Workshops: Development of a roadmap for the next decade of microbial systematics research

微生物世界的多样性令人难以置信，在所有生物地球化学循环中发挥着关键作用。然而，描述和分类微生物的过程仍然是非常具有挑战性的。细菌和古细菌的主要分类系统依赖于对单一物种培养的仔细描述，这源于深深扎根于微生物学历史的传统。近几十年来，微生物学家越来越依赖于分子研究，包括单细胞基因组学和宏基因组学，它们提供了对原核生物的深入了解，而不依赖于实验室培养。与此同时，在基因组学时代，微生物系统学的重构也取得了进展，这在原则上可以使分类结构的扩展包括未培养的生物。然而，未培养的微生物在命名法中没有地位，目前也没有系统来命名未培养的微生物。该项目将在大约18个月的时间里召开三次会议，召集一批世界专家制定一个有凝聚力的计划，将未培育的原核生物整合到一个系统框架中。最终，将制定一项可行的计划，修改管理微生物命名法的代码，并发布未来十年原核生物系统学的蓝图。该项目的结果将影响所有微生物学家，包括微生物生态学家和临床医生，为所有原核生物的命名系统提供一个强有力的计划。该项目还将吸引在STEM领域代表性不足的群体，并为早期职业科学家提供领导机会。该项目将包括三个讲习班。研讨会1将邀请原核生物和真核生物的系统学和基因组学专家，并将考虑几个现有的建议，并将未培养的微生物整合到一个命名系统中，包括呼吁修改候选物种状态指南，呼吁将基因组材料用作分类建议的类型材料，以及更积极的建议，即使用基因组数据重新校准所有微生物系统学。研讨会还将审查用于分类学目的的基因组数据标准化的两项不同提案。研讨会2将讨论与微生物分类学相关的现有数据库，如命名法中有地位的原核生物名称列表，微生物基因组图谱，数字原始数据库和基因组分类学数据库，目的是更好地整合和开发系统，将不同的数据集直接链接到分类学数据。第3次讲习班将由一个小型工作组负责汇集两次讲习班的成果，综合各项建议，并就如何进行和执行这些建议提出建议。研讨会的结果将是一个可操作的计划，将未培育的生物纳入一个命名系统，并制定一个路线图，指导下一个十年的微生物系统。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The microbial world is incredibly diverse and plays critical roles in all biogeochemical cycles. However, the process describing and classifying microorganisms continues to be very challenging. The dominant taxonomic system for Bacteria and Archaea relies on the careful description of single-species cultures, stemming from traditions rooted deeply in the history of microbiology. In recent decades, microbiologists have increasingly relied on molecular investigations, including single-cell genomics and metagenomics, which provide insight into prokaryotes without reliance on cultivation in the laboratory. In parallel, progress has been made to reframe microbial systematics in the genomics age, which in principle could enable expansion of the taxonomic structure to include uncultivated organisms. However, uncultivated microorganisms have no status within the code of nomenclature and currently there is no system to name uncultivated organisms. This project will involve three meetings over the course of ~18 months to convene a group of world experts to develop a cohesive plan to integrate uncultivated prokaryotes into a systematics framework. Ultimately, an actionable plan will be created to modify the code governing microbial nomenclature and to publish a blueprint for prokaryotic systematics for the next decade. The results of this project will impact all microbiologists, including microbial ecologists and clinicians, by providing a robust plan for a system of nomenclature for all prokaryotes. The project will also engage groups that are underrepresented in STEM fields and provide leadership opportunities for early-career scientists. The project will involve three workshops. Workshop 1 will engage experts on the systematics and genomics of prokaryotes and eukaryotes, and will consider several existing proposals and to integrate uncultivated microorganisms into a system of nomenclature, including a call to modify guidelines for Candidatus status, a call to enable genomic material to be used as type material for taxonomic proposals, and more aggressive proposals to recalibrate all of microbial systematics using genomic data. The workshop will also review two different proposals for the standardization of genomic data for taxonomic purposes. Workshop 2 will discuss existing databases that are relevant to microbial taxonomy such as the List of Prokaryotic Names with Standing in Nomenclature, the Microbial Genomes Atlas, the Digital Protologue Database, and the Genome Taxonomy Database with a goal of better integration and development of systems to link diverse datasets directly to taxonomic data. Workshop 3 will engage a small working group to pull together the findings of the two workshops, synthesize recommendations and provide recommendations on how to proceed and implement these recommendations. The outcome of the workshops will be an actionable plan to integrate uncultivated organisms into a system of nomenclature and a roadmap to guide microbial systematics for the next decade.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.