Xiaohui Chen , Zhouqing Zheng , Feina Li , Xiao Ma , Feng Chen , Mingsheng Chen , Li Tuo
{"title":"Bruguiera gymnorhiza Bruguiera Nocardioides sp11 .的描述和基因组特征","authors":"Xiaohui Chen , Zhouqing Zheng , Feina Li , Xiao Ma , Feng Chen , Mingsheng Chen , Li Tuo","doi":"10.1016/j.syapm.2022.126391","DOIUrl":null,"url":null,"abstract":"<div><p>Strains BSK12Z-3<sup>T</sup><span><span> and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall </span>peptidoglycan of strain BSK12Z-3</span><sup>T</sup> was LL-diaminopimelic acid and MK-8(H<sub>4</sub><span><span><span>) was the predominant menaquinone. The polar </span>lipids comprised diphosphatidylglycerol (DPG), </span>phosphatidylglycerol<span> (PG) and phospholipid (PL). The major fatty acids was </span></span><em>iso</em>-C<sub>16:0</sub><span>. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus </span><span><em>Nocardioides</em></span>, appearing most closely related to <em>Nocardioides ginkgobilobae</em> KCTC 39594<sup>T</sup> (97.5–97.6 % sequence similarity) and <em>Nocardioides marinus</em> DSM 18248<sup>T</sup> (97.4–97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3<sup>T</sup> and BSK12Z-4 formed a distinct phylogenetic cluster within the genus <em>Nocardioides</em>. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3<sup>T</sup>, BSK12Z-4 with their most related species <em>N</em>. <em>marinus</em> DSM18248<sup>T</sup> were within the ranges of 77.2–77.3 % and 21.3–21.4 %, respectively, clearly indicated that strains BSK12Z-3<sup>T</sup>, BSK12Z-4 represented novel species. Strains BSK12Z-3<sup>T</sup><span><span> and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on </span>phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3</span><sup>T</sup> and BSK12Z-4 could be classified as a novel species of the genus <em>Nocardioides</em>, for which the name <em>Nocardioides bruguierae</em> sp. nov., is proposed. The type strain is BSK12Z-3<sup>T</sup> (=CGMCC 4.7709<sup>T</sup> = JCM 34554<sup>T</sup>).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 2","pages":"Article 126391"},"PeriodicalIF":3.3000,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":"{\"title\":\"Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza\",\"authors\":\"Xiaohui Chen , Zhouqing Zheng , Feina Li , Xiao Ma , Feng Chen , Mingsheng Chen , Li Tuo\",\"doi\":\"10.1016/j.syapm.2022.126391\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Strains BSK12Z-3<sup>T</sup><span><span> and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall </span>peptidoglycan of strain BSK12Z-3</span><sup>T</sup> was LL-diaminopimelic acid and MK-8(H<sub>4</sub><span><span><span>) was the predominant menaquinone. The polar </span>lipids comprised diphosphatidylglycerol (DPG), </span>phosphatidylglycerol<span> (PG) and phospholipid (PL). The major fatty acids was </span></span><em>iso</em>-C<sub>16:0</sub><span>. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus </span><span><em>Nocardioides</em></span>, appearing most closely related to <em>Nocardioides ginkgobilobae</em> KCTC 39594<sup>T</sup> (97.5–97.6 % sequence similarity) and <em>Nocardioides marinus</em> DSM 18248<sup>T</sup> (97.4–97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3<sup>T</sup> and BSK12Z-4 formed a distinct phylogenetic cluster within the genus <em>Nocardioides</em>. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3<sup>T</sup>, BSK12Z-4 with their most related species <em>N</em>. <em>marinus</em> DSM18248<sup>T</sup> were within the ranges of 77.2–77.3 % and 21.3–21.4 %, respectively, clearly indicated that strains BSK12Z-3<sup>T</sup>, BSK12Z-4 represented novel species. Strains BSK12Z-3<sup>T</sup><span><span> and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on </span>phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3</span><sup>T</sup> and BSK12Z-4 could be classified as a novel species of the genus <em>Nocardioides</em>, for which the name <em>Nocardioides bruguierae</em> sp. nov., is proposed. The type strain is BSK12Z-3<sup>T</sup> (=CGMCC 4.7709<sup>T</sup> = JCM 34554<sup>T</sup>).</p></div>\",\"PeriodicalId\":22124,\"journal\":{\"name\":\"Systematic and applied microbiology\",\"volume\":\"46 2\",\"pages\":\"Article 126391\"},\"PeriodicalIF\":3.3000,\"publicationDate\":\"2023-04-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"1\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Systematic and applied microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0723202022000984\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Systematic and applied microbiology","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0723202022000984","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza
Strains BSK12Z-3T and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall peptidoglycan of strain BSK12Z-3T was LL-diaminopimelic acid and MK-8(H4) was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phospholipid (PL). The major fatty acids was iso-C16:0. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Nocardioides, appearing most closely related to Nocardioides ginkgobilobae KCTC 39594T (97.5–97.6 % sequence similarity) and Nocardioides marinus DSM 18248T (97.4–97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus Nocardioides. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3T, BSK12Z-4 with their most related species N. marinus DSM18248T were within the ranges of 77.2–77.3 % and 21.3–21.4 %, respectively, clearly indicated that strains BSK12Z-3T, BSK12Z-4 represented novel species. Strains BSK12Z-3T and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3T and BSK12Z-4 could be classified as a novel species of the genus Nocardioides, for which the name Nocardioides bruguierae sp. nov., is proposed. The type strain is BSK12Z-3T (=CGMCC 4.7709T = JCM 34554T).
期刊介绍：
Systematic and Applied Microbiology deals with various aspects of microbial diversity and systematics of prokaryotes. It focuses on Bacteria and Archaea; eukaryotic microorganisms will only be considered in rare cases. The journal perceives a broad understanding of microbial diversity and encourages the submission of manuscripts from the following branches of microbiology:
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