Khaoula Bouznada, Rafika Saker, Hadj Ahmed Belaouni, Atika Meklat
{"title":"系统发生组分析支持将粪钙单胞菌(Winter 等人,1988 年)重新分类 Bouanane-Darenfed 等人(2015 年)将其列为 Yokoyama 等人(2010 年)的钙单胞菌 oshimai 的后异型同义词","authors":"Khaoula Bouznada, Rafika Saker, Hadj Ahmed Belaouni, Atika Meklat","doi":"10.1007/s00284-024-03878-4","DOIUrl":null,"url":null,"abstract":"<p>This study employs genome-based methodologies to explore the taxonomic relationship between <i>Caldicoprobacter faecalis</i> DSM 20678<sup>T</sup> and <i>Caldicoprobacter oshimai</i> DSM 21659<sup>T</sup>. The genome-based similarity indices calculations consisting of digital DNA–DNA Hybridization (dDDH), Average Amino Aid Identity (AAI), and Average Nucleotide Identity (ANI) between the genomes of these two type strains yielded percentages of 91.2%, 98.9%, and 99.1%, respectively. These values were above the recommended thresholds of 70% (dDDH) and 95–96% (ANI and AAI) for bacterial species delineation, indicating a shared taxonomic position for <i>C. faecalis</i> and <i>C. oshimai</i>. Furthermore, analysis utilizing the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and constructing a Maximum Likelihood core-genes tree using FastTree2 consistently demonstrated the close relationship between <i>C</i>. <i>faecalis</i> DSM 20678<sup>T</sup> and <i>C</i>. <i>oshimai</i> DSM 21659<sup>T</sup>, evident from their clustering in the core-genes phylogenomic tree. Based on these comprehensive findings, we propose the reclassification of <i>C</i>. <i>faecalis</i> as a later heterotypic synonym of <i>C</i>. <i>oshimai</i>.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"15 1","pages":""},"PeriodicalIF":2.3000,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Phylogenomic Analysis Supports the Reclassification of Caldicoprobacter faecalis (Winter et al. 1988) Bouanane-Darenfed et al. (2015) as a Later Heterotypic Synonym of Caldicoprobacter oshimai Yokoyama et al. (2010)\",\"authors\":\"Khaoula Bouznada, Rafika Saker, Hadj Ahmed Belaouni, Atika Meklat\",\"doi\":\"10.1007/s00284-024-03878-4\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>This study employs genome-based methodologies to explore the taxonomic relationship between <i>Caldicoprobacter faecalis</i> DSM 20678<sup>T</sup> and <i>Caldicoprobacter oshimai</i> DSM 21659<sup>T</sup>. The genome-based similarity indices calculations consisting of digital DNA–DNA Hybridization (dDDH), Average Amino Aid Identity (AAI), and Average Nucleotide Identity (ANI) between the genomes of these two type strains yielded percentages of 91.2%, 98.9%, and 99.1%, respectively. These values were above the recommended thresholds of 70% (dDDH) and 95–96% (ANI and AAI) for bacterial species delineation, indicating a shared taxonomic position for <i>C. faecalis</i> and <i>C. oshimai</i>. Furthermore, analysis utilizing the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and constructing a Maximum Likelihood core-genes tree using FastTree2 consistently demonstrated the close relationship between <i>C</i>. <i>faecalis</i> DSM 20678<sup>T</sup> and <i>C</i>. <i>oshimai</i> DSM 21659<sup>T</sup>, evident from their clustering in the core-genes phylogenomic tree. Based on these comprehensive findings, we propose the reclassification of <i>C</i>. <i>faecalis</i> as a later heterotypic synonym of <i>C</i>. <i>oshimai</i>.</p>\",\"PeriodicalId\":11360,\"journal\":{\"name\":\"Current Microbiology\",\"volume\":\"15 1\",\"pages\":\"\"},\"PeriodicalIF\":2.3000,\"publicationDate\":\"2024-09-17\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Current Microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1007/s00284-024-03878-4\",\"RegionNum\":3,\"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":"Current Microbiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s00284-024-03878-4","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
Phylogenomic Analysis Supports the Reclassification of Caldicoprobacter faecalis (Winter et al. 1988) Bouanane-Darenfed et al. (2015) as a Later Heterotypic Synonym of Caldicoprobacter oshimai Yokoyama et al. (2010)
This study employs genome-based methodologies to explore the taxonomic relationship between Caldicoprobacter faecalis DSM 20678T and Caldicoprobacter oshimai DSM 21659T. The genome-based similarity indices calculations consisting of digital DNA–DNA Hybridization (dDDH), Average Amino Aid Identity (AAI), and Average Nucleotide Identity (ANI) between the genomes of these two type strains yielded percentages of 91.2%, 98.9%, and 99.1%, respectively. These values were above the recommended thresholds of 70% (dDDH) and 95–96% (ANI and AAI) for bacterial species delineation, indicating a shared taxonomic position for C. faecalis and C. oshimai. Furthermore, analysis utilizing the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and constructing a Maximum Likelihood core-genes tree using FastTree2 consistently demonstrated the close relationship between C. faecalis DSM 20678T and C. oshimai DSM 21659T, evident from their clustering in the core-genes phylogenomic tree. Based on these comprehensive findings, we propose the reclassification of C. faecalis as a later heterotypic synonym of C. oshimai.
期刊介绍:
Current Microbiology is a well-established journal that publishes articles in all aspects of microbial cells and the interactions between the microorganisms, their hosts and the environment.
Current Microbiology publishes original research articles, short communications, reviews and letters to the editor, spanning the following areas:
physiology, biochemistry, genetics, genomics, biotechnology, ecology, evolution, morphology, taxonomy, diagnostic methods, medical and clinical microbiology and immunology as applied to microorganisms.