Strain identifier

BacDive ID: 17313

Type strain: Yes

Species: Vibrio gigantis

Strain history: CIP <- 2005, M. Gay, IFREMER, La Tremblaye, France: strain LGP 13

NCBI tax ID(s): 296199 (species)

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General

@ref: 7582

BacDive-ID: 17313

DSM-Number: 18531

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

description: Vibrio gigantis DSM 18531 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from haemolymph of oysters .

NCBI tax id

  • NCBI tax id: 296199
  • Matching level: species

strain history

@refhistory
7582<- CIP <- M. Gay, IFREMER; LGP 13
400482005, M. Gay, IFREMER, La Tremblaye, France: strain LGP 13
119615CIP <- 2005, M. Gay, IFREMER, La Tremblaye, France: strain LGP 13

doi: 10.13145/bacdive17313.20230509.8.1

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 gigantis
  • full scientific name: Vibrio gigantis Le Roux et al. 2005

@ref: 7582

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio gigantis

full scientific name: Vibrio gigantis Le Roux et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilitycell shape
31486negative2.5 µm1 µmyes
119615negativeyesrod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7582BACTO 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
40048Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119615CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7582positivegrowth25mesophilic
31486positiveoptimum4psychrophilic
40048positivegrowth22psychrophilic
61148positivegrowth30mesophilic
119615positivegrowth5-30
119615nogrowth37mesophilic
119615nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31486facultative anaerobe
61148aerobe
119615facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
31486NaClpositivegrowth01-07 %
31486NaClpositiveoptimum4 %
119615NaClpositivegrowth2-8 %
119615NaClnogrowth0 %
119615NaClnogrowth10 %

observation

  • @ref: 31486
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3148617057cellobiose+carbon source
3148628757fructose+carbon source
3148628260galactose+carbon source
3148617234glucose+carbon source
3148617754glycerol+carbon source
3148628087glycogen+carbon source
3148629864mannitol+carbon source
3148637684mannose+carbon source
3148628053melibiose+carbon source
31486506227N-acetylglucosamine+carbon source
3148633942ribose+carbon source
3148627082trehalose+carbon source
314864853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
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
11961516947citrate-carbon source
1196154853esculin+hydrolysis
11961517234glucose+fermentation
11961517716lactose-fermentation
11961517632nitrate+reduction
11961516301nitrite-reduction
119615132112sodium thiosulfate-builds gas from
11961517234glucose+degradation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
11961535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
11961515688acetoin-
11961517234glucose-

enzymes

@refvalueactivityec
31486catalase+1.11.1.6
31486gelatinase+
31486cytochrome 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
119615oxidase+
119615beta-galactosidase-3.2.1.23
119615alcohol dehydrogenase-1.1.1.1
119615gelatinase+
119615amylase+
119615caseinase+3.4.21.50
119615catalase+1.11.1.6
119615tween esterase+
119615gamma-glutamyltransferase-2.3.2.2
119615lecithinase-
119615lipase+
119615lysine decarboxylase-4.1.1.18
119615ornithine decarboxylase-4.1.1.17
119615phenylalanine ammonia-lyase-4.3.1.24
119615protease+
119615tryptophan deaminase-
119615urease-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
119615-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7582+++--++++-++++++-++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119615+---+----++++----+---+--+/--++-++/-+---++---------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119615+++++-+--++---++--++-----------+-----------------++--+-----++--------------+--++--+------+-+-+-----

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
7582haemolymph of oysters (Crassostrea gigas)Crassostrea gigasFranceFRAEurope
61148Haemolymph of oyster (Crassostrea gigas)FranceFRAEurope
119615Japanese oyster, C. GigasFranceFRAEuropeLa Tremblaye2001

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Mollusca
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_929.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_361;98_409;99_929&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: AJ582810
  • Sequence Identity:
  • Total samples: 6265
  • soil counts: 160
  • aquatic counts: 5115
  • animal counts: 960
  • plant counts: 30

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7582yes1Risk group (German classification)
1196152Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio gigantis strain CAIM 25 16S ribosomal RNA gene, partial sequenceEF0948881498ena296199
7582Vibrio gigantis partial 16S rRNA gene, type strain LGP 13AJ5828101202ena296199

Genome sequences

  • @ref: 66792
  • description: Vibrio gigantis LMG 22741
  • accession: GCA_024347515
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 296199

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes89.556no
gram-positiveno98.855yes
anaerobicno97.416yes
aerobicyes87.611no
halophileyes52.621no
spore-formingno94.575no
motileyes90.249yes
glucose-fermentyes86.553no
thermophileno99.688yes
glucose-utilyes91.614yes

External links

@ref: 7582

culture collection no.: DSM 18531, CIP 108656, LMG 22741, CCUG 56969, LGP 13

straininfo link

  • @ref: 86313
  • straininfo: 281472

literature

  • topic: Phylogeny
  • Pubmed-ID: 16280478
  • title: Vibrio gigantis sp. nov., isolated from the haemolymph of cultured oysters (Crassostrea gigas).
  • authors: Roux FL, Goubet A, Thompson FL, Faury N, Gay M, Swings J, Saulnier D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63666-0
  • year: 2005
  • mesh: Animals, Crassostrea/*microbiology, DNA Gyrase/*genetics, DNA, Bacterial/analysis/chemistry, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNA, Vibrio/*classification/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7582Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18531)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18531
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
31486Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127784
40048Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6309
61148Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56969)https://www.ccug.se/strain?id=56969
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)
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
86313Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281472.1StrainInfo: A central database for resolving microbial strain identifiers
119615Curators of the CIPCollection of Institut Pasteur (CIP 108656)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108656