Strain identifier

BacDive ID: 17330

Type strain: Yes

Species: Vibrio tubiashii

Strain history: CIP <- 1987, NCIB <- 1965, H.S. Tubiash: strain Milford 74, type J, Vibrio anguillarum

NCBI tax ID(s): 1051646 (strain), 29498 (species)

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General

@ref: 7839

BacDive-ID: 17330

DSM-Number: 19142

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, animal pathogen

description: Vibrio tubiashii DSM 19142 is an aerobe, mesophilic, motile animal pathogen that was isolated from Moribund larvae of hard clam,Mercenaria mercenaria.

NCBI tax id

NCBI tax idMatching level
1051646strain
29498species

strain history

@refhistory
7839<- CAIM <- LMG <- NCIMB <- H. Tubiash [Vibrio mercenaria]
123680CIP <- 1987, NCIB <- 1965, H.S. Tubiash: strain Milford 74, type J, Vibrio anguillarum

doi: 10.13145/bacdive17330.20230509.8.1

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 tubiashii
  • full scientific name: Vibrio tubiashii Hada et al. 1984

@ref: 7839

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio tubiashii

full scientific name: Vibrio tubiashii Hada et al. 1984 emend. Prado et al. 2015 emend. Dubert et al. 2016

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.127
6948099.982negative
123680yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7839BACTO 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
42194Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123680CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7839positivegrowth28mesophilic
42194positivegrowth25mesophilic
54251positivegrowth20-22psychrophilic
123680positivegrowth15-37
123680nogrowth5psychrophilic
123680nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54251aerobe
123680facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.939

halophily

@refsaltgrowthtested relationconcentration
123680NaClpositivegrowth2-8 %
123680NaClnogrowth0 %
123680NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836930849L-arabinose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan+energy source
6836917632nitrate+reduction
12368016947citrate-carbon source
1236804853esculin-hydrolysis
12368017234glucose+fermentation
12368017716lactose-fermentation
12368017632nitrate+reduction
12368016301nitrite-reduction
123680132112sodium thiosulfate-builds gas from
12368017234glucose-degradation
12368017632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
12368035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
12368015688acetoin-
12368017234glucose-

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
123680oxidase+
123680beta-galactosidase+3.2.1.23
123680alcohol dehydrogenase+1.1.1.1
123680gelatinase+
123680amylase+
123680DNase+
123680caseinase+3.4.21.50
123680catalase+1.11.1.6
123680tween esterase+
123680gamma-glutamyltransferase+2.3.2.2
123680lecithinase+
123680lipase+
123680lysine decarboxylase-4.1.1.18
123680ornithine decarboxylase-4.1.1.17
123680phenylalanine ammonia-lyase-4.3.1.24
123680protease+
123680tryptophan deaminase-
123680urease-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
123680-+++-+----++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7839++++-++++/--+/-+/--++--+--+
7839++++-++++-+++++--++-+
7839++++-++++/--+/-+/--++--+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123680+++++-++-+++-+++-+++-----------+-+---------------+----+----++--------------+---++-+---+-+++++++---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
54251Moribund larvae of hard clam,Mercenaria mercenariaConnecticut,MilfordUSAUSANorth America
7839juvenile larvae of hard clam (Mercenaria mercenaria)LagendaFranceFRAEurope
123680Animal, Moribund larvae and juvenile hard clamsConnecticutUnited States of AmericaUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_578.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_312;98_347;99_578&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: X74725
  • Sequence Identity:
  • Total samples: 208
  • soil counts: 2
  • aquatic counts: 195
  • animal counts: 10
  • plant counts: 1

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7839yes1Risk group (German classification)
1236802Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio tubiashii DNA, 16S-23S rRNA intergenic spacer type 1 and 23S rRNA, partial sequence, strain: ATCC 19109AB255736261ena1051646
20218Vibrio tubiashii DNA, 16S-23S rRNA intergenic spacer type 2 and 23S rRNA, partial sequence, strain: ATCC 19109AB255737240ena1051646
20218Vibrio tubiashii strain ATCC 19109 16S ribosomal RNA gene, partial sequenceHQ8904641471ena1051646
7839V.tubiashi (ATCC 19109T) gene for 16S ribosomal RNAX747251436ena1051646

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio tubiashii ATCC 19109GCA_000772105completencbi1051646
66792Vibrio tubiashii ATCC 19109GCA_000222665contigncbi1051646
66792Vibrio tubiashii ATCC 191091051646.3wgspatric1051646
66792Vibrio tubiashii ATCC 191091051646.20plasmidpatric1051646
66792Vibrio tubiashii ATCC 191091051646.9completepatric1051646
66792Vibrio tubiashii ATCC 191091051646.21plasmidpatric1051646
66792Vibrio tubiashii ATCC 191091051646.22plasmidpatric1051646
66792Vibrio tubiashii ATCC 191091051646.23plasmidpatric1051646
66792Vibrio tubiashii ATCC 191092512047081draftimg1051646
66792Vibrio tubiashii ATCC 191092627854020completeimg1051646

GC content

  • @ref: 7839
  • GC-content: 44
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.805no
flagellatedyes92.675no
gram-positiveno98.655no
anaerobicno97.354yes
aerobicyes88.487yes
halophileyes55.682no
spore-formingno94.183no
thermophileno99.706no
glucose-utilyes90.555no
glucose-fermentyes83.506yes

External links

@ref: 7839

culture collection no.: DSM 19142, ATCC 19109, CAIM 313, CCUG 19118, CECT 4196, CIP 102760, LMG 10936, NBRC 15644, NCIMB 1340, CCUG 38428

straininfo link

  • @ref: 86330
  • straininfo: 5124

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599703Vibrio porteresiae sp. nov., a diazotrophic bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka).Rameshkumar N, Fukui Y, Sawabe T, Nair SInt J Syst Evol Microbiol10.1099/ijs.0.65604-02008Molecular Sequence Data, *Nitrogen Fixation, Oryza/*microbiology, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Verbenaceae, Vibrio/*classification/genetics/isolation & purificationGenetics
Phylogeny21930677Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea.Hoffmann M, Monday SR, Allard MW, Strain EA, Whittaker P, Naum M, McCarthy PJ, Lopez JV, Fischer M, Brown EWInt J Syst Evol Microbiol10.1099/ijs.0.032375-02011Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Likelihood Functions, Molecular Sequence Data, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/*classification/genetics/*isolation & purificationGenetics
Enzymology25344234Mortalities of Eastern and Pacific oyster Larvae caused by the pathogens Vibrio coralliilyticus and Vibrio tubiashii.Richards GP, Watson MA, Needleman DS, Church KM, Hase CCAppl Environ Microbiol10.1128/AEM.02930-142014Animals, Crassostrea/*microbiology, Larva/microbiology, Lethal Dose 50, Vibrio/*isolation & purification/pathogenicity, Vibrio Infections/microbiology/*mortality/*veterinary, VirulencePhylogeny
Genetics25523763Complete Genome Sequence of the Larval Shellfish Pathogen Vibrio tubiashii Type Strain ATCC 19109.Richards GP, Needleman DS, Watson MA, Bono JLGenome Announc10.1128/genomeA.01252-142014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7839Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19142)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19142
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
42194Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14482
54251Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38428)https://www.ccug.se/strain?id=38428
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
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
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
86330Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5124.1StrainInfo: A central database for resolving microbial strain identifiers
123680Curators of the CIPCollection of Institut Pasteur (CIP 102760)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102760