Strain identifier

BacDive ID: 17308

Type strain: Yes

Species: Vibrio crassostreae

Strain history: CIP <- 2004, D. Mazel, Inst. Pasteur, Paris, France: strain LGP 7

NCBI tax ID(s): 246167 (species)

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General

@ref: 6822

BacDive-ID: 17308

DSM-Number: 17220

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, animal pathogen

description: Vibrio crassostreae DSM 17220 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from oyster Crassostreae gigas.

NCBI tax id

  • NCBI tax id: 246167
  • Matching level: species

strain history

@refhistory
6822<- M. Stahlberger, IFREMER <- D. Saulnier, IFREMER; LGP7
339432004, D. Mazel, Inst. Pasteur, Paris, France: strain LGP 7
118779CIP <- 2004, D. Mazel, Inst. Pasteur, Paris, France: strain LGP 7

doi: 10.13145/bacdive17308.20230509.8.1

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 crassostreae
  • full scientific name: Vibrio crassostreae Faury et al. 2004

@ref: 6822

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio crassostreae

full scientific name: Vibrio crassostreae Faury et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilitycell shape
31294negative2 µm1 µmyes
118779negativeyesrod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6822REACTIVATION 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
33943Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118779CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6822positivegrowth28mesophilic
33943positivegrowth20psychrophilic
61087positivegrowth30mesophilic
118779positivegrowth5-30
118779nogrowth37mesophilic
118779nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31294facultative anaerobe
61087aerobe
118779facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
31294NaClpositivegrowth01-07 %
31294NaClpositiveoptimum4 %
118779NaClpositivegrowth2-6 %
118779NaClnogrowth0 %
118779NaClnogrowth8 %
118779NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3129417057cellobiose+carbon source
3129433984fucose+carbon source
3129428260galactose+carbon source
3129417234glucose+carbon source
3129417754glycerol+carbon source
3129428087glycogen+carbon source
3129429864mannitol+carbon source
3129437684mannose+carbon source
3129428053melibiose+carbon source
31294506227N-acetylglucosamine+carbon source
3129433942ribose+carbon source
3129417992sucrose+carbon source
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan+energy source
6836917632nitrate+reduction
6836817632nitrate+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
11877916947citrate-carbon source
1187794853esculin+hydrolysis
11877917234glucose+fermentation
11877917716lactose+fermentation
11877917632nitrate+reduction
11877916301nitrite-reduction
118779132112sodium thiosulfate-builds gas from

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11877935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
6836815688acetoin-
6836835581indole+
11877915688acetoin-
11877917234glucose-

enzymes

@refvalueactivityec
31294catalase+1.11.1.6
31294cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68368cytochrome oxidase+1.9.3.1
68368gelatinase+
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
118779oxidase+
118779beta-galactosidase-3.2.1.23
118779alcohol dehydrogenase-1.1.1.1
118779gelatinase+
118779amylase+
118779caseinase+3.4.21.50
118779catalase+1.11.1.6
118779tween esterase+
118779gamma-glutamyltransferase+2.3.2.2
118779lecithinase+
118779lipase-
118779lysine decarboxylase-4.1.1.18
118779ornithine decarboxylase-4.1.1.17
118779phenylalanine ammonia-lyase-4.3.1.24
118779protease+
118779tryptophan deaminase-
118779urease-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
118779-+++-+--+-++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
6822-------++-+++---+++-++-
6822--------+-+++---+++-+
6822--------+-+++---+++-+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6822+++--++++-+++++--++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118779--+++-+--++---+++--+----+------+-----------------+----+----++--------------+---++--------++++++---+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
6822oyster Crassostreae gigasCrassostrea gigasLa TrembladeFranceFRAEurope
61087Pacific cupped oyster Crassostrea gigas haemolymphLa TrembladeFranceFRAEurope
118779Animal, Oyster, hemolymphLa TrembladeFranceFRAEurope2004

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Mollusca

taxonmaps

  • @ref: 69479
  • File name: preview.99_1337.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_361;98_409;99_1337&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: AJ582808
  • Sequence Identity:
  • Total samples: 10101
  • soil counts: 499
  • aquatic counts: 6829
  • animal counts: 1668
  • plant counts: 1105

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6822yes1Risk group (German classification)
1187792Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio crassostreae strain CAIM 1405 16S ribosomal RNA gene, partial sequenceEF0948871496ena246167
6822Vibrio crassostreae partial 16S rRNA gene, strain LGP 7AJ5828081214ena246167

Genome sequences

  • @ref: 66792
  • description: Vibrio crassostreae LMG 22240
  • accession: GCA_024347415
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 246167

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes91.068no
gram-positiveno98.796yes
anaerobicno97.428yes
aerobicyes86.021no
halophileyes56.962no
spore-formingno95.265no
motileyes90.811yes
glucose-fermentyes85.839yes
thermophileno99.556yes
glucose-utilyes90.445yes

External links

@ref: 6822

culture collection no.: DSM 17220, CIP 108327, LMG 22240, CCUG 56778, Le Roux LGP 7, LGP 7

straininfo link

  • @ref: 86308
  • straininfo: 131141

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545447
  • title: Vibrio crassostreae sp. nov., isolated from the haemolymph of oysters (Crassostrea gigas).
  • authors: Faury N, Saulnier D, Thompson FL, Gay M, Swings J, Roux FL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63232-0
  • year: 2004
  • mesh: Animals, Bacterial Proteins/genetics, DNA Fingerprinting, DNA Gyrase/genetics, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Hemolymph/*microbiology, Hydrolases/analysis, Molecular Sequence Data, Nitrogen Dioxide/metabolism, Nucleic Acid Hybridization, Ostreidae/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/*classification/*isolation & purification, beta-Galactosidase/analysis
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6822Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17220)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17220
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
31294Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127613
33943Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5937
61087Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56778)https://www.ccug.se/strain?id=56778
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)
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86308Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131141.1StrainInfo: A central database for resolving microbial strain identifiers
118779Curators of the CIPCollection of Institut Pasteur (CIP 108327)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108327