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走出阴影——该科分类法的解析

Out From the Shadows - Resolution of the Taxonomy of the Family .

作者信息

Bowman John P

机构信息

Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia.

出版信息

Front Microbiol. 2020 May 5;11:795. doi: 10.3389/fmicb.2020.00795. eCollection 2020.

Abstract

The family for many years has been a poorly defined taxonomic group within the order , phylum . Members of the , apparently consisting of multiple-family level clades, have been mostly but not exclusively detected in saline ecosystems. The problems with the taxonomy of this group have stemmed from inadequate resolution of taxonomic groups using 16S rRNA gene sequences, sparse numbers of cultivated taxa, and limited phenotypic distinctiveness. The Genome Tiaxonomc Database (GTDB), which is based on normalized taxonomic ranks includes as containing the genera and . This is at odds with the official taxonomy that places these genera in the family . The other affiliated species have even more uncertain taxonomic positions including . To clarify the taxonomy of , genomes were generated for all type strains of the family lacking such data. The GTDB-toolkit (GTDB-tk) was used to place taxa in the GTDB, which revealed novelty at the family level for some of these type strains. 16S rRNA gene sequences and concatenated protein sequences were used to further evaluate the taxonomy of the order . From the data, the GTDB enabled successful clarification of the taxonomy of the family . A number of placeholder families were given Latinized names. It is proposed that the family is emended to include only the species . The family is emended to account for the expansion of its membership. represents a new family designated fam. nov. is the representative of fam. nov. while represents fam. nov.

摘要

多年来,该科在门、纲的分类群中一直是一个分类定义不明确的类群。该纲的成员显然由多个科级分支组成,大多(但并非全部)在盐生生态系统中被检测到。该类群分类学上的问题源于使用16S rRNA基因序列对分类群的分辨率不足、可培养分类单元数量稀少以及表型差异有限。基于标准化分类等级的基因组分类数据库(GTDB)将该纲包含的属定为属和属。这与将这些属归入科的官方分类法不一致。其他相关物种的分类地位甚至更不确定,包括。为了澄清该纲的分类,为该科所有缺乏此类数据的模式菌株生成了基因组。使用GTDB工具包(GTDB-tk)将分类单元归入GTDB,这揭示了其中一些模式菌株在科级水平上的新颖性。使用16S rRNA基因序列和串联蛋白序列进一步评估该纲的分类。从数据来看,GTDB成功地澄清了该科的分类。一些占位科被赋予了拉丁化名称。建议修订科,使其仅包括物种。修订科以考虑其成员的扩充。代表一个新科,命名为科。是科的代表,而代表科。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e5a4/7214798/c646bc3fb37e/fmicb-11-00795-g001.jpg

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