澳大利亚昆士兰大学Donovan H. Parks研究团队探究了细菌和古生菌域到物种的分类学。相关论文发表在2020年4月27日的《自然—生物技术》上。

研究人员通过使用公认的平均核苷酸同一标准来设定物种界限，解决了许多未知基因簇缺少种名这一局限，并提供了涵盖所有公共可获得细菌和古细菌基因组的物种簇。

与之前的平均核苷酸同一性研究不同，该研究选择了一个代表性的基因组作为定义每个物种有效命名法的“类型”。在已知的24706个物种簇中，有8792个是已有报道其命名。研究人员为剩余的15914个物种簇分配了占位符名称，以为越来越多的未研究物种的基因组提供名称。

该研究为细菌和古细菌基因组提供了一个完整的域到物种分类学框架，这将促进对未知物种的研究并有利于科学成果的交流。

据了解，基因组分类数据库是系统发育的、基于基因组的分类法，可为大约15万个细菌和古细菌基因组提供从域到属的等级归一化分类。但是，基因组分类数据库中大约有40％的基因组缺少物种名称。

附：英文原文

Title: A complete domain-to-species taxonomy for Bacteria and Archaea

Author: Donovan H. Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J. Mussig, Philip Hugenholtz

Issue&Volume: 2020-04-27

Abstract: The Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus. However, almost 40% of the genomes in the Genome Taxonomy Database lack a species name. We address this limitation by using commonly accepted average nucleotide identity criteria to set bounds on species and propose species clusters that encompass all publicly available bacterial and archaeal genomes. Unlike previous average nucleotide identity studies, we chose a single representative genome to serve as the effective nomenclatural ‘type’ defining each species. Of the 24,706 proposed species clusters, 8,792 are based on published names. We assigned placeholder names to the remaining 15,914 species clusters to provide names to the growing number of genomes from uncultivated species. This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results.

DOI: 10.1038/s41587-020-0501-8

Source: https://www.nature.com/articles/s41587-020-0501-8