Genome-based analyses of family Oxalobacteraceae reveal the taxonomic classification

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology Pub Date : 2023-09-01 DOI:10.1016/j.resmic.2023.104076

Tengfei Ma, Han Xue, Chungen Piao, Ning Jiang, Yong Li

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引用次数: 0

Abstract

Family Oxalobacteraceae is known for the indicator of bacterial diversity in the environment and many of which are important beneficial bacteria. Previous studies on the taxonomic structure of family Oxalobacteraceae mostly relied on 16S rRNA gene analysis, or core-genome phylogeny of a limited number of species and resulted in taxonomic confusion within several genera. Developments in sequencing technologies have allowed more genome sequences to be obtained, enabling the revision of family Oxalobacteraceae. Here, we report a comprehensive analysis of phylogenomic trees, concatenated protein and up-to-date bacterial core gene phylogenetic trees, and genomic metrics for genus demarcation on 135 genomes of Oxalobacteraceae species to elucidate their interrelationships. Following this framework for classification of species in family Oxalobacteraceae, all the proposed genera formed monophyletic lineages in the phylogenomic trees and could also be clearly separated from others in the genomic similarity indexes of average amino acid identity, percentage of conserved proteins and core-proteome average amino acid identity.

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基于基因组的分析揭示了牛杆菌科的分类。

牛杆菌科以指示环境中细菌多样性而闻名，其中许多是重要的有益细菌。先前对牛杆菌科分类结构的研究大多依赖于有限数量物种的16S rRNA基因分析或核心基因组系统发育，并导致几个属的分类混乱。测序技术的发展使人们能够获得更多的基因组序列，从而能够对牛杆菌科进行修订。在这里，我们报道了对牛杆菌科135个基因组的系统发育树、连接蛋白和最新细菌核心基因系统发育树以及属划分的基因组指标的全面分析，以阐明它们之间的相互关系。根据该分类框架，所有提出的属在系统发育树上形成了单系谱系，并且在平均氨基酸同一性、保守蛋白百分比和核心蛋白质组平均氨基酸同性的基因组相似性指数上也可以与其他属明显分离。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Research in microbiology 生物-微生物学

CiteScore

4.10

自引率

3.80%

发文量

审稿时长

16 days

期刊介绍： Research in Microbiology is the direct descendant of the original Pasteur periodical entitled Annales de l''Institut Pasteur, created in 1887 by Emile Duclaux under the patronage of Louis Pasteur. The Editorial Committee included Chamberland, Grancher, Nocard, Roux and Straus, and the first issue began with Louis Pasteur''s "Lettre sur la Rage" which clearly defines the spirit of the journal:"You have informed me, my dear Duclaux, that you intend to start a monthly collection of articles entitled "Annales de l''Institut Pasteur". You will be rendering a service that will be appreciated by the ever increasing number of young scientists who are attracted to microbiological studies. In your Annales, our laboratory research will of course occupy a central position, but the work from outside groups that you intend to publish will be a source of competitive stimulation for all of us."That first volume included 53 articles as well as critical reviews and book reviews. From that time on, the Annales appeared regularly every month, without interruption, even during the two world wars. Although the journal has undergone many changes over the past 100 years (in the title, the format, the language) reflecting the evolution in scientific publishing, it has consistently maintained the Pasteur tradition by publishing original reports on all aspects of microbiology.