Strain identifier

BacDive ID: 17329

Type strain: Yes

Species: Vibrio splendidus

Strain history: CIP <- 1987, NCIB, Beneckea splendida <- 1958, R. Spencer <- A.J. Kluyver <- H. J. van Zutphen, Photobacterium splendidum

NCBI tax ID(s): 29497 (species)

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General

@ref: 8230

BacDive-ID: 17329

DSM-Number: 19640

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, psychrophilic, motile, animal pathogen

description: Vibrio splendidus DSM 19640 is a facultative anaerobe, psychrophilic, motile animal pathogen that was isolated from marine fish.

NCBI tax id

  • NCBI tax id: 29497
  • Matching level: species

strain history

@refhistory
8230<- NCIMB <- R. Spencer <- A. J. Kluyver <- H. van Zutphen
123268CIP <- 1987, NCIB, Beneckea splendida <- 1958, R. Spencer <- A.J. Kluyver <- H. J. van Zutphen, Photobacterium splendidum

doi: 10.13145/bacdive17329.20230509.8.1

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 splendidus
  • full scientific name: Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981

  • synonyms

    @refsynonym
    20215Photobacter splendidum
    20215Beneckea splendida
    20215Vibrio hemicentroti

@ref: 8230

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio splendidus

full scientific name: Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.817
6948099.988negative
123268yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8230BACTO 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
40473Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123268CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8230positivegrowth20psychrophilic
40473positivegrowth22psychrophilic
123268positivegrowth15-30
123268nogrowth5psychrophilic
123268nogrowth37mesophilic
123268nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123268
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.781

halophily

@refsaltgrowthtested relationconcentration
123268NaClpositivegrowth2-8 %
123268NaClnogrowth0 %
123268NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
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
68371gentiobiose-builds acid from28066
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
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-sorbose-builds acid from17266
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
68371glycerol-builds acid from17754
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369L-arabinose-assimilation30849
68369gelatin+hydrolysis5291
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68368L-arabinose-fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin+hydrolysis5291
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
123268citrate-carbon source16947
123268esculin-hydrolysis4853
123268glucose-fermentation17234
123268lactose-fermentation17716
123268nitrate+reduction17632
123268nitrite-reduction16301
123268sodium thiosulfate-builds gas from132112
123268glucose-degradation17234

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836816136hydrogen sulfideno
12326835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
6836815688acetoin-
12326815688acetoin-
12326817234glucose-

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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
123268oxidase+
123268beta-galactosidase-3.2.1.23
123268alcohol dehydrogenase-1.1.1.1
123268gelatinase+
123268caseinase+3.4.21.50
123268catalase+1.11.1.6
123268tween esterase+
123268gamma-glutamyltransferase+2.3.2.2
123268lecithinase+
123268lipase+
123268lysine decarboxylase-4.1.1.18
123268ornithine decarboxylase-4.1.1.17
123268phenylalanine ammonia-lyase-4.3.1.24
123268protease+
123268tryptophan deaminase-
123268urease-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
123268-++++++-+-++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
8230+---------+++----++-+
8230+-------+-+++----++-+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8230-----+/-+++-+++++--++-+
8230+++--+++------------+
8230+++--+++------------+
8230+++---+++-+++++--++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123268-----------+/-+/--+/----------+/-+/-+/-+/---+/-+/--+/---+/-+/--------+/---+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123268---------------------------------------------------------------------------+---++---------+--------

Isolation, sampling and environmental information

isolation

@refsample type
8230marine fish
123268Animal, Sea fish

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Fishes

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
8230yes2Risk group (German classification)
1232682Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio splendidus strain ATCC 33125 16S-23S ribosomal RNA intergenic spacer, partial sequenceAF413021394ena29497
20218Vibrio splendidus strain ATCC 33125 16S-23S ribosomal RNA intergenic spacer, partial sequenceAF413022394ena29497
20218Vibrio splendidus strain ATCC 33125 16S-23S ribosomal RNA intergenic spacer, partial sequenceAF413023278ena29497
20218Vibrio splendidus strain ATCC 33125 16S-23S ribosomal RNA intergenic spacer, partial sequenceAF413024448ena29497
20218Vibrio splendidus partial 16S rRNA gene, strain LMG 4042, clone bAJ5152301321ena29497
20218V.splendidus (ATCC 33125T) gene for 16S ribosomal RNAX747241468ena29497
8230Vibrio splendidus partial 16S rRNA gene, strain LMG 4042, clone aAJ5152291321ena29497

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio splendidus DSM 19640GCA_002737025contigncbi29497
66792Vibrio splendidus NCCB 53037GCA_001558015contigncbi29497
66792Vibrio splendidus strain DSM 1964029497.30wgspatric29497
66792Vibrio splendidus strain NCCB 5303729497.15wgspatric29497
66792Vibrio splendidus DSM 196402916752974draftimg29497

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.784no
anaerobicno97.21no
halophileyes59.065no
spore-formingno95.594no
glucose-utilyes91.982no
motileyes91.042no
flagellatedyes90.928no
aerobicyes87.452no
thermophileno99.724no
glucose-fermentyes85.701no

External links

@ref: 8230

culture collection no.: DSM 19640, ATCC 33125, CECT 528, LMG 4042, NCCB 53037, NCIMB 1, CIP 102893, KCTC 12679

straininfo link

  • @ref: 86329
  • straininfo: 5122

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10229952Polyphasic approach to the characterisation of marine luminous bacteria.Caccamo D, Di Cello F, Fani R, Gugliandolo C, Maugeri TLRes Microbiol10.1016/s0923-2508(99)80039-41999Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Luminescent Measurements, Molecular Sequence Data, Phenotype, Plasmids/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Restriction Mapping, Seawater/*microbiology, Sequence Analysis, DNA, Vibrionaceae/*classification/genetics/*isolation & purificationGenetics
Phylogeny10347874Characterization by numerical taxonomy and ribotyping of Vibrio splendidus biovar I and Vibrio scophthalmi strains associated with turbot cultures.Farto R, Montes M, Perez MJ, Nieto TP, Larsen JL, Pedersen KJ Appl Microbiol10.1046/j.1365-2672.1999.00730.x1999Animals, *Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fish Diseases/*microbiology, Flatfishes/*microbiology, Phenotype, Seawater, Vibrio/*classification/isolation & purification/pathogenicity, Vibrio Infections/*veterinary, Water MicrobiologyPhenotype
10594718Pathogenicity of vibrio splendidus strains associated with turbot larvae, scophthalmus maximusGatesoupe FJ, Lambert C, Nicolas JLJ Appl Microbiol10.1046/j.1365-2672.1999.00922.x1999
Phylogeny22066815Historical microbiology: revival and phylogenetic analysis of the luminous bacterial cultures of M. W. Beijerinck.Figge MJ, Robertson LA, Ast JC, Dunlap PVFEMS Microbiol Ecol10.1111/j.1574-6941.2011.01177.x2011Bacterial Typing Techniques, DNA, Bacterial/genetics, France, Genes, Bacterial, Genetic Variation, Japan, *Luminescence, Mexico, Microbial Viability, Multilocus Sequence Typing, Norway, Photobacterium/*classification/genetics/isolation & purification, *Phylogeny, Seawater/microbiology, Sequence Analysis, DNA, Uruguay, Vibrio/*classification/genetics/isolation & purificationEnzymology
Phylogeny25586509A European epidemiological survey of Vibrio splendidus clade shows unexplored diversity and massive exchange of virulence factors.Nasfi H, Travers MA, de Lorgeril J, Habib C, Sannie T, Sorieul L, Gerard J, Avarre JC, Haffner P, Tourbiez D, Renault T, Furones D, Roque A, Pruzzo C, Cheslett D, Gdoura R, Vallaeys TWorld J Microbiol Biotechnol10.1007/s11274-015-1800-y2015Animals, Aquatic Organisms/*microbiology, Cluster Analysis, DNA, Ribosomal/chemistry/genetics, Europe, *Genetic Variation, Genotype, Minisatellite Repeats, *Molecular Typing, Phylogeny, RNA, Ribosomal, 16S/genetics, Real-Time Polymerase Chain Reaction, Seafood/*microbiology, Seawater/microbiology, Vibrio/classification/*genetics/*isolation & purification, Virulence Factors/*geneticsGenetics
Phylogeny28150577Whole genome sequences reveal Vibrio hemicentroti Kim et al. 2013 as a later heterotypic synonym of Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981.Lucena T, Carmen Macian M, Arahal DR, Rodrigo-Torres L, Pujalte MJInt J Syst Evol Microbiol10.1099/ijsem.0.0018422017Bacterial Typing Techniques, DNA, Bacterial/genetics, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Sequence Analysis, DNA, Vibrio/*classification/geneticsTranscriptome
Genetics29192085Draft Genome Sequence of Vibrio splendidus DSM 19640.Chibani CM, Poehlein A, Roth O, Liesegang H, Wendling CCGenome Announc10.1128/genomeA.01368-172017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8230Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19640)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19640
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
40473Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14629
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
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
86329Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5122.1StrainInfo: A central database for resolving microbial strain identifiers
123268Curators of the CIPCollection of Institut Pasteur (CIP 102893)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102893