Strain identifier

BacDive ID: 136180

Type strain: No

Species: Vibrio vulnificus

Strain history: CIP <- 1988, NCIB <- 1979, M. Nishibuchi: strain ES-7601, Vibrio sp.

NCBI tax ID(s): 672 (species)

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General

@ref: 35507

BacDive-ID: 136180

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

description: Vibrio vulnificus CIP 103196 is a facultative anaerobe, mesophilic, Gram-negative bacterium of the family Vibrionaceae.

NCBI tax id

  • NCBI tax id: 672
  • Matching level: species

strain history

  • @ref: 35507
  • history: CIP <- 1988, NCIB <- 1979, M. Nishibuchi: strain ES-7601, Vibrio sp.

doi: 10.13145/bacdive136180.20250331.9.3

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 vulnificus
  • full scientific name: Vibrio vulnificus (Reichelt et al. 1979) Farmer 1980

  • synonyms

    • @ref: 20215
    • synonym: Beneckea vulnifica

@ref: 35507

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales

family: Vibrionaceae

genus: Vibrio

species: Vibrio vulnificus

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125438negative100
125439negative98.6
35507negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35507MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
35507CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
35507positivegrowth30
35507positivegrowth15-41
35507nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
35507facultative anaerobe
125439obligate aerobe96.7

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.2

halophily

@refsaltgrowthtested relationconcentration
35507NaClpositivegrowth2-6 %
35507NaClnogrowth0 %
35507NaClnogrowth8 %
35507NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3550716947citrate-carbon source
355074853esculin+hydrolysis
3550717234glucose+fermentation
3550717716lactose-fermentation
3550717632nitrate+reduction
3550716301nitrite-reduction
35507132112sodium thiosulfate-builds gas from
3550717234glucose+degradation
3550717632nitrate+respiration
6837118305arbutin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
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
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+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
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

antibiotic resistance

  • @ref: 35507
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 35507
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3550715688acetoin-
3550717234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
35507oxidase+
35507beta-galactosidase-3.2.1.23
35507alcohol dehydrogenase-1.1.1.1
35507gelatinase+
35507amylase+
35507DNase+
35507caseinase+3.4.21.50
35507catalase+1.11.1.6
35507tween esterase+
35507gamma-glutamyltransferase-2.3.2.2
35507lecithinase+
35507lipase+
35507lysine decarboxylase+4.1.1.18
35507ornithine decarboxylase-4.1.1.17
35507phenylalanine ammonia-lyase+4.3.1.24
35507protease+
35507tryptophan deaminase-
35507urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
35507-++++++---++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
35507+---+----++++--------++/-+++++---+---++-+-------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
35507++++-----++----+++++-----------+----------------+++--++----++--------------+--+++-+---+--++++++--++

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample type
35507JapanJPNAsia
35507JapanJPNAsiaEnvironment, Diseased pond-cultured eels

Safety information

risk assessment

  • @ref: 35507
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
124043Vibrio vulnificus strain ATCC 33147 16S ribosomal RNA gene, partial sequence.JQ2539671394nuccore672
124043V.vulnificus (ATCC 33147) gene for 16S ribosomal RNA (partial)Z22992199nuccore672

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio vulnificus ATCC 33147GCA_000764895contigncbi672
66792Vibrio vulnificus ATCC 33147672.93wgspatric672
66792Vibrio vulnificus ATCC 331472651869775draftimg672

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno100no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.005yes
125438spore-formingspore-formingAbility to form endo- or exosporesno86.768no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no71.439yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.5no
125438motile2+flagellatedAbility to perform flagellated movementyes89.687no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.2
125439BacteriaNetmotilityAbility to perform movementyes82.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.7

External links

@ref: 35507

culture collection no.: CIP 103196, ATCC 33147, NCIMB 2136

straininfo link

  • @ref: 93409
  • straininfo: 40356

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity16227349Vibrionaceae as a possible source of Qnr-like quinolone resistance determinants.Poirel L, Liard A, Rodriguez-Martinez JM, Nordmann PJ Antimicrob Chemother10.1093/jac/dki3712005Amino Acid Sequence, Anti-Bacterial Agents/*pharmacology, Bacterial Proteins/chemistry/genetics, DNA, Bacterial/chemistry/genetics, Drug Resistance, Bacterial/*genetics, Escherichia coli/drug effects/genetics, *Gene Transfer, Horizontal, *Genes, Bacterial, Microbial Sensitivity Tests, Molecular Sequence Data, Photobacterium/drug effects/genetics, Polymerase Chain Reaction, Quinolones/*pharmacology, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Vibrio parahaemolyticus/drug effects/genetics, Vibrio vulnificus/drug effects/genetics, Vibrionaceae/*drug effects/*geneticsGenetics
Cultivation21515718Comparison of the effects of environmental parameters on growth rates of Vibrio vulnificus biotypes I, II, and III by culture and quantitative PCR analysis.Chase E, Harwood VJAppl Environ Microbiol10.1128/AEM.00135-112011*Bacterial Load, Bacterial Typing Techniques, Culture Media/chemistry, *Environmental Microbiology, Hydrogen-Ion Concentration, Israel, Polymerase Chain Reaction/methods, Sodium Chloride/metabolism, Temperature, Vibrio vulnificus/drug effects/*growth & development/isolation & purification/radiation effectsMetabolism

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
35507Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103196Collection of Institut Pasteur (CIP 103196)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
93409Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID40356.1
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG