Strain identifier

BacDive ID: 17349

Type strain: Yes

Species: Vibrio azureus

Strain Designation: LC2-005

Strain history: <- NBRC <- S. Yoshizawa, Ocean Res. Inst., Univ. Tokyo, Japan; LC2-005

NCBI tax ID(s): 1219077 (strain), 512649 (species)

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General

@ref: 16779

BacDive-ID: 17349

DSM-Number: 23306

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped

description: Vibrio azureus LC2-005 is a mesophilic, Gram-negative, motile bacterium that was isolated from seawater.

NCBI tax id

NCBI tax idMatching level
1219077strain
512649species

strain history

  • @ref: 16779
  • history: <- NBRC <- S. Yoshizawa, Ocean Res. Inst., Univ. Tokyo, Japan; LC2-005

doi: 10.13145/bacdive17349.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Vibrio
  • species: Vibrio azureus
  • full scientific name: Vibrio azureus Yoshizawa et al. 2009

@ref: 16779

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio azureus

full scientific name: Vibrio azureus Yoshizawa et al. 2009

strain designation: LC2-005

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29024negativerod-shapedyes
69480yes98.361
69480negative99.993

pigmentation

  • @ref: 29024
  • production: no

Culture and growth conditions

culture medium

  • @ref: 16779
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16779positivegrowth28mesophilic
29024positivegrowth10-37
29024positiveoptimum23.5psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.899

halophily

@refsaltgrowthtested relationconcentration
29024NaClpositivegrowth0.5-6 %
29024NaClpositiveoptimum3.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2902417234glucose+carbon source
2902425017leucine+carbon source

metabolite production

  • @ref: 29024
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29024
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29024alkaline phosphatase+3.1.3.1
29024catalase+1.11.1.6
29024cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 16779
  • sample type: seawater
  • geographic location: Kuroshio Region (32° 30' N 138° 00' E; depth: 200 m)
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

Safety information

risk assessment

  • @ref: 16779
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio azureus gene for 16S rRNA, partial sequence, strain: NBRC 104587AB6822111477ena512649
16779Vibrio azureus gene for 16S rRNA, partial sequence, strain: LC2-005 (= NBRC 104587)AB4288971298ena512649

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio azureus LC2-005GCA_002849855chromosomencbi512649
66792Vibrio azureus NBRC 104587GCA_000467165contigncbi1219077
66792Vibrio azureus NBRC 104587GCA_000400265scaffoldncbi1219077
66792Vibrio azureus NBRC 1045871219077.3wgspatric1219077
66792Vibrio azureus NBRC 1045871219077.9wgspatric1219077
66792Vibrio azureus strain LC2-005512649.4patric512649
66792Vibrio azureus LC2-0052806310741completeimg1219077
66792Vibrio azureus NBRC 1045872600255073draftimg1219077
66792Vibrio azureus NBRC 1045872579778795draftimg1219077

GC content

  • @ref: 16779
  • GC-content: 45.2

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 16779

culture collection no.: DSM 23306, KCTC 22352, NBRC 104587

straininfo link

  • @ref: 86350
  • straininfo: 361418

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19542136Vibrio azureus sp. nov., a luminous marine bacterium isolated from seawater.Yoshizawa S, Wada M, Kita-Tsukamoto K, Ikemoto E, Yokota A, Kogure KInt J Syst Evol Microbiol10.1099/ijs.0.004283-02009Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Japan, *Luminescence, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA/methods, Species Specificity, Vibrio/*classification/genetics/isolation & purification/physiologyGenetics
Metabolism22268378Vibrio azureus emits blue-shifted light via an accessory blue fluorescent protein.Yoshizawa S, Karatani H, Wada M, Kogure KFEMS Microbiol Lett10.1111/j.1574-6968.2012.02507.x2012Bacterial Proteins/genetics/*metabolism, DNA, Bacterial/chemistry/genetics, *Light, Luminescent Proteins/genetics/*metabolism, Molecular Sequence Data, Sequence Analysis, DNA, Spectrum Analysis, Vibrio/genetics/*physiologyGenetics
Genetics23710045Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences.Urbanczyk H, Ogura Y, Hayashi TInt J Syst Evol Microbiol10.1099/ijs.0.051110-02013Bacterial Typing Techniques, DNA, Bacterial/genetics, *Genome, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/*classification/geneticsPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16779Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23306)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23306
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29024Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125454
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86350Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID361418.1StrainInfo: A central database for resolving microbial strain identifiers