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, mesophilic, Gram-negative, motile, rod-shaped

description: Vibrio hangzhouensis DSM 100627 is an aerobe, mesophilic, Gram-negative 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/bacdive130765.20230509.8.1

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 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 shapemotility
29211negative1.5 µm0.65 µmrod-shapedyes
119834negativerod-shapedyes

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

@refgrowthtypetemperaturerange
21979positivegrowth30mesophilic
29211positivegrowth20-37
29211positiveoptimum30mesophilic
38268positivegrowth30mesophilic
67770positivegrowth30mesophilic

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: ena
  • 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

traitpredictionconfidencetraining_data
gram-positiveno98.926yes
anaerobicno95.775yes
halophileyes52.56no
spore-formingno95.28yes
glucose-utilyes92.974yes
aerobicyes83.56yes
flagellatedyes89.89no
motileyes90.852yes
thermophileno99.045yes
glucose-fermentyes89.575yes

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
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)