Strain identifier

BacDive ID: 17293

Type strain: Yes

Species: Vibrio ruber

Strain Designation: VR1

Strain history: CIP <- 2003, JCM <- W.Y. Shieh: strain VR1

NCBI tax ID(s): 1123498 (strain), 184755 (species)

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General

@ref: 6407

BacDive-ID: 17293

DSM-Number: 16370

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile

description: Vibrio ruber VR1 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from seawater.

NCBI tax id

NCBI tax idMatching level
184755species
1123498strain

strain history

@refhistory
6407<- W. Y. Shieh; VR1 <- Y.-W. Chen
67770W. Y. Shieh VR1.
122279CIP <- 2003, JCM <- W.Y. Shieh: strain VR1

doi: 10.13145/bacdive17293.20230509.8.1

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 ruber
  • full scientific name: Vibrio ruber Shieh et al. 2003

@ref: 6407

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio ruber

full scientific name: Vibrio ruber Shieh et al. 2003

strain designation: VR1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.689
6948099.895negative
122279yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6407BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
39970Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122279CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
122279CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6407positivegrowth28mesophilic
39970positivegrowth25mesophilic
67770positivegrowth30mesophilic
122279positivegrowth15-37
122279nogrowth5psychrophilic
122279nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122279
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.798

halophily

@refsaltgrowthtested relationconcentration
122279NaClpositivegrowth2-10 %
122279NaClnogrowth0 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate+assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol+assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin+hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose+fermentation17634
68369tryptophan-energy source27897
68369nitrate+reduction17632
122279citrate+carbon source16947
122279esculin+hydrolysis4853
122279glucose+fermentation17234
122279lactose-fermentation17716
122279nitrate+reduction17632
122279nitrite-reduction16301
122279sodium thiosulfate-builds gas from132112
122279glucose-degradation17234
122279nitrate+respiration17632

antibiotic resistance

  • @ref: 122279
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12227935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12227915688acetoin-
12227917234glucose-

enzymes

@refvalueactivityec
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
122279beta-galactosidase+3.2.1.23
122279alcohol dehydrogenase-1.1.1.1
122279gelatinase+
122279amylase+
122279DNase+
122279caseinase+3.4.21.50
122279catalase+1.11.1.6
122279tween esterase+
122279gamma-glutamyltransferase+2.3.2.2
122279lecithinase+
122279lipase-
122279lysine decarboxylase-4.1.1.18
122279ornithine decarboxylase-4.1.1.17
122279phenylalanine ammonia-lyase-4.3.1.24
122279protease+
122279tryptophan deaminase-
122279urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122279-+++-+----++-+--+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6407+-+--++++++++++--++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122279+/---+++---++++----+---+-++++++/-++----++-+/-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122279+++-+-++-+++++++++++++---------+-+---------------++--++----++----------+-+-+---++-----+--+++--+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6407seawaterKeelungTaiwanTWNAsia
67770Seawater
122279Environment, Sea waterShallow coastal region of KeelTaiwanTWNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64071Risk group (German classification)
1222792Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6407Vibrio ruber 16S ribosomal RNA gene, partial sequenceAF4624581460ena184755
67770Vibrio ruber JCM 11486 gene for 16S ribosomal RNA, partial sequenceLC5074431464ena184755

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio ruber DSM 16370 strain CECT 78781123498.5wgspatric1123498
66792Vibrio ruber DSM 163702916703105draftimg1123498
66792Vibrio ruber DSM 163702574179726draftimg1123498
67770Vibrio ruber DSM 16370 CECT 7878TGCA_900163965contigncbi1123498

GC content

  • @ref: 67770
  • GC-content: 45.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.762no
flagellatedyes77.617no
gram-positiveno99.225no
anaerobicno93.713no
aerobicno68.578no
halophileno50no
spore-formingno93.242no
glucose-utilyes95.202yes
thermophileno98.961no
glucose-fermentyes87.999yes

External links

@ref: 6407

culture collection no.: DSM 16370, CCRC 17186, JCM 11486, BCRC 17186, CIP 107960

straininfo link

  • @ref: 86294
  • straininfo: 88493

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710616Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water.Shieh WY, Chen YW, Chaw SM, Chiu HHInt J Syst Evol Microbiol10.1099/ijs.0.02307-02003Anaerobiosis, Anti-Bacterial Agents/pharmacology, Base Composition, DNA, Bacterial, Fermentation, Glucose/*metabolism, Microbial Sensitivity Tests, Molecular Sequence Data, Phylogeny, Pigments, Biological, Seawater/*microbiology, Sodium Chloride, Vibrio/*classification/drug effects/*metabolism/physiology, *Water MicrobiologyMetabolism
Phylogeny17911290Vibrio rhizosphaerae sp. nov., a red-pigmented bacterium that antagonizes phytopathogenic bacteria.Kumar NR, Nair SInt J Syst Evol Microbiol10.1099/ijs.0.65017-02007Aerobiosis/physiology, Anaerobiosis/physiology, *Antibiosis, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Escherichia coli Proteins/genetics, Genes, Suppressor, Genes, rRNA, India, Molecular Sequence Data, Oryza/*microbiology, Phylogeny, Pigments, Biological/*biosynthesis, Plant Roots/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Rec A Recombinases/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature, Transferases/genetics, Vibrio/*classification/genetics/*isolation & purification/physiologyMetabolism
Phylogeny20402787Vibrio mangrovi sp. nov., a diazotrophic bacterium isolated from mangrove-associated wild rice (Poteresia coarctata Tateoka).Rameshkumar N, Sproer C, Lang E, Nair SFEMS Microbiol Lett10.1111/j.1574-6968.2010.01958.x2010Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, India, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/*classification/genetics/*isolation & purification/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitle
6407Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16370)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16370
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
39970Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5529
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
86294Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88493.1StrainInfo: A central database for resolving microbial strain identifiers
122279Curators of the CIPCollection of Institut Pasteur (CIP 107960)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107960