Strain identifier
BacDive ID: 17265
Type strain:
Species: Vibrio natriegens
Strain Designation: 111
Strain history: CIP <- 1988, NCIB <- 1961, W.J. Payne, Pseudomonas natriegens
NCBI tax ID(s): 1219067 (strain), 691 (species)
General
@ref: 431
BacDive-ID: 17265
DSM-Number: 759
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Vibrio natriegens 111 is a mesophilic, motile bacterium that was isolated from salt marsh mud.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1219067 | strain |
691 | species |
strain history
@ref | history |
---|---|
431 | <- NCMB <- W.J. Payne (Pseudomonas natriegens). |
121244 | CIP <- 1988, NCIB <- 1961, W.J. Payne, Pseudomonas natriegens |
doi: 10.13145/bacdive17265.20230509.8.1
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 natriegens
- full scientific name: Vibrio natriegens (Payne et al. 1961) Baumann et al. 1981
synonyms
@ref synonym 20215 Beneckea natriegens 20215 Pseudomonas natriegens
@ref: 431
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Vibrio
species: Vibrio natriegens
full scientific name: Vibrio natriegens (Payne et al. 1961) Baumann et al. 1981
strain designation: 111
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 95.707 | ||
69480 | 99.988 | negative | ||
121244 | yes | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
431 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: 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 |
431 | VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) | yes | https://mediadive.dsmz.de/medium/115 | Name: VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) Composition: NaCl 15.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
37063 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
431 | SEA WATER AGAR (DSMZ Medium 246) | yes | https://mediadive.dsmz.de/medium/246 | Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water |
121244 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 | |
121244 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
431 | positive | growth | 30 | mesophilic |
37063 | positive | growth | 25 | mesophilic |
431 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
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 | 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 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
68368 | 17997 | dinitrogen | no |
68368 | 16301 | nitrite | no |
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
68369 | 35581 | indole | - | |
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
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 | 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 |
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 | NO2 | N2 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
431 | - | - | - | - | + | - | - | - | - | - | + | + | + | - | - | + | + | - | + | + | + | - | - |
431 | - | - | - | - | + | - | - | - | - | - | + | + | + | - | - | + | + | - | + | + | + | ||
431 | - | - | - | - | + | - | - | - | - | - | + | + | + | - | - | + | + | - | + | + | + | ||
431 | - | - | - | - | - | - | - | - | - | - | +/- | + | + | - | - | + | + | - | + | + | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
431 | + | - | + | - | - | + | + | - | + | + | - | + | + | + | + | + | - | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
431 | salt marsh mud | Georgia, Sapelo island | USA | USA | North America |
121244 | Environment, Salt marsh mud | Sapelo Island, Georgia | United States of America | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Salt marsh |
#Environmental | #Terrestrial | #Mud (Sludge) |
#Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_89.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_74;98_81;99_89&stattab=map
- Last taxonomy: Vibrio
- 16S sequence: X74714
- Sequence Identity:
- Total samples: 5164
- soil counts: 169
- aquatic counts: 3075
- animal counts: 1856
- plant counts: 64
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
431 | 1 | Risk group (German classification) |
121244 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Vibrio natriegens 16S ribosomal RNA gene, partial sequence | DQ068938 | 1470 | ena | 1219067 |
20218 | Vibrio natriegens 16S ribosomal RNA gene, partial sequence | HM771343 | 1471 | ena | 1219067 |
20218 | V.natrigens 16S ribosomal RNA | X56581 | 1483 | ena | 1219067 |
20218 | V.natriegens (ATCC 14048T) gene for 16S ribosomal RNA | X74714 | 1466 | ena | 1219067 |
20218 | Vibrio natriegens 16S rRNA | D11211 | 214 | ena | 691 |
20218 | Vibrio natriegens 16S rRNA | D11260 | 214 | ena | 691 |
20218 | Vibrio natriegens 16S rRNA | D11309 | 192 | ena | 691 |
20218 | Vibrio natriegens gene for 16S rRNA, partial sequence, strain: NBRC 15636 | AB680922 | 1478 | ena | 1219067 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | GCA_001456255 | complete | ncbi | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | GCA_001680025 | complete | ncbi | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | GCA_001591085 | contig | ncbi | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | GCA_000417905 | contig | ncbi | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | GCA_000438785 | scaffold | ncbi | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | 1219067.6 | wgs | patric | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | 1219067.11 | wgs | patric | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | 1219067.7 | wgs | patric | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 | 1219067.12 | complete | patric | 1219067 |
66792 | Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 strain ATCC 14048 | 1219067.16 | complete | patric | 1219067 |
66792 | Vibrio natriegens ATCC 14048 | 2811995373 | complete | img | 1219067 |
66792 | Vibrio natriegens ATCC 14048 | 2811995319 | complete | img | 1219067 |
GC content
- @ref: 431
- GC-content: 46.4
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 89.076 | no |
gram-positive | no | 98.343 | no |
anaerobic | no | 96.999 | no |
halophile | yes | 63.538 | no |
spore-forming | no | 95.957 | no |
glucose-util | yes | 92.827 | yes |
motile | yes | 90.729 | no |
aerobic | yes | 89.731 | no |
thermophile | no | 99.373 | yes |
glucose-ferment | yes | 85.211 | yes |
External links
@ref: 431
culture collection no.: DSM 759, ATCC 14048, NCMB 857, CIP 103193, CCUG 4980, LMG 10935, NCIMB 857
straininfo link
- @ref: 86264
- straininfo: 92285
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh |
---|---|---|---|---|---|---|---|
Genetics | 23929482 | Draft Genome Sequence of the Fast-Growing Marine Bacterium Vibrio natriegens Strain ATCC 14048. | Wang Z, Lin B, Hervey WJ 4th, Vora GJ | Genome Announc | 10.1128/genomeA.00589-13 | 2013 | |
Pathogenicity | 28659560 | Environmental Impact of Tributyltin-Resistant Marine Bacteria in the Indigenous Microbial Population of Tributyltin-Polluted Surface Sediments. | Mimura H, Yagi M, Yoshida K | Biocontrol Sci | 10.4265/bio.22.89 | 2017 | DNA, Ribosomal, *Drug Resistance, Microbial, Geologic Sediments/*microbiology, Photobacterium/*drug effects/growth & development, Trialkyltin Compounds/*pharmacology, Water Microbiology, Water Pollutants, Chemical/pharmacology |
31253674 | Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens. | Pfeifer E, Michniewski S, Gatgens C, Munch E, Muller F, Polen T, Millard A, Blombach B, Frunzke J | Appl Environ Microbiol | 10.1128/AEM.00853-19 | 2019 | *DNA Damage, *Osmotic Pressure, Prophages/*physiology, Vibrio/*physiology/virology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
431 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 759) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-759 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
37063 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14963 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68368 | Automatically annotated from API 20E | |||||
68369 | Automatically annotated from API 20NE | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
86264 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92285.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121244 | Curators of the CIP | Collection of Institut Pasteur (CIP 103193) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103193 |