Strain identifier

BacDive ID: 17264

Type strain: No

Species: Vibrio harveyi

Strain Designation: 1116b

Strain history: CIP <- 1994, R. Ruimy, CNRS, Villefrance/Mer, France, Vibrio carchariae <- D.J. Grimes and R.R. Colwell: strain 1116b

NCBI tax ID(s): 669 (species)

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General

@ref: 16687

BacDive-ID: 17264

DSM-Number: 23069

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

description: Vibrio harveyi 1116b is an aerobe, mesophilic, motile human pathogen that was isolated from kidney of brown shark Carcharhinus plumbeus.

NCBI tax id

  • NCBI tax id: 669
  • Matching level: species

strain history

@refhistory
16687<- CCUG <- R. Colwell, Maryland, USA; 1116b
119846CIP <- 1994, R. Ruimy, CNRS, Villefrance/Mer, France, Vibrio carchariae <- D.J. Grimes and R.R. Colwell: strain 1116b

doi: 10.13145/bacdive17264.20230509.8.1

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 harveyi
  • full scientific name: Vibrio harveyi (Johnson and Shunk 1936) Baumann et al. 1981

  • synonyms

    @refsynonym
    20215Achromobacter harveyi
    20215Beneckea harveyi
    20215Lucibacterium harveyi
    20215Vibrio trachuri
    20215Vibrio carchariae

@ref: 16687

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio harveyi

full scientific name: Vibrio harveyi (Johnson and Shunk 1936) Baumann et al. 1981

strain designation: 1116b

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.634
6948099.964negative
119846yesnegativerod-shaped

multimedia

  • @ref: 16687
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23069.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16687BACTO 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
41717Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119846CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
16687positivegrowth28mesophilic
41717positivegrowth30mesophilic
46964positivegrowth30mesophilic
119846positivegrowth41thermophilic
119846nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 46964
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.019

halophily

@refsaltgrowthtested relationconcentration
119846NaClpositivegrowth2-10 %
119846NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
11984616947citrate+carbon source
11984617234glucose+fermentation
11984617716lactose-fermentation
11984617632nitrate+reduction
11984616301nitrite-reduction
119846132112sodium thiosulfate-builds gas from
6837418257ornithine-degradation
6837429016arginine-hydrolysis
6837425094lysine-degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol-builds acid from
6837417306maltose-builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan+energy source
6837417634D-glucose+builds acid from
6837417992sucrose+builds acid from
6837430849L-arabinose-builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose-builds acid from
6837462345L-rhamnose-builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol-builds acid from

antibiotic resistance

  • @ref: 119846
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleyes
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11984635581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole+
6836815688acetoin-
6836835581indole+
11984615688acetoin-
11984617234glucose+

enzymes

@refvalueactivityec
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase-3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase-3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase+
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
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
119846oxidase+
119846beta-galactosidase-3.2.1.23
119846alcohol dehydrogenase-1.1.1.1
119846gelatinase+
119846amylase+
119846DNase+
119846catalase+1.11.1.6
119846lysine decarboxylase+4.1.1.18
119846ornithine decarboxylase+4.1.1.17
119846urease+3.5.1.5

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
46964--+-----+--++---+-+-+

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
46964-------++-------+--++-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119846+++++--+-++----+--++-----------+-+----+----------+---++-----+--------------+---++-+------++++++--+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
16687kidney of brown shark Carcharhinus plumbeusCarcharhinus plumbeusUSAUSANorth America
46964Kidney of brown shark,Carcharhinus plumbeus
119846Brown shark, kidneyUnited States of AmericaUSANorth AmericaBaltimore, Maryland

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Tunicata
#Host Body-Site#Urogenital tract#Kidney

taxonmaps

  • @ref: 69479
  • File name: preview.99_864.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_74;98_81;99_864&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: X74693
  • Sequence Identity:
  • Total samples: 2725
  • soil counts: 65
  • aquatic counts: 1572
  • animal counts: 1045
  • plant counts: 43

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
16687yes, in single casesyes1Risk group (German classification)
1198462Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio harveyi DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: ATCC 35084AB255713252ena669
20218Vibrio harveyi VIB 286 16S ribosomal RNA gene, partial sequenceAF426814744ena669
20218Vibrio carchariae 16S rRNAD11194217ena669
20218Vibrio carchariae 16S rRNAD11243215ena669
20218Vibrio carchariae 16S rRNAD11292191ena669
20218Vibrio harveyi ATCC:35084 16S ribosomal RNA gene, partial sequenceEU1304751474ena669
20218Vibrio harveyi strain ATCC 35084 16S ribosomal RNA gene, partial sequenceGQ3705281062ena669
20218Vibrio harveyi 16S ribosomal RNA gene, partial sequenceHM7713421470ena669
20218V.carchiariae (ATCC 35084T) gene for 16S ribosomal RNAX746931465ena669

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio harveyi strain ATCC 35084669.48wgspatric669
66792Vibrio carchariae ATCC 350842916716654draftimg669

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.725no
anaerobicno97.959yes
halophileyes50.635no
spore-formingno93.876no
glucose-utilyes92.426no
thermophileno99.248yes
flagellatedyes89.238no
motileyes91.237no
aerobicyes87.329yes
glucose-fermentyes87.462yes

External links

@ref: 16687

culture collection no.: DSM 23069, ATCC 35084, CCUG 19116, LMG 7890, CIP 104172

straininfo link

  • @ref: 86263
  • straininfo: 5058

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism19058134Pathogenic Vibrio harveyi, in contrast to non-pathogenic strains, intervenes with the p38 MAPK pathway to avoid an abalone haemocyte immune response.Travers MA, Le Bouffant R, Friedman CS, Buzin F, Cougard B, Huchette S, Koken M, Paillard CJ Cell Biochem10.1002/jcb.219902009Animals, Gastropoda/microbiology, Hemocytes/*immunology, *MAP Kinase Signaling System, Reactive Oxygen Species/metabolism, Vibrio/classification/*pathogenicity, Vibrio Infections/immunology, Virulence, p38 Mitogen-Activated Protein Kinases/*metabolismPhylogeny
23756730Characterization of abalone Haliotis tuberculata-Vibrio harveyi interactions in gill primary cultures.Pichon D, Cudennec B, Huchette S, Djediat C, Renault T, Paillard C, Auzoux-Bordenave SCytotechnology10.1007/s10616-013-9583-12013
33065306Photocatalytic, antiproliferative and antimicrobial properties of copper nanoparticles synthesized using Manilkara zapota leaf extract: A photodynamic approach.Kiriyanthan RM, Sharmili SA, Balaji R, Jayashree S, Mahboob S, Al-Ghanim KA, Al-Misned F, Ahmed Z, Govindarajan M, Vaseeharan BPhotodiagnosis Photodyn Ther10.1016/j.pdpdt.2020.1020582020Animals, Anti-Bacterial Agents/pharmacology, *Anti-Infective Agents, Ascomycota, Chlorocebus aethiops, Copper/pharmacology, *Manilkara, *Metal Nanoparticles, *Photochemotherapy/methods, Photosensitizing Agents/pharmacology, Plant Extracts/pharmacology, Rhizoctonia, Spectroscopy, Fourier Transform Infrared, Vero Cells, Vibrio

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16687Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23069)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23069
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
41717Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16051
46964Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 19116)https://www.ccug.se/strain?id=19116
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
68374Automatically annotated from API ID32E
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
86263Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5058.1StrainInfo: A central database for resolving microbial strain identifiers
119846Curators of the CIPCollection of Institut Pasteur (CIP 104172)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104172