, serve an important outreach function to educate the community about the principles and implementation of the SeqCode and provide a conduit for community feedback.
通过路径2对已经发布的名称(包括Candidatus名称)应用SeqCode。
SeqCode还支持注册以前发布的名字，如符合其规则的Candidatus名字。候选人是一种临时地位，在命名法上缺乏优先和地位，被归入ICNP的非立法附件11。它是为“不仅仅是一个核酸序列”的生物开发的18。从一开始，自然样本中的分类单元可视化就被推荐18,19，但这很少实现。有人争辩说，在ICNP第20项下应给予候选人姓名优先;然而，这一提议也被ICSP8否决了。结果，许多候选人的名字可能被证明是短暂的。根据SeqCode对这些名称进行验证将优先考虑它们，可删除候选菌属的名称(图1，路径2)。这些名称特别重要，因为已经编制了1000多个候选菌属名称的目录21，最近发表了917个候选菌属名称，作为鸡粪便微生物组研究的一部分22。SeqCode是有意开发的，在有效的出版物中很少要求，以允许这些名称和其他名称进行验证(表2)。事实上，文献中的任何Candidatus名称都可以在路径2下进行验证，只要该类群在有效的出版物中命名，并且基因组满足命名自然类型所需的数据质量标准(参见补充信息中的示例)。这是可能的，因为关键数据，包括命名自然类型的指定，可以在验证期间在SeqCode注册表中捕获。我们计划启动这项工作，将与社区合作完成。但是，我们欢迎Candidatus taxa的作者自己验证已经有效发表并满足序列质量标准的名称。因为SeqCode注册中心已经开始运作了，这可以立即开始。验证大量念珠菌名称的基本程序是:(1)评估分配给每个念珠菌分类单元的基因组序列的数据质量;(2)如果序列有足够的质量作为类型，联系作者检查SeqCode注册表生成的自动填充模板，并完成缺失的数据字段;(3)在SeqCode注册表中完成验证;并且(4)与来自社区的合作者发表一篇论文，宣布对名称的验证。该项目将验证Candidatus名称，集中这些分类的名称和元数据，提供一个重要的扩展功能，教育社区关于SeqCode的原则和实现，并为社区提供一个反馈渠道。
Data standards. Table 3 summarizes the SeqCode Organizing Committee’s recommendations on minimal standards for data and reporting requirements. These standards were chosen to enable the accurate delineation of species 1,23 and incorporated many of the recommendations of the Genomic Standards Consortium 16,24. The SeqCode Organizing Committee discussed the criteria for the original publication of new names using DNA sequences as type at length. The majority felt that the publication requirements should enable the naming of all scientifically well-supported names. For instance, it is not necessary to require the genome accession number in the publication because it will be readily available in the SeqCode Registry. This will allow post hoc registration of Candidatus names where the type genomes may not have been explicitly identified. However, it is highly recommended that publications in the future contain the accession number. Similarly, whether the 16S ribosomal RNA sequence should be required or recommended was discussed. The majority opinion was that the 16S rRNA sequence is not necessary for the diagnosis of species and it should not be required. Nevertheless, the entire Committee recognized that the modern taxonomy of prokaryotes is based on the phylogeny of the 16S rRNA and inclusion of an accurate 16S rRNA sequence provides access to this taxonomy as well as an enormous database of environmental ribotypes. For those reasons, the inclusion of an accurate 16S rRNA sequence is highly recommended, although we recognize that rRNA genes can be difficult to assemble and bin accurately because they are often present in multiple copies and do not conform to nucleotide word frequency patterns of coding sequences. While outside the code itself, these standards are in an appendix to the SeqCode and should generally be applied unless there is a strong justification for validating names with lower quality genomes as types (for example, medium-quality genomes with large datasets on physiology, ecology or evolution). We expect that these standards will evolve to keep pace with community feedback and methodological improvements.
数据标准。表3总结了SeqCode组委会关于数据和报告要求的最低标准的建议。选择这些标准是为了准确描述物种1,23，并纳入了基因组标准联盟的许多建议16,24。SeqCode组织委员会详细讨论了使用DNA序列作为类型的新名称的原始发布标准。大多数人认为，发表要求应能够命名所有科学上得到充分支持的名称。例如，没有必要在出版物中要求基因组登录号，因为它可以在SeqCode Registry中随时获得。这将允许在尚未明确识别类型基因组的情况下对候选菌名进行临时注册。但是，强烈建议今后的出版物应载有登记号。同样，讨论了是否需要或推荐16S核糖体RNA序列。大多数的意见是，16S rRNA序列不是物种诊断的必要条件，不应该被要求。尽管如此，整个委员会都认识到，原核生物的现代分类学是基于16S rRNA的系统发育，包含一个精确的16S rRNA序列提供了该分类学以及一个巨大的环境核型数据库的访问。由于这些原因，我们强烈建议包含一个精确的16S rRNA序列，尽管我们认识到rRNA基因可能很难组装和准确bin，因为它们经常出现在多个副本中，不符合编码序列的核苷酸词频模式。虽然在代码本身之外，这些标准是SeqCode的附录，但通常应该应用这些标准，除非有强有力的理由验证具有较低质量基因组的名称作为类型(例如，具有生理学、生态学或进化方面的大型数据集的中等质量基因组)。我们期望这些标准将随着社区反馈和方法改进而不断发展。
While the SeqCode itself is necessarily comprehensive, we have also developed resources to guide the community, including a glossary and examples of the types of data for naming (Supplementary Information).
虽然SeqCode本身必然是全面的，但我们也开发了指导社区的资源，包括一个词汇表和用于命名的数据类型的例子（补充资料）。
Discussion
One goal of the SeqCode is to reverse the trend wherein taxonomic names are published in the primary literature but not validly published. Although the community is free to publish taxonomic names that do not comply with codes of nomenclature, we argue that codes of nomenclature and taxonomic frameworks serve the greater community by promoting objectivity, best practices, communication and data interoperability. However, the unique restrictions of the ICNP regarding viable and accessible type strains have alienated many microbiologists and engendered a sense of normalcy in publishing names outside of the regulation of the ICNP. The SeqCode addresses this problem by providing an efficient and user-friendly resource that serves the common interests of the wider research community. The SeqCode embraces findability, accessibility, interoperability and reusability (FAIR) principles and the Registry was developed with interoperable data structures to promote sharing of SeqCode names across global biodiversity inventories within microbiology and the broader biology research communities (for example, NCBI 25, GTDB26, MiGA27, LPSN28, Catalogue of Life29 and Global Biodiversity Information Facility 30).
SeqCode的一个目标是扭转分类学名称在主要文献中发表但没有有效发表的趋势。尽管社区可以自由发表不符合命名法则的分类学名称，但我们认为命名法则和分类学框架通过促进客观性、最佳实践、交流和数据互操作性来为更大的社区服务。然而，ICNP对可行的和可获得的类型菌株的独特限制疏远了许多微生物学家，并使他们对在ICNP规定之外发表名称产生了正常感。SeqCode通过提供一个有效的和用户友好的资源来解决这个问题，以满足更广泛的研究团体的共同利益。SeqCode包含了可查找性、可访问性、互操作性和可重用性（FAIR）的原则，注册表是用可互操作的数据结构开发的，以促进SeqCode名称在微生物学和更广泛的生物学研究界的全球生物多样性目录中的共享（例如，NCBI 25、GTDB26、MiGA27、LPSN28、生命目录29和全球生物多样性信息机构30）。
In closing, we emphasize a few important points. First, the SeqCode is not intended to discourage cultivation. Cultivation of mixed or pure cultures enables testing of properties predicted from genomes under controlled conditions. Furthermore, investigators are strongly encouraged to deposit strains to culture collections to improve strain availability, enable assessment of reproducibility of phenotypic traits, provide resources for biochemistry and biotechnology and promote international cooperation. Second, like all other codes of nomenclature, the SeqCode does not provide rules or recommendations on the delineation of taxa. Existing and improving approaches and data structures are available for that purpose 26,27 and proposals for description of previously undescribed taxa must be settled through peer review. Finally, this is the first version of the SeqCode and we hope that it will evolve as the community engages in further development of the system. Because of our desire to serve the broad microbiology research community, we will engage the community to gather feedback and develop bylaws for SeqCode administration. This code is driven by bottom-up desires to improve communication across the microbial sciences. Thus, we view this ‘SeqCode v.1.0’ as a necessary first step toward a unified system of nomenclature to communicate the full diversity of prokaryotes and we will cooperate with the community toward the realization of this vision.
最后，我们强调几个重要的问题。首先，SeqCode的目的不是要阻止培养。混合或纯培养物的培养可以在受控条件下测试从基因组预测的特性。此外，我们强烈鼓励研究者将菌株存入培养物中，以提高菌株的可用性，使表型性状的可重复性得到评估，为生物化学和生物技术提供资源并促进国际合作。第二，像所有其他的命名法则一样，SeqCode并没有提供关于分类群划分的规则或建议。现有的和正在改进的方法和数据结构可用于这一目的26,27，关于描述以前未描述的分类群的建议必须通过同行评审来解决。最后，这是SeqCode的第一个版本，我们希望它能随着社区对系统的进一步开发而不断发展。由于我们希望为广大的微生物学研究界服务，我们将让社区参与进来，收集反馈意见并制定SeqCode的管理细则。这个代码是由自下而上的愿望驱动的，以改善整个微生物科学的交流。因此，我们认为这个 "SeqCode v.1.0 "是迈向一个统一的命名系统的必要的第一步，以沟通原核生物的全部多样性，我们将与社区合作以实现这个愿景。
Methods
Public outreach and consensus building. Over the course of the project, considerable effort was spent to communicate with the research community to build consensus on the path forward in microbial systematics. To obtain consensus, four major workshop series were held. The first outreach effort was a three-part web workshop series entitled ‘Microbial systematics for the next decade’, which was held in October 2018. The workshops were intended to engage a diversity of stakeholders in discussions about key issues that affect the landscape of microbial systematics. Each workshop included two 15 min presentations, followed by 15 min of discussion in breakout groups of four to five participants and 15 min of reporting by the breakout groups. Postworkshop questionnaires captured responses to general questions about the future direction of prokaryotic systematics. To maximize productivity, all participants were given reading assignments and asked to develop opinions and ideas for discussions before each seminar. To ensure broad viewpoints, speakers included experts in microbial systematics and from the related fields of plant and protozoal taxonomy. The three workshop themes were as follows. (1) What’s in a name? The importance (and limitations) of formal codes of taxonomic nomenclature. (2) Candidatus status: current system and proposed modifications. (3) Efforts to scale and systematize taxonomy in the twenty-first century. Thirty-nine participants from four continents contributed to this first workshop series, which provided a strong foundation for the more decisive and more inclusive workshops to come.
方法
公共宣传和建立共识。在项目实施过程中，我们花了大量的精力与研究界沟通，以便在微生物系统学的发展道路上建立共识。为了获得共识，我们举办了四个主要的系列研讨会。第一个推广工作是由三部分组成的网络系列研讨会，题为 "未来十年的微生物系统学"，于2018年10月举行。这些研讨会的目的是让不同的利益相关者参与讨论影响微生物系统学前景的关键问题。每个研讨会包括两个15分钟的演讲，然后是15分钟的四至五人分组讨论，以及15分钟的分组报告。研讨会后的调查问卷收集了对原核生物系统学未来发展方向的一般问题的回答。为了最大限度地提高工作效率，所有参与者都有阅读任务，并被要求在每次研讨会前提出讨论的意见和想法。为了确保广泛的观点，发言者包括微生物系统学的专家和来自植物和原生动物分类学相关领域的专家。三个研讨会的主题如下。(1) 名字有什么用？正式的分类学命名代码的重要性（和局限性）。(2) 候选状态：目前的系统和拟议的修改。(3) 21世纪分类学的规模化和系统化的努力。来自四大洲的39位与会者为这第一个系列研讨会做出了贡献，这为以后更有决定性和更有包容性的研讨会奠定了坚实的基础。
This initial workshop was followed by two in-person workshops. At the first, 28–31 October 2018, in Hood River, Oregon, United States, 24 participants used poll responses from the first set of workshops to narrow in on major issues in microbial systematics and possible solutions. Following plenary presentations and discussions, breakout groups focused on: (1) microbial systematics within a broader perspective; (2) current proposals on the nomenclature of SAGs and MAGs (DNA as a category of nomenclatural type, granting priority to Candidatus names, erecting a parallel system of nomenclature or no action); (3) the genomic tree of life; and (4) microbial nomenclature—progressivism versus conservatism. This workshop, in addition to the initial online series led to a consensus statement 2 proposing two possible paths forward, ‘plan A’, amendment of the ICNP to allow DNA sequence data to serve as a category of nomenclatural type or, pending failure of ‘plan A’, the alternative ‘plan B’, entailing development of a new code of nomenclature based on DNA sequence data as the unifying category of nomenclatural type for cultivated and uncultivated prokaryotes.
在这个最初的研讨会之后，又举行了两次面对面的研讨会。在2018年10月28日至31日在美国俄勒冈州胡德河举行的第一次研讨会上，24名与会者利用第一组研讨会的民意调查结果，缩小了微生物系统学的主要问题和可能的解决方案。在全体发言和讨论之后，分组讨论的重点是：（1）更广泛视角下的微生物系统学；（2）目前关于SAG和MAG命名的建议（DNA作为命名类型的一个类别，给予Candidatus名称优先权，建立一个平行的命名系统或不采取行动）；（3）生命的基因组树；以及（4）微生物命名-进步主义与保守主义。这次研讨会，除了最初的在线系列之外，还产生了一份共识声明2，提出了两条可能的发展道路："A计划"，即修正ICNP，允许DNA序列数据作为命名类型的一个类别；或者，在 "A计划 "失败之前，另一个 "B计划"，即开发一个基于DNA序列数据的新命名法，作为栽培和非栽培原核生物的统一命名类别。
The second in-person workshop was held on 8–9 April 2019, in Walnut Creek, California, United States with 27 participants. It focused on scalability and database development related to microbial nomenclature under the two possible plans resulting from the previous workshops. The location and timing of this workshop was coordinated with the US Department of Energy’s Joint Genome Institute (JGI) ‘Genomics of energy and environment meeting’ to take advantage of strong database and bioinformatics expertise available at the JGI and among attendees. Major questions that were a focus of the workshop were as follows. (1) What are the most pressing taxonomic database issues that can help launch microbial taxonomy into the next decade? (2) Is there a way to reach a consensus for a common nomenclature or taxonomy that is treated equally or cross-referenced faithfully in multiple databases? (3) Is there way to facilitate data-rich systematics in the future? This workshop, combined with the subsequent negative vote on previous proposals to amend the ICNP to include DNA sequence data as an alternative category of nomenclatural type 8 (‘plan A’), finally triggered the writing of the first draft the SeqCode (‘plan B’).
第二次面授研讨会于2019年4月8-9日在美国加州核桃溪举行，有27人参加。它的重点是在前几次研讨会产生的两个可能的计划下，与微生物命名法有关的可扩展性和数据库开发。本次研讨会的地点和时间与美国能源部联合基因组研究所（JGI）的 "能源和环境的基因组学会议 "相协调，以利用JGI和与会者中强大的数据库和生物信息学专业知识。作为研讨会的重点，主要问题如下。(1) 哪些是最紧迫的分类数据库问题，可以帮助将微生物分类学推向下一个十年？(2) 是否有办法达成共识，使共同的命名法或分类法在多个数据库中被平等对待或忠实地交叉引用？(3) 是否有办法在未来促进数据丰富的系统学？这次研讨会，再加上随后对以前关于修改ICNP以包括DNA序列数据作为命名法类型8的替代类别的建议的反对投票（"计划A"），最终引发了SeqCode第一稿的撰写（"计划B"）。
In lieu of a session and subsequent in-person workshop at the ISME18 conference originally scheduled in Cape Town in 2020, which was cancelled due to the COVID19 pandemic, a last series of online workshops was held in February 2021 (SeqCode Workshops, ISME (https://www.isme-microbes.org)). These workshops centred around the first complete draft of the SeqCode, which was shared with all participants before the workshop to drive critical review of the document and its underlying principles. This final series comprised two workshops, each of which had two sessions, one timed for the convenience of participants in Europe, Africa and the Americas and one timed for participants from Asia and Oceania. It was cosponsored by the International Society of Microbial Ecology as part of a developing partnership for administration of the SeqCode. The first workshop was entitled the ‘Path forward for naming the uncultivated’ and included six prerecorded lectures introducing the various topics and discussion and breakout sessions. The second workshop was entitled ‘Path forward to implementations and adoption of the SeqCode’ and included 13 presentations on eukaryotic systematics, databases and related topics. The workshops were highly anticipated and attended by a broad group of microbiologists from all over the world, including 848 registrants and at least 575 attendees from 42 countries on 6 continents. Participants identified with a broad range of subdisciplines within microbiology, including microbial ecologists and systematists. These two communities do not often interact and the strong participation of both groups was a strength of the workshops. A total of 26% of respondents identified as graduate students. We note that training for microbial systematics is almost non-existent, despite the large number of scientists using taxonomic names. Thus, career development was a significant outcome of these workshops. A total of 95% of respondents said the content and outcomes of the workshops will be useful to them and/or their field and 90% said they are likely to use SeqCode in the future. Given the strong participation and near-unanimous support for SeqCode, the SeqCode committee incorporated feedback from breakout groups that tackled key questions about the SeqCode, which were carefully considered and acted on by the SeqCode Committee, as summarized in Supplementary Table 1.
在原定于2020年在开普敦举行的ISME18会议上，由于COVID19大流行而取消了一次会议和随后的现场研讨会，最后一系列在线研讨会于2021年2月举行（SeqCode研讨会，ISME（https://www.isme-microbes.org））。这些研讨会围绕着SeqCode的第一份完整的草案，在研讨会前与所有参与者分享，以推动对该文件及其基本原则的批判性审查。最后一个系列包括两个研讨会，每个都有两个会议，一个是为方便欧洲、非洲和美洲的参与者而安排的，一个是为亚洲和大洋洲的参与者安排的。它是由国际微生物生态学会共同主办的，作为SeqCode管理的发展伙伴关系的一部分。第一次研讨会的主题是 "为未种植的植物命名的前进之路"，包括六个预先录制的讲座，介绍各种主题和讨论及分组会议。第二次研讨会的主题是 "SeqCode的实施和采用之路"，包括13个关于真核生物系统学、数据库和相关主题的演讲。这些研讨会备受期待，来自世界各地的广大微生物学家参加了会议，包括来自6大洲42个国家的848名注册者和至少575名与会者。与会者认同微生物学中广泛的分支学科，包括微生物生态学家和系统论者。这两个群体并不经常互动，两个群体的大力参与是研讨会的一个优势。共有26%的受访者认为自己是研究生。我们注意到，尽管有大量的科学家使用分类学名称，但微生物系统学的培训几乎是不存在的。因此，职业发展是这些研讨会的一个重要成果。共有95%的受访者表示研讨会的内容和成果对他们和/或他们的领域是有用的，90%的受访者表示他们将来可能会使用SeqCode。鉴于SeqCode的强烈参与和近乎一致的支持，SeqCode委员会纳入了分组的反馈，这些分组解决了关于SeqCode的关键问题，SeqCode委员会仔细考虑并采取了行动，如补充表1所总结的。