Strain identifier

BacDive ID: 130765

Type strain: Yes

Species: Vibrio hangzhouensis

Strain history: CIP <- 2009, JCM <- 2008, X.W. Xu, Lab. Marine Ecosyst. and Biogeochem., Hangzhou, China: strain CN83

NCBI tax ID(s): 462991 (species)

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General

@ref: 21979

BacDive-ID: 130765

DSM-Number: 100627

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

description: Vibrio hangzhouensis DSM 100627 is an aerobe, Gram-negative, motile bacterium that was isolated from sediment at a depth of 49.

NCBI tax id

  • NCBI tax id: 462991
  • Matching level: species

strain history

@refhistory
21979<- JCM <- X.-W. Xu, Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou
67770X.-W. Xu CN83.
119834CIP <- 2009, JCM <- 2008, X.W. Xu, Lab. Marine Ecosyst. and Biogeochem., Hangzhou, China: strain CN83

doi: 10.13145/bacdive130765.20240916.9.1

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 hangzhouensis
  • full scientific name: Vibrio hangzhouensis Xu et al. 2009

@ref: 21979

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio hangzhouensis

full scientific name: Vibrio hangzhouensis Xu et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29211negative1.5 µm0.65 µmrod-shapedyes
119834negativerod-shapedyes
69480yes90.527
69480negative100

pigmentation

  • @ref: 29211
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21979REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)yeshttps://mediadive.dsmz.de/medium/514cName: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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
38268Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119834CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
21979positivegrowth30
29211positivegrowth20-37
29211positiveoptimum30
38268positivegrowth30
67770positivegrowth30

culture pH

@refabilitytypepHPH range
29211positivegrowth6.0-10alkaliphile
29211positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29211
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29211
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29211NaClpositivegrowth0.5-7.5 %
29211NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2921130089acetate+carbon source
2921116449alanine+carbon source
2921129016arginine+carbon source
2921122653asparagine+carbon source
2921135391aspartate+carbon source
2921117057cellobiose+carbon source
2921116947citrate+carbon source
2921128757fructose+carbon source
2921128260galactose+carbon source
2921124265gluconate+carbon source
2921117234glucose+carbon source
2921129987glutamate+carbon source
2921117754glycerol+carbon source
2921115428glycine+carbon source
2921127570histidine+carbon source
2921124996lactate+carbon source
2921117716lactose+carbon source
2921125115malate+carbon source
2921117306maltose+carbon source
2921129864mannitol+carbon source
2921137684mannose+carbon source
2921118257ornithine+carbon source
2921126271proline+carbon source
2921117272propionate+carbon source
2921115361pyruvate+carbon source
2921133942ribose+carbon source
2921117822serine+carbon source
2921130031succinate+carbon source
2921117992sucrose+carbon source
2921127082trehalose+carbon source
2921153424tween 20+carbon source
292114853esculin+hydrolysis
2921117632nitrate+reduction
6836830849L-arabinose-fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11983417632nitrate+reduction
11983416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2921116136hydrogen sulfideyes
2921135581indoleyes
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11983435581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
2921135581indole+
6836815688acetoin-
6836835581indole+

enzymes

@refvalueactivityec
29211acid phosphatase+3.1.3.2
29211alkaline phosphatase+3.1.3.1
29211catalase+1.11.1.6
29211gelatinase+
29211cytochrome oxidase+1.9.3.1
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
119834oxidase+
119834catalase+1.11.1.6
119834urease-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
119834-++--+----++---+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21979--------+--++---+++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
21979sediment at a depth of 49East China SeaChinaCHNAsia27.3325120.575
67770Marine sediment sample from ZhejiangChinaCHNAsia
119834Environment, Sea, sedimentEastChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
219791Risk group (German classification)
1198342Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21979
  • description: Vibrio sp. cn83 16S ribosomal RNA gene, partial sequence
  • accession: EU082035
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 462991

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio hangzhouensis strain CGMCC 1.7062462991.9wgspatric462991
66792Vibrio hangzhouensis CGMCC 1.70622617270906draftimg462991
67770Vibrio hangzhouensis CGMCC 1.7062GCA_900107935contigncbi462991

GC content

@refGC-contentmethod
2921144.9
6777044.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno100yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.971yes
69480spore-formingspore-formingAbility to form endo- or exosporesno89.862yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no55.959yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.939no
69480flagellatedmotile2+Ability to perform flagellated movementyes90.527no

External links

@ref: 21979

culture collection no.: DSM 100627, CGMCC 1.7062, CIP 110023, JCM 15146, CN 83

straininfo link

  • @ref: 89262
  • straininfo: 364202

literature

  • topic: Phylogeny
  • Pubmed-ID: 19605706
  • title: Vibrio hangzhouensis sp. nov., isolated from sediment of the East China Sea.
  • authors: Xu XW, Wu YH, Wang CS, Oren A, Wu M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.008698-0
  • year: 2009
  • mesh: Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Locomotion, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/*classification/genetics/*isolation & purification/physiology
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21979Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100627Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100627)
29211Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172563228776041
38268Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7834
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
89262Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID364202.1
119834Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110023Collection of Institut Pasteur (CIP 110023)