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，并在所有生物地球化学循环中发挥关键作用。然而，描述和分类微生物的过程仍然非常具有挑战性。细菌和古生菌的主要分类系统依赖于对单一物种培养的仔细描述，这些培养源于深深植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元基因组学，这些研究提供了对原核生物的洞察，而不依赖于实验室培养。与此同时，在基因组学时代在重新构建微生物系统学方面也取得了进展，原则上可以扩大分类结构，将未耕种的生物体包括在内。然而，未培养的微生物在命名法中没有地位，目前还没有为未培养的生物命名的系统。该项目将在大约18个月的时间里举行三次会议，召集一个世界专家小组，制定一项将未种植的原核生物纳入系统学框架的统一计划。最终，将制定一项可行的计划，以修改管理微生物命名的代码，并公布下一个十年的原核生物系统学蓝图。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，并为职业生涯早期的科学家提供领导机会。该项目将包括三个讲习班。讲习班1将邀请原核生物和真核生物的分类学和基因组学方面的专家参加，并将审议若干现有提案，将未耕作的微生物纳入命名系统，包括呼吁修改假丝酵母地位准则，呼吁将基因组材料用作分类提案的模式材料，以及更激进的提案，利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目的的基因组数据标准化的两个不同提案。讲习班2将讨论与微生物分类学有关的现有数据库，例如具有命名标准的原核生物名录、微生物基因组图谱、数字原型数据库和基因组分类数据库，目的是更好地整合和开发系统，将不同的数据集直接与分类数据联系起来。讲习班3将聘请一个小型工作组，汇集两个讲习班的调查结果，综合建议，并就如何推进和执行这些建议提出建议。研讨会的成果将是一项可操作的计划，将未种植的有机体整合到命名系统中，并制定路线图，指导未来十年的微生物系统学。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.