Strain identifier
BacDive ID: 130763
Type strain:
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)
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 id | Matching level |
---|---|
1408478 | strain |
666 | species |
strain history
@ref | history |
---|---|
21977 | <- CIP; CIP 62.13 <- NCTC; NCTC 8021 <- H.J. Bensted, PHLS - Colindale; strain 3 |
118251 | CIP <- 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
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.91 | ||
118251 | negative | rod-shaped | yes |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
21977 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
21977 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf | |
39747 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
118251 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
118251 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
21977 | positive | growth | 30 | mesophilic |
39747 | positive | growth | 30 | mesophilic |
118251 | positive | growth | 15-41 | |
118251 | no | growth | 5 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 118251
- oxygen tolerance: facultative anaerobe
antibiogram
@ref | medium | incubation temperature | oxygen condition | Penicillin G | oxacillin | ampicillin | ticarcillin | mezlocillin | cefalotin | cefazolin | cefotaxime | aztreonam | imipenem | tetracycline | chloramphenicol | gentamycin | amikacin | vancomycin | erythromycin | lincomycin | ofloxacin | norfloxacin | colistin | pipemidic acid | nitrofurantoin | bacitracin | polymyxin b | kanamycin | neomycin | doxycycline | ceftriaxone | clindamycin | fosfomycin | moxifloxacin | linezolid | nystatin | quinupristin/dalfopristin | teicoplanin | piperacillin/tazobactam |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21977 | Mueller-Hinton Agar | 30 | aerob | 16 | 0 | 20 | 32 | 34-36 | 30 | 26 | 44 | 34 | 28 | 34-36 | 38 | 24 | 24 | 0 | 22 | 8 | 42 | 46 | 12-14 | 36 | 28 | 0 | 14-16 | 24-26 | 20-22 | 32 | 42 | 10 | 10 | 40 | 28 | 0 | 14 | 0 | 32 |
21977 | Mueller-Hinton Agar | 30 | aerob | 16 | 0 | 20 | 30 | 32-34 | 30 | 24 | 42 | 34 | 28 | 36 | 36 | 22 | 22 | 0 | 20 | 0 | 40 | 40 | 14 | 34 | 30 | 0 | 16 | 24 | 20 | 34 | 38-40 | 10 | 12-14 | 36-38 | 30 | 12-14 | 16 | 10 | 34 |
21977 | Mueller-Hinton Agar | 30 | aerob | 16 | 0 | 20 | 30 | 32-34 | 30 | 24 | 42 | 34 | 28 | 36 | 36 | 22 | 22 | 0 | 20 | 0 | 40 | 40 | 14 | 34 | 30 | 0 | 16 | 24 | 20 | 34 | 38-40 | 10 | 12-14 | 36-38 | 30 | 12-14 | 16 | 10 | 34 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.962 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
118251 | NaCl | positive | growth | 0-8 % |
118251 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | + | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | + | fermentation |
68369 | 27897 | tryptophan | + | energy source |
68369 | 17632 | nitrate | + | reduction |
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | - | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | + | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | + | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | + | hydrolysis |
68368 | 27897 | tryptophan | + | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | + | degradation |
68368 | 25094 | lysine | + | degradation |
68368 | 29016 | arginine | - | hydrolysis |
118251 | 16947 | citrate | + | carbon source |
118251 | 4853 | esculin | - | hydrolysis |
118251 | 17234 | glucose | + | fermentation |
118251 | 17716 | lactose | - | fermentation |
118251 | 17632 | nitrate | + | reduction |
118251 | 16301 | nitrite | - | reduction |
118251 | 132112 | sodium 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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | yes |
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | yes |
68368 | 16136 | hydrogen sulfide | no |
118251 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test | methylred-test |
---|---|---|---|---|---|
68369 | 35581 | indole | + | ||
68368 | 15688 | acetoin | + | ||
68368 | 35581 | indole | + | ||
118251 | 15688 | acetoin | - | ||
118251 | 17234 | glucose | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | + | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
68368 | cytochrome oxidase | + | 1.9.3.1 |
68368 | gelatinase | + | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | + | 4.1.1.17 |
68368 | lysine decarboxylase | + | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
118251 | oxidase | + | |
118251 | beta-galactosidase | + | 3.2.1.23 |
118251 | alcohol dehydrogenase | - | 1.1.1.1 |
118251 | gelatinase | + | |
118251 | amylase | + | |
118251 | DNase | + | |
118251 | caseinase | + | 3.4.21.50 |
118251 | catalase | + | 1.11.1.6 |
118251 | tween esterase | + | |
118251 | gamma-glutamyltransferase | + | 2.3.2.2 |
118251 | lecithinase | + | |
118251 | lipase | + | |
118251 | lysine decarboxylase | + | 4.1.1.18 |
118251 | ornithine decarboxylase | + | 4.1.1.17 |
118251 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
118251 | tryptophan deaminase | - | |
118251 | urease | - | 3.5.1.5 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21977 | + | - | + | + | + | - | - | - | + | + | + | + | + | - | - | - | + | - | - | - | + |
21977 | + | - | + | + | + | - | - | - | + | + | + | + | + | - | - | - | + | - | - | - | + |
21977 | + | - | + | + | + | - | - | - | + | + | + | + | + | - | - | - | + | - | - | - | + |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21977 | + | + | + | - | - | - | + | + | + | - | + | + | + | + | + | - | - | + | + | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 21977
- geographic location: unknown?
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
21977 | 2 | Risk group (German classification) |
118251 | 2 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Vibrio cholerae CECT 514 | GCA_013155105 | complete | ncbi | 666 |
66792 | Vibrio cholerae ATCC 14035 | 1408478.3 | wgs | patric | 1408478 |
66792 | Vibrio cholerae strain CECT 514 | 666.5088 | complete | patric | 666 |
66792 | Vibrio cholerae ATCC 14035 | 2556921658 | draft | img | 1408478 |
66792 | Vibrio cholerae NCTC8021 | GCA_028120825 | contig | ncbi | 666 |
66792 | Vibrio cholerae ATCC 14035 | GCA_000621645 | scaffold | ncbi | 1408478 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 79.908 | no |
gram-positive | no | 98.869 | no |
anaerobic | no | 94.762 | no |
aerobic | yes | 80.186 | no |
halophile | no | 61.386 | no |
spore-forming | no | 96.82 | no |
glucose-util | yes | 87.608 | yes |
thermophile | no | 98.681 | no |
motile | yes | 85.465 | no |
glucose-ferment | yes | 85.257 | yes |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 7474354 | [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 T | Nihon Saikingaku Zasshi | 10.3412/jsb.50.863 | 1995 | Animals, Decapoda/*microbiology, Luminescent Measurements, Serotyping, Vibrio cholerae/*classification/isolation & purification/metabolism | Enzymology |
Metabolism | 7567791 | Characterization of the melanogenic system in Vibrio cholerae, ATCC 14035. | Ruzafa C, Sanchez-Amat A, Solano F | Pigment Cell Res | 10.1111/j.1600-0749.1995.tb00656.x | 1995 | Chromatography, 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/*metabolism | Cultivation |
Metabolism | 9734339 | Comparative 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 F | Comp Biochem Physiol B Biochem Mol Biol | 10.1016/s0305-0491(98)00028-5 | 1998 | *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/metabolism | Enzymology |
Enzymology | 10049907 | Role of surface proteins in Vibrio cholerae attachment to chitin. | Tarsi R, Pruzzo C | Appl Environ Microbiol | 10.1128/AEM.65.3.1348-1351.1999 | 1999 | Acetylglucosamine/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/pharmacology | Metabolism |
Pathogenicity | 10347079 | Response of pathogenic Vibrio species to high hydrostatic pressure. | Berlin DL, Herson DS, Hicks DT, Hoover DG | Appl Environ Microbiol | 10.1128/AEM.65.6.2776-2780.1999 | 1999 | Colony Count, Microbial, Disinfection/methods, Humans, *Hydrostatic Pressure, Vibrio/growth & development/isolation & purification/*physiology, Vibrio Infections/microbiology | Enzymology |
Enzymology | 23508422 | Comparison of two recombinant systems for expression of cholera toxin B subunit from Vibrio cholerae. | Boustanshenas M, Bakhshi B, Ghorbani M, Norouzian D | Indian J Med Microbiol | 10.4103/0255-0857.108705 | 2013 | Cholera Toxin/*biosynthesis/genetics, Cloning, Molecular, Escherichia coli/genetics, *Gene Expression, Genetic Vectors, Plasmids, Polymerase Chain Reaction, Recombinant Proteins/biosynthesis/genetics, Vibrio cholerae/genetics | |
24165439 | The hows and whys of constructing a native recombinant cholera vaccine. | Boustanshenas M, Bakhshi B | Bioengineered | 10.4161/bioe.26420 | 2013 | Animals, Cholera Toxin/*immunology, Cholera Vaccines/*immunology, Female | ||
Enzymology | 24842138 | A single point mutation within the coding sequence of cholera toxin B subunit will increase its expression yield. | Bakhshi B, Boustanshenas M, Ghorbani M | Iran Biomed J | 10.6091/ibj.1165.2014 | 2014 | Amino 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/metabolism | Metabolism |
Phylogeny | 29665368 | Streptomyces 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 M | J Microbiol Methods | 10.1016/j.mimet.2018.04.008 | 2018 | Algeria, 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 effects | Pathogenicity |
30636952 | Growth Inhibitory Effect of Lactocare on Vibrio cholerae. | Asadi M, Fazeli MR, Sabokbar A | Iran J Pathol | 2018 | ||||
31143687 | Capsaicin inhibitory effects on Vibrio cholerae toxin genes expression. | Erfanimanesh S, Eslami G, Taherpour A, Hashemi A | Avicenna J Phytomed | 2019 | ||||
32944045 | Genetic 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 AA | Iran J Pathol | 10.30699/ijp.2020.127793.2393 | 2020 | |||
Pathogenicity | 33913531 | Vibrio 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 M | Microbiol Immunol | 10.1111/1348-0421.12889 | 2021 | Antigens, 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 | |
Metabolism | 35171023 | Pufferfish (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 SK | Microbiol Spectr | 10.1128/spectrum.01221-21 | 2022 | Animals, 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/*metabolism | Pathogenicity |
35368520 | Investigation of the Antibacterial and Antibiofilm Activity of Selenium Nanoparticles against Vibrio cholerae as a Potent Therapeutics. | Bagheri-Josheghani S, Bakhshi B | Can J Infect Dis Med Microbiol | 10.1155/2022/3432235 | 2022 | |||
35737135 | Bacterial 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 H | AMB Express | 10.1186/s13568-022-01423-9 | 2022 |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
21977 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100200 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100200) | |
39747 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/9958 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68368 | Automatically annotated from API 20E | |||
68369 | Automatically annotated from API 20NE | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
89261 | Reimer, 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 identifiers | 10.60712/SI-ID389338.1 | |
118251 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2062.13 | Collection of Institut Pasteur (CIP 62.13) |