{"title":"从黑梳蜂蜜中分离出的新双歧杆菌(Bifidobacterium favimelis sp.","authors":"Yu Li, Qiujie Song, Haizhu Yang, Yue Wei, Bilege Menghe, Wenjun Liu","doi":"10.1099/ijsem.0.006573","DOIUrl":null,"url":null,"abstract":"<p><p>A strain of the bacterial genus <i>Bifidobacterium</i>, IMAU50987<sup>T</sup>, that was isolated from black comb honey from Lianghe County, Dehong Autonomous Prefecture, Yunnan Province, China, could not be accurately identified as a known species using 16S rRNA gene sequencing. In this study, the taxonomic status of strain IMAU50987<sup>T</sup> was evaluated using whole-genome sequencing combined with phenotypic analyses. Strain IMAU50987<sup>T</sup> was Gram-positive, non-motile and non-spore-forming. Comparative of 16S rRNA gene sequence similarity analysis indicated that strain IMAU50987<sup>T</sup> could be attributed to the genus <i>Bifidobacterium</i> and most closely related to the <i>B. mellis</i> Bin7N<sup>T</sup> (98.5% identity). Comparative sequence analysis of eight housekeeping genes (<i>pyrG</i>, <i>thrS</i>, <i>glnA1</i>, <i>recA</i>, <i>tuf</i>, <i>dnaB</i>, <i>rpoC</i> and <i>xfp</i>) showed that strain IMAU50987<sup>T</sup> was different from closely related species. Phylogenomic analysis based on the 88 single-copy genes in the phylogenetic tree showed that strain IMAU50987<sup>T</sup> belonged to the <i>B. asteroides</i> group. The highest average nucleotide identity value for strain IMAU50987<sup>T</sup> was 77.0% in comparison with <i>B. choladohabitans</i> B14384H11<sup>T</sup> and <i>B. apis</i> F753-1<sup>T</sup>. However, the highest digital DNA-DNA hybridization value was 23.1% compared with <i>B. apis</i> F753-1<sup>T</sup> and <i>B. xylocopae</i> XV2<sup>T</sup>; the highest average amino acid identity value was 73.2% compared with <i>B. polysaccharolyticum</i> W8117<sup>T</sup>. These values are below the accepted threshold for novel species boundaries. The draft genome size of strain IMAU50987<sup>T</sup> was 1.9 Mb, and the DNA G+C content was 63.5%. The major cellular fatty acids of strain IMAU50987<sup>T</sup> were C<sub>16 : 0</sub>, C<sub>18 : 1</sub> <i> ω</i>9c and Sum in Feature 7 (C<sub>19 : 1</sub> <i> ω</i>7c/C<sub>19 : 1</sub> <i> ω</i>6c). The cell-wall peptidoglycan was of the A3α l-Lys-Gly type. Based on data from this study, a novel species, <i>Bifidobacterium favimelis</i> sp. nov., is proposed with the type strain IMAU50987<sup>T</sup> (= GDMCC 1.4189<sup>T</sup> = JCM 36315<sup>T</sup>).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"74 11","pages":""},"PeriodicalIF":2.0000,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"<i>Bifidobacterium favimelis</i> sp. nov., isolated from black comb honey.\",\"authors\":\"Yu Li, Qiujie Song, Haizhu Yang, Yue Wei, Bilege Menghe, Wenjun Liu\",\"doi\":\"10.1099/ijsem.0.006573\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>A strain of the bacterial genus <i>Bifidobacterium</i>, IMAU50987<sup>T</sup>, that was isolated from black comb honey from Lianghe County, Dehong Autonomous Prefecture, Yunnan Province, China, could not be accurately identified as a known species using 16S rRNA gene sequencing. In this study, the taxonomic status of strain IMAU50987<sup>T</sup> was evaluated using whole-genome sequencing combined with phenotypic analyses. Strain IMAU50987<sup>T</sup> was Gram-positive, non-motile and non-spore-forming. Comparative of 16S rRNA gene sequence similarity analysis indicated that strain IMAU50987<sup>T</sup> could be attributed to the genus <i>Bifidobacterium</i> and most closely related to the <i>B. mellis</i> Bin7N<sup>T</sup> (98.5% identity). Comparative sequence analysis of eight housekeeping genes (<i>pyrG</i>, <i>thrS</i>, <i>glnA1</i>, <i>recA</i>, <i>tuf</i>, <i>dnaB</i>, <i>rpoC</i> and <i>xfp</i>) showed that strain IMAU50987<sup>T</sup> was different from closely related species. Phylogenomic analysis based on the 88 single-copy genes in the phylogenetic tree showed that strain IMAU50987<sup>T</sup> belonged to the <i>B. asteroides</i> group. The highest average nucleotide identity value for strain IMAU50987<sup>T</sup> was 77.0% in comparison with <i>B. choladohabitans</i> B14384H11<sup>T</sup> and <i>B. apis</i> F753-1<sup>T</sup>. However, the highest digital DNA-DNA hybridization value was 23.1% compared with <i>B. apis</i> F753-1<sup>T</sup> and <i>B. xylocopae</i> XV2<sup>T</sup>; the highest average amino acid identity value was 73.2% compared with <i>B. polysaccharolyticum</i> W8117<sup>T</sup>. These values are below the accepted threshold for novel species boundaries. The draft genome size of strain IMAU50987<sup>T</sup> was 1.9 Mb, and the DNA G+C content was 63.5%. The major cellular fatty acids of strain IMAU50987<sup>T</sup> were C<sub>16 : 0</sub>, C<sub>18 : 1</sub> <i> ω</i>9c and Sum in Feature 7 (C<sub>19 : 1</sub> <i> ω</i>7c/C<sub>19 : 1</sub> <i> ω</i>6c). The cell-wall peptidoglycan was of the A3α l-Lys-Gly type. Based on data from this study, a novel species, <i>Bifidobacterium favimelis</i> sp. nov., is proposed with the type strain IMAU50987<sup>T</sup> (= GDMCC 1.4189<sup>T</sup> = JCM 36315<sup>T</sup>).</p>\",\"PeriodicalId\":14390,\"journal\":{\"name\":\"International journal of systematic and evolutionary microbiology\",\"volume\":\"74 11\",\"pages\":\"\"},\"PeriodicalIF\":2.0000,\"publicationDate\":\"2024-11-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"International journal of systematic and evolutionary microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1099/ijsem.0.006573\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"International journal of systematic and evolutionary microbiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1099/ijsem.0.006573","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
Bifidobacterium favimelis sp. nov., isolated from black comb honey.
A strain of the bacterial genus Bifidobacterium, IMAU50987T, that was isolated from black comb honey from Lianghe County, Dehong Autonomous Prefecture, Yunnan Province, China, could not be accurately identified as a known species using 16S rRNA gene sequencing. In this study, the taxonomic status of strain IMAU50987T was evaluated using whole-genome sequencing combined with phenotypic analyses. Strain IMAU50987T was Gram-positive, non-motile and non-spore-forming. Comparative of 16S rRNA gene sequence similarity analysis indicated that strain IMAU50987T could be attributed to the genus Bifidobacterium and most closely related to the B. mellis Bin7NT (98.5% identity). Comparative sequence analysis of eight housekeeping genes (pyrG, thrS, glnA1, recA, tuf, dnaB, rpoC and xfp) showed that strain IMAU50987T was different from closely related species. Phylogenomic analysis based on the 88 single-copy genes in the phylogenetic tree showed that strain IMAU50987T belonged to the B. asteroides group. The highest average nucleotide identity value for strain IMAU50987T was 77.0% in comparison with B. choladohabitans B14384H11T and B. apis F753-1T. However, the highest digital DNA-DNA hybridization value was 23.1% compared with B. apis F753-1T and B. xylocopae XV2T; the highest average amino acid identity value was 73.2% compared with B. polysaccharolyticum W8117T. These values are below the accepted threshold for novel species boundaries. The draft genome size of strain IMAU50987T was 1.9 Mb, and the DNA G+C content was 63.5%. The major cellular fatty acids of strain IMAU50987T were C16 : 0, C18 : 1 ω9c and Sum in Feature 7 (C19 : 1 ω7c/C19 : 1 ω6c). The cell-wall peptidoglycan was of the A3α l-Lys-Gly type. Based on data from this study, a novel species, Bifidobacterium favimelis sp. nov., is proposed with the type strain IMAU50987T (= GDMCC 1.4189T = JCM 36315T).
期刊介绍:
Published by the Microbiology Society and owned by the International Committee on Systematics of Prokaryotes (ICSP), a committee of the Bacteriology and Applied Microbiology Division of the International Union of Microbiological Societies, International Journal of Systematic and Evolutionary Microbiology is the leading forum for the publication of novel microbial taxa and the ICSP’s official journal of record for prokaryotic names.
The journal welcomes high-quality research on all aspects of microbial evolution, phylogenetics and systematics, encouraging submissions on all prokaryotes, yeasts, microfungi, protozoa and microalgae across the full breadth of systematics including:
Identification, characterisation and culture preservation
Microbial evolution and biodiversity
Molecular environmental work with strong taxonomic or evolutionary content
Nomenclature
Taxonomy and phylogenetics.