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

微生物世界极其多样化，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非常具有挑战性。细菌和古细菌的主要分类系统依赖于对单物种培养物的仔细描述，这些描述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分子研究，包括单细胞基因组学和宏基因组学，这些研究可以在不依赖实验室培养的情况下深入了解原核生物。与此同时，在基因组学时代重构微生物系统学方面也取得了进展，原则上这可以扩展分类结构以包括未培养的生物体。然而，未培养的微生物在命名法中没有地位，并且目前没有系统来命名未培养的生物体。该项目将在大约 18 个月的时间内召开 3 次会议，召集一组世界专家来制定一项有凝聚力的计划，将未培养的原核生物整合到系统学框架中。最终，将制定一项可行的计划来修改管理微生物命名法的代码，并发布未来十年原核系统学的蓝图。该项目的结果将为所有原核生物的命名系统提供强有力的计划，从而影响所有微生物学家，包括微生物生态学家和临床医生。该项目还将吸引 STEM 领域代表性不足的群体参与，并为早期职业科学家提供领导机会。该项目将涉及三个研讨会。研讨会 1 将邀请原核生物和真核生物系统学和基因组学专家参与，并将考虑几项现有提案，并将未培养的微生物整合到命名系统中，包括呼吁修改候选状态指南、呼吁将基因组材料用作分类学提案的类型材料，以及使用基因组数据重新校准所有微生物系统学的更积极的提案。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，例如具有命名法的原核生物名称列表、微生物基因组图谱、数字原语数据库和基因组分类数据库，目标是更好地集成和开发系统，将不同的数据集直接链接到分类数据。第三次研讨会将聘请一个小型工作组来汇总两次研讨会的调查结果，综合建议，并就如何继续和实施这些建议提供建议。研讨会的成果将是一个将未培养的生物体纳入命名系统的可行计划，以及指导未来十年微生物系统学的路线图。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力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.