Strain identifier

BacDive ID: 130763

Type strain: Yes

Species: Vibrio cholerae

Strain Designation: strain 3, J4308, 3

Strain history: CIP <- 1962, NCTC, Vibrio cholerae asiaticus <- 1949, H.J. Bensted: strain 3

NCBI tax ID(s): 1408478 (strain), 666 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 21977

BacDive-ID: 130763

DSM-Number: 100200

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

description: Vibrio cholerae strain 3 is a facultative anaerobe, mesophilic, Gram-negative bacterium that has multiple antibiotic resistances.

NCBI tax id

NCBI tax idMatching level
1408478strain
666species

strain history

@refhistory
21977<- CIP; CIP 62.13 <- NCTC; NCTC 8021 <- H.J. Bensted, PHLS - Colindale; strain 3
118251CIP <- 1962, NCTC, Vibrio cholerae asiaticus <- 1949, H.J. Bensted: strain 3

doi: 10.13145/bacdive130763.20230509.8.1

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 cholerae
  • full scientific name: Vibrio cholerae Pacini 1854 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Vibrio albensis

@ref: 21977

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio cholerae

full scientific name: Vibrio cholerae Pacini 1854

strain designation: strain 3, J4308, 3

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.91
118251negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21977COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
21977TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
39747MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118251CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
118251CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
21977positivegrowth30mesophilic
39747positivegrowth30mesophilic
118251positivegrowth15-41
118251nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118251
  • oxygen tolerance: facultative anaerobe

antibiogram

@refmediumincubation temperatureoxygen conditionPenicillin Goxacillinampicillinticarcillinmezlocillincefalotincefazolincefotaximeaztreonamimipenemtetracyclinechloramphenicolgentamycinamikacinvancomycinerythromycinlincomycinofloxacinnorfloxacincolistinpipemidic acidnitrofurantoinbacitracinpolymyxin bkanamycinneomycindoxycyclineceftriaxoneclindamycinfosfomycinmoxifloxacinlinezolidnystatinquinupristin/dalfopristinteicoplaninpiperacillin/tazobactam
21977Mueller-Hinton Agar30aerob160203234-36302644342834-363824240228424612-143628014-1624-2620-22324210104028014032
21977Mueller-Hinton Agar30aerob160203032-343024423428363622220200404014343001624203438-401012-1436-383012-14161034
21977Mueller-Hinton Agar30aerob160203032-343024423428363622220200404014343001624203438-401012-1436-383012-14161034

spore formation

@refspore formationconfidence
69481no100
69480no99.962

halophily

@refsaltgrowthtested relationconcentration
118251NaClpositivegrowth0-8 %
118251NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
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
11825116947citrate+carbon source
1182514853esculin-hydrolysis
11825117234glucose+fermentation
11825117716lactose-fermentation
11825117632nitrate+reduction
11825116301nitrite-reduction
118251132112sodium thiosulfate-builds gas from

antibiotic resistance

  • @ref: 118251
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno
11825135581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
6836815688acetoin+
6836835581indole+
11825115688acetoin-
11825117234glucose+

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
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
118251oxidase+
118251beta-galactosidase+3.2.1.23
118251alcohol dehydrogenase-1.1.1.1
118251gelatinase+
118251amylase+
118251DNase+
118251caseinase+3.4.21.50
118251catalase+1.11.1.6
118251tween esterase+
118251gamma-glutamyltransferase+2.3.2.2
118251lecithinase+
118251lipase+
118251lysine decarboxylase+4.1.1.18
118251ornithine decarboxylase+4.1.1.17
118251phenylalanine ammonia-lyase-4.3.1.24
118251tryptophan deaminase-
118251urease-3.5.1.5

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21977+-+++---+++++---+---+
21977+-+++---+++++---+---+
21977+-+++---+++++---+---+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21977+++---+++-+++++--++-+

Isolation, sampling and environmental information

isolation

  • @ref: 21977
  • geographic location: unknown?

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
219772Risk group (German classification)
1182512Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21977
  • description: V.cholerae (CECT 514 T) 16S rRNA gene
  • accession: X76337
  • length: 1538
  • database: ena
  • NCBI tax ID: 666

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio cholerae CECT 514GCA_013155105completencbi666
66792Vibrio cholerae ATCC 140351408478.3wgspatric1408478
66792Vibrio cholerae strain CECT 514666.5088completepatric666
66792Vibrio cholerae ATCC 140352556921658draftimg1408478
66792Vibrio cholerae NCTC8021GCA_028120825contigncbi666
66792Vibrio cholerae ATCC 14035GCA_000621645scaffoldncbi1408478

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes79.908no
gram-positiveno98.869no
anaerobicno94.762no
aerobicyes80.186no
halophileno61.386no
spore-formingno96.82no
glucose-utilyes87.608yes
thermophileno98.681no
motileyes85.465no
glucose-fermentyes85.257yes

External links

@ref: 21977

culture collection no.: CCUG 9118 A, DSM 100200, ATCC 14035, CCUG 9118, CIP 62.13, NCTC 8021, CECT 514

straininfo link

  • @ref: 89261
  • straininfo: 389338

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7474354[Causative agent of the so-called "light disease of shrimps" is luminescent Vibrio cholerae non-O1].Shimada T, Arakawa E, Itoh K, Kosako Y, Okitsu T, Yamai S, Nishino M, Nakajima TNihon Saikingaku Zasshi10.3412/jsb.50.8631995Animals, Decapoda/*microbiology, Luminescent Measurements, Serotyping, Vibrio cholerae/*classification/isolation & purification/metabolismEnzymology
Metabolism7567791Characterization of the melanogenic system in Vibrio cholerae, ATCC 14035.Ruzafa C, Sanchez-Amat A, Solano FPigment Cell Res10.1111/j.1600-0749.1995.tb00656.x1995Chromatography, High Pressure Liquid, Culture Media, Homogentisic Acid/metabolism, Hydrogen-Ion Concentration, Kinetics, Melanins/*biosynthesis, Monophenol Monooxygenase/metabolism, Phenylpyruvic Acids/metabolism, Transaminases/metabolism, Tyrosine, Vibrio cholerae/*metabolismCultivation
Metabolism9734339Comparative tyrosine degradation in Vibrio cholerae strains. The strain ATCC 14035 as a prokaryotic melanogenic model of homogentisate-releasing cell.Sanchez-Amat A, Ruzafa C, Solano FComp Biochem Physiol B Biochem Mol Biol10.1016/s0305-0491(98)00028-51998*Dioxygenases, Enzyme Induction, Homogentisate 1,2-Dioxygenase, Homogentisic Acid/metabolism, Hydrolases/biosynthesis/metabolism, Kinetics, Models, Biological, Oxygenases/biosynthesis/metabolism, Serotyping, Tyrosine/*metabolism, Vibrio cholerae/*classification/growth & development/*metabolism, cis-trans-Isomerases/biosynthesis/metabolismEnzymology
Enzymology10049907Role of surface proteins in Vibrio cholerae attachment to chitin.Tarsi R, Pruzzo CAppl Environ Microbiol10.1128/AEM.65.3.1348-1351.19991999Acetylglucosamine/pharmacology, *Bacterial Adhesion/drug effects, Chitin/*physiology, Disaccharides/pharmacology, Electrophoresis, Polyacrylamide Gel, Membrane Proteins/*metabolism, Periodic Acid/pharmacology, Pronase/metabolism, Vibrio cholerae/*physiology, Wheat Germ Agglutinins/pharmacologyMetabolism
Pathogenicity10347079Response of pathogenic Vibrio species to high hydrostatic pressure.Berlin DL, Herson DS, Hicks DT, Hoover DGAppl Environ Microbiol10.1128/AEM.65.6.2776-2780.19991999Colony Count, Microbial, Disinfection/methods, Humans, *Hydrostatic Pressure, Vibrio/growth & development/isolation & purification/*physiology, Vibrio Infections/microbiologyEnzymology
Enzymology23508422Comparison of two recombinant systems for expression of cholera toxin B subunit from Vibrio cholerae.Boustanshenas M, Bakhshi B, Ghorbani M, Norouzian DIndian J Med Microbiol10.4103/0255-0857.1087052013Cholera Toxin/*biosynthesis/genetics, Cloning, Molecular, Escherichia coli/genetics, *Gene Expression, Genetic Vectors, Plasmids, Polymerase Chain Reaction, Recombinant Proteins/biosynthesis/genetics, Vibrio cholerae/genetics
24165439The hows and whys of constructing a native recombinant cholera vaccine.Boustanshenas M, Bakhshi BBioengineered10.4161/bioe.264202013Animals, Cholera Toxin/*immunology, Cholera Vaccines/*immunology, Female
Enzymology24842138A single point mutation within the coding sequence of cholera toxin B subunit will increase its expression yield.Bakhshi B, Boustanshenas M, Ghorbani MIran Biomed J10.6091/ibj.1165.20142014Amino Acid Sequence, Blotting, Western, Cholera Toxin/*genetics/*metabolism, Cloning, Molecular, DNA/metabolism, Electrophoresis, Agar Gel, Electrophoresis, Polyacrylamide Gel, Mutant Proteins/metabolism, Open Reading Frames/*genetics, Point Mutation/*genetics, Polymerase Chain Reaction, Recombinant Proteins/metabolismMetabolism
Phylogeny29665368Streptomyces thermoviolaceus SRC3 strain as a novel source of the antibiotic adjuvant streptazolin: A statistical approach toward the optimized production.Djinni I, Djoudi W, Souagui S, Rabia F, Rahmouni S, Mancini I, Kecha MJ Microbiol Methods10.1016/j.mimet.2018.04.0082018Algeria, Anti-Infective Agents/*isolation & purification/*metabolism, Bacteriological Techniques, Candida albicans/drug effects, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments/microbiology, Methicillin-Resistant Staphylococcus aureus/drug effects, Piperidines/*isolation & purification/*metabolism, RNA, Ribosomal, 16S/genetics, Rivers/microbiology, Salmonella typhi/drug effects, Sequence Analysis, DNA, Streptomyces/classification/*growth & development/isolation & purification/*metabolism, Time Factors, Vibrio cholerae/drug effectsPathogenicity
30636952Growth Inhibitory Effect of Lactocare on Vibrio cholerae.Asadi M, Fazeli MR, Sabokbar AIran J Pathol2018
31143687Capsaicin inhibitory effects on Vibrio cholerae toxin genes expression.Erfanimanesh S, Eslami G, Taherpour A, Hashemi AAvicenna J Phytomed2019
32944045Genetic Diversity of ctxB Gene Among Classical O1 and El Tor Strains of Vibrio cholerae using High-Resolution Melting Curve Analysis.Mahboobi M, Mirnejad R, Sedighian H, Piranfar V, Imani Fooladi AAIran J Pathol10.30699/ijp.2020.127793.23932020
Pathogenicity33913531Vibrio cholerae toxin coregulated pilus provokes inflammatory responses in Coculture model of Caco-2 and peripheral blood mononuclear cells (PBMC) leading to increased colonization.Ghasemi M, Bakhshi B, Khashei R, Soudi S, Boustanshenas MMicrobiol Immunol10.1111/1348-0421.128892021Antigens, CD/immunology, Caco-2 Cells, Cell Adhesion Molecules/immunology, *Cholera, Cholera Toxin/*immunology, Coculture Techniques, Cytokines/immunology, Fimbriae Proteins/*immunology, Humans, Leukocytes, Mononuclear/*immunology/microbiology, *Vibrio cholerae
Metabolism35171023Pufferfish (Tetraodon cutcutia) Sampled from a Freshwater River Serves as an Intermediate Reservoir of a Sucrose Nonfermenting Variant of Vibrio cholerae PS-4.Das L, Deb S, Arakawa E, Yamasaki S, Das SKMicrobiol Spectr10.1128/spectrum.01221-212022Animals, Bacterial Proteins/genetics/metabolism, Cholera/microbiology, Disease Reservoirs/*microbiology, Endotoxins/metabolism, Fermentation, Fructose/metabolism, Genome, Bacterial, Glucose/metabolism, Humans, Phosphotransferases/genetics/metabolism, Rivers/microbiology, Skin/microbiology, Sucrose/*metabolism, Tetraodontiformes/*microbiology, Vibrio cholerae/genetics/isolation & purification/*metabolismPathogenicity
35368520Investigation of the Antibacterial and Antibiofilm Activity of Selenium Nanoparticles against Vibrio cholerae as a Potent Therapeutics.Bagheri-Josheghani S, Bakhshi BCan J Infect Dis Med Microbiol10.1155/2022/34322352022
35737135Bacterial community structure and bacterial isolates having antimicrobial potential in shrimp pond aquaculture.Ali S, Xie J, Zada S, Hu Z, Zhang Y, Cai R, Wang HAMB Express10.1186/s13568-022-01423-92022

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
21977Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100200Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100200)
39747Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9958
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
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89261Reimer, 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-ID389338.1
118251Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2062.13Collection of Institut Pasteur (CIP 62.13)