OrthoANI: An improved algorithm and software for calculating average nucleotide identity

Lee, Imchang; Kim, Yeong Ouk; Park, Sang Cheol; Chun, Jongsik

doi:10.1099/ijsem.0.000760

Cited by 2,434 publications

(1,800 citation statements)

References 15 publications

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“…In addition to ANIb, other measurements of genomic relatedness were calculated. These included ANI calculated with the MUMmer algorithm (ANIm) and tetranucleotide nucleotide frequency distribution (Tetra) measurements, calculated using JSpecies software, orthology ANI (orthoANI) measurement, calculated using OAT tool version 1.20 (Lee et al, 2015), as well as genome-to-genome distance comparison (GGDC) calculated using GGDC 2.1 tool with formula 2 available on http://ggdc.dsmz.de website (Meier-Kolthoff et al, 2013). Results of ANIm, orthoANI and GGDC calculations (Tables S3-S5) support classification of CECT 7692 T and the five analyzed V. jasicida strains as members of the same species.…”

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Genomic evidence that Vibrio inhibens is a heterotypic synonym of Vibrio jasicida

Urbanczyk

Ogura

Hayashi

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Vibrio inhibens is a marine bacterium species of the genus Vibrio (Vibrionaceae, Gammaproteobacteria). The species has been shown to be closely related to members of the genus Vibrio in the so-called Harveyi clade. The clade includes at least 11 closely related species with similar physiological and biochemical properties. Due to these similarities, species of the Harveyi clade are difficult to characterize taxonomically. Previously phenotypic and genotypic properties of the V. inhibens type strain were compared with six species of the Harveyi clade, resulting in the possibility that V. inhibens could be a synonym of a previously described species. In this study, the taxonomic status of V. inhibens was analyzed using genomic approaches. The whole-genome sequence of the type strain of V. inhibens, CECT 7692 T , was obtained and analyzed. Calculations of average nucleotide identity with the BLAST algorithm (ANIb) showed that CECT 7692 T has an ANIb of 97.5 % or higher to five strains of Vibrio. jasicida, including the type strain, but an ANIb lower than 93.5 % to other members of the Harveyi clade Vibrio. Phylogenetic analysis based on nucleotide sequences of 133 protein-coding genes showed a close evolutionary relationship of CECT 7692 T to V. jasicida. Based on these results, Vibrio inhibens is proposed to be a later heterotypic synonym of V. jasicida.Strain CECT 7692 T was isolated from feces of wild longsnouted seahorse (Hippocampus guttulatus) (Balcazar et al., 2012). Based on a phylogenetic analysis of sequences of five genes, as well as a chemophenotypic analysis the strain was taxonomically classified as representing a novel species of the genus Vibrio (family Vibrionaceae, Gammaproteobacteria), Vibrio inhibens (Balcazar et al., 2012). So far, the species type strain (CECT 7692 T =DSM 23440 T =BFLP-10 T ) is the only strain of V. inhibens described in the literature. The type strain of V. inhibens, CECT 7692 T , was obtained from the Spanish Type Culture Collection (CECT). Genomic DNA of CECT 7692 T was isolated using a DNeasy Blood and Tissue kit (Qiagen). The whole-genome sequence was generated using an Illumina MiSeq platform and a Nextera XT DNA Sample Prep kit (Illumina). Pairedend sequencing resulted in 2 367 933 reads (after quality trimming), which were assembled using Platanus assembler version 1.2.1 with the option for haploid genome (Katijani et al., 2014) into 237 scaffolds of over 300 bp in length, with approximately 132-fold coverage. The draft genome was 5 945 135 bp in length, with a DNA G+C content of 43.82 %. The CECT 7692 T genome sequence was submitted Abbreviations: MLSA, multi-locus sequence analysis; ANI, average nucleotide identity; GGDC, genome-to-genome distance comparison; ANIb, ANI calculated with the blast algorithm; ANIm, ANI calculated with the MUMmer algorithm; orthoANI, orthology ANI .V. inhibens CECT 7692 T 16S rRNA sequence obtained in this study has GenBank accession number KU360274. CECT 7692 T genome sequence has DDBJ accession numbers DF977004 to DF977445.Six supple...

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confidence: 99%

Genomic evidence that Vibrio inhibens is a heterotypic synonym of Vibrio jasicida

Urbanczyk

Ogura

Hayashi

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…AQXF00000000) was retrieved from the GenBank database. The average nucleotide identity (ANI) between two genomes was calculated using the algorithm of EZGenome web service (Goris et al, 2007) and Orthologous Average Nucleotide Identity Tool (OAT software) (Lee et al, 2016). The genome-to-genome distance was calculated by GGDC (Meier-Kolthoff et al, 2013).…”

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Kordiimonas lipolytica sp. nov., isolated from seawater

Jian

Meng

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, aerobic, rod-shaped bacterium, designated M41 T , was isolated from a surface seawater sample collected from the western Pacific Ocean. The isolate grew in medium containing 0.5-10.0 % (w/v) NaCl (optimally at 1.0-3.0 %) at 15-45 C and pH 5.5-9.5. Positive for oxidase, catalase and nitrate reduction. The respiratory quinone is Q-10. The major fatty acids (>10 %) are iso-C 15:0 , iso-C 17:1 !9c and summed feature 3 (comprising C 16:1 !7c and/or iso-C 15:0 2-OH). The major polar lipids are phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, and three unidentified glycolipids.The genomic DNA G +C content is 56.3 mol %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M41 T should be assigned to the genus Kordiimonas. The 16S rRNA gene sequence similarities between the isolate and the type strains of species of the genus Kordiimonas with validly published names were in the range 96.2-98.6 %. Strain M41 T exhibited average nucleotide identity (ANI) values of 81.7 and 72.3 % with respect to Kordiimonas. lacus S3-22 T and Kordiimonas gwangyangensis JCM 12864 T , respectively. The genome-to-genome distance analysis revealed that strain M41 T shared 51.4 % DNA-DNA relatedness with K. lacus S3-22 T and 16.3 % with K. gwangyangensis JCM 12864 T . On the basis of phenotypic and genotypic characteristics, strain M41 T represents a novel species of the genus Kordiimonas, for which the name Kordiimonas lipolytica sp. nov. is proposed. The type strain is M41 T (=CGMCC 1.15304 T =JCM 30877 T ). An emended description of Kordiimonas lacus is also provided.

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“…The average nucleotide identity (ANI) is a similarity measure between two genome sequences that can be used to replace DNA-DNA hybridization (Goris et al, 2007;Richter et al, 2009). In the present study, the ANIs of strain 7Y-4 T with 'Sphingobacterium paucimobilis' HER1398, Sphingobacterium spiritivorum ATCC 33861 T , Sphingobacterium thalpophilum DSM 11723 T and Olivibacter sitiensis DSM 17696 T were determined using OrthoANI (Lee et al, 2015).…”

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Sphingobacterium populi sp. nov., isolated from bark of Populus × euramericana

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, aerobic, non-motile bacterial strain, 7Y-4 T , was isolated from bark tissue of Populus Â euramericana. The isolate was able to grow between 10 and 37 C, with optimal growth occurring at 28-30 C. Strain 7Y-4 T was positive for oxidase and catalase activities, but did not reduce nitrite from nitrate. Positive reactions were observed for the activities of b-galactosidase, urease and b-glucosidase, but negative reactions for the activities of gelatinase and the production of indole, acetoin and H 2 S. Citrate was not utilized. The major fatty acids of strain 7Y-4 T are iso-C 15 : 0 (28.6 %), C 16 : 1 !7c/C 16 : 1 !6c (31.8 %) and iso-C 17 : 0 3-OH (23.3 %).The major polar lipids of the novel isolate include phosphatidylethanolamine, three unknown phospholipids (PL1-3) and six unknown lipids (L1-6), and the predominant menaquinone is MK-7. The DNA G+C content is 41.7 mol%. Analysis of 16S rRNA gene sequences revealed that the novel isolate shared the greatest sequence similarity with Sphingobacterium hotanense XH4 T (93.50 %). On the basis of phenotypic and genotypic characteristics, strain 7Y-4 T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium populi is proposed. The type strain is 7Y-4 T (=CFCC 11742 T =KCTC 42247 T ).

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OrthoANI: An improved algorithm and software for calculating average nucleotide identity

Cited by 2,434 publications

References 15 publications

Genomic evidence that Vibrio inhibens is a heterotypic synonym of Vibrio jasicida

Genomic evidence that Vibrio inhibens is a heterotypic synonym of Vibrio jasicida

Kordiimonas lipolytica sp. nov., isolated from seawater

Sphingobacterium populi sp. nov., isolated from bark of Populus × euramericana

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