Tengfei Ma, Han Xue, Chungen Piao, Ning Jiang, Yong Li
{"title":"基于基因组的分析揭示了牛杆菌科的分类。","authors":"Tengfei Ma, Han Xue, Chungen Piao, Ning Jiang, Yong Li","doi":"10.1016/j.resmic.2023.104076","DOIUrl":null,"url":null,"abstract":"<div><p>Family <span><em>Oxalobacteraceae</em></span> 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 <em>Oxalobacteraceae</em><span> 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 </span><em>Oxalobacteraceae</em><span><span>. Here, we report a comprehensive analysis of phylogenomic trees, concatenated protein and up-to-date bacterial core gene </span>phylogenetic trees, and genomic metrics for genus demarcation on 135 genomes of </span><em>Oxalobacteraceae</em> species to elucidate their interrelationships. Following this framework for classification of species in family <em>Oxalobacteraceae</em><span>, 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.</span></p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":null,"pages":null},"PeriodicalIF":2.5000,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genome-based analyses of family Oxalobacteraceae reveal the taxonomic classification\",\"authors\":\"Tengfei Ma, Han Xue, Chungen Piao, Ning Jiang, Yong Li\",\"doi\":\"10.1016/j.resmic.2023.104076\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Family <span><em>Oxalobacteraceae</em></span> 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 <em>Oxalobacteraceae</em><span> 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 </span><em>Oxalobacteraceae</em><span><span>. Here, we report a comprehensive analysis of phylogenomic trees, concatenated protein and up-to-date bacterial core gene </span>phylogenetic trees, and genomic metrics for genus demarcation on 135 genomes of </span><em>Oxalobacteraceae</em> species to elucidate their interrelationships. Following this framework for classification of species in family <em>Oxalobacteraceae</em><span>, 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.</span></p></div>\",\"PeriodicalId\":21098,\"journal\":{\"name\":\"Research in microbiology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2023-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Research in microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0923250823000517\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Research in microbiology","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0923250823000517","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
Genome-based analyses of family Oxalobacteraceae reveal the taxonomic classification
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.
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.
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