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RISS 인기검색어
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- 주제어 : average nucleotide identity (검색결과 5 건)
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Yoon, Seok-Hwan,Ha, Sung-Min,Kwon, Soonjae,Lim, Jeongmin,Kim, Yeseul,Seo, Hyungseok,Chun, Jongsik Microbiology Society 2017 International journal of systematic and evolutiona Vol.67 No.5
<P>The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the <I>Bacteria</I> and <I>Archaea</I>. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the <I>Bacteria</I> and <I>Archaea</I>, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the <I>Bacteria</I> and <I>Archaea</I>. The database and related search tools are available at www.ezbiocloud.net/.</P>
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Yang, Seung-Jo,Kim, Byung-Yong,Chun, Jongsik Society for General Microbiology 2017 International journal of systematic and evolutiona Vol.67 No.11
<P> Lactobacillus bobalius, Lactobacillus kimchii and Lactobacillus paralimentarius belong to the genus Lactobacillus and show close phylogenetic relationships. In a previous study, L. bobalius and L. kimchii were proposed to be reclassified as later heterotypic synonyms of L. paralimentarius using high 16S rRNA gene sequence similarities (≥99.5 %) and DNA-DNA hybridization values (≥82 %). We determined high quality whole genome assemblies of the type strains of L. bobalius and L. kimchii, which were then compared with that of L. paralimentarius. Average nucleotide identity values among three genomes ranged from 91.4 to 92.3%which are clearly below 95~96 %, the generally recognized cutoff value for bacterial species boundaries. On the basis of comparative genomic evidence, L. bobalius, L. kimchii, and L. paralimentarius should stand as separate species in the genus Lactobacillus. We therefore suggest rejecting the previous proposal to combine these three species into a single species. </P>
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Park, Soon-Nang,Lim, Yun Kyong,Kook, Joong-Ki 대한구강생물학회 2020 International Journal of Oral Biology Vol.45 No.2
The aim of this study was to identify strain KCOM 1265 isolated from subgingival plaque at the species level by comparing 16S ribosomal RNA gene (16S rDNA) and genome sequences. The whole genome of strain KCOM 1265 was extracted using the phenol-chloroform extraction method. 16S rDNA was amplified using polymerase chain reaction and sequenced using the dideoxy chain termination method. Pairwise genome comparison was performed using average nucleotide identity (ANI) and genome-to-genome distance (GGD) analyses. The data showed that the percent similarity of 16S rDNA sequence of strain KCOM 1265 was 99.6% as compared with those of Fusobacterium polymorphum ATCC 10953<sup>T</sup> and Fusobacterium hwasookii KCOM 1249<sup>T</sup>. The ANI values of strain KCOM 1265 with F. polymorphum ATCC 10953<sup>T</sup> and F. hwasookii KCOM 1249<sup>T</sup> were 95.8% and 93.0%, respectively. The GGD values of strain KCOM 1265 with F. polymorphum ATCC 10953<sup>T</sup> and F. hwasookii KCOM 1249<sup>T</sup> were 63.9% and 49.6%, respectively. These results indicate that strain KCOM 1265 belongs to F. polymorphum.
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Whole-genome sequence analysis through online web interfaces: a review
Gunasekara, A.W.A.C.W.R.,Rajapaksha, L.G.T.G.,Tung, T.L. Korea Genome Organization 2022 Genomics & informatics Vol.20 No.1
The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.
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Tongchu Deng,Youfen Qian,Xingjuan Chen,Xunan Yang,Jun Guo,Guoping Sun,Meiying Xu 한국미생물학회 2020 The journal of microbiology Vol.58 No.5
A nitrate-reducing Fe(II)-oxidizing bacterial strain, F8825T, was isolated from the Fe(II)-rich sediment of an urban creek in Pearl River Delta, China. The strain was Gram-negative, facultative chemolithotrophic, facultative anaerobic, nonspore- forming, and rod-shaped with a single flagellum. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that it belongs to the genus Ciceribacter and is most closely related to C. lividus MSSRFBL1T (99.4%), followed by C. thiooxidans F43bT (98.8%) and C. azotifigens A.slu09T (98.0%). Fatty acid, polar lipid, respiratory quinone, and DNA G + C content analyses supported its classification in the genus Ciceribacter. Multilocus sequence analysis of concatenated 16S rRNA, atpD, glnII, gyrB, recA, and thrC suggested that the isolate was a novel species. DNA–DNA hybridization and genome sequence comparisons (90.88 and 89.86%, for values of ANIm and ANIb between strains F8825T with MSSRFBL1T, respectively) confirmed that strain F8825T was a novel species, different from C. lividus MSSRFBL1T, C. thiooxidans F43bT, and C. azotifigens A.slu09T. The physiological and biochemical properties of the strain, such as carbon source utilization, nitrate reduction, and ferrous ion oxidation, further supported that this is a novel species. Based on the polyphasic taxonomic results, strain F8825T was identified as a novel species in the genus Ciceribacter, for which the name Ciceribacter ferrooxidans sp. nov. is proposed. The type strain is F8825T (= CCTCC AB 2018196T = KCTC 62948T).
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