Strain identifier

BacDive ID: 17265

Type strain: Yes

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)

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General

@ref: 431

BacDive-ID: 17265

DSM-Number: 759

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped

description: Vibrio natriegens 111 is a mesophilic, Gram-negative, motile bacterium that was isolated from salt marsh mud.

NCBI tax id

NCBI tax idMatching level
691species
1219067strain

strain history

@refhistory
431<- NCMB <- W.J. Payne (Pseudomonas natriegens).
121244CIP <- 1988, NCIB <- 1961, W.J. Payne, Pseudomonas natriegens

doi: 10.13145/bacdive17265.20250331.9.3

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 natriegens
  • full scientific name: Vibrio natriegens (Payne et al. 1961) Baumann et al. 1981

  • synonyms

    @refsynonym
    20215Pseudomonas natriegens
    20215Beneckea 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

@refgram stainconfidencemotilitycell shape
125439negative93.7
12543890.101yes
125438negative99.5
121244negativeyesrod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
431BACTO 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
431VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115)yeshttps://mediadive.dsmz.de/medium/115Name: 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
37063Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
431SEA WATER AGAR (DSMZ Medium 246)yeshttps://mediadive.dsmz.de/medium/246Name: 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
121244CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
121244CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
431positivegrowth30
37063positivegrowth25
431positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 96

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 94.7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+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
6836927897tryptophan-energy source
6836917632nitrate+reduction
6836817632nitrate-reduction
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose-fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
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
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
431----+-----+++--++-+++--
431----+-----+++--++-+++
431----+-----+++--++-+++
431----------+/-++--++-+++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
431+-+--++-++-+++++-++++
431+----++-++-+++-+-+-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
431salt marsh mudGeorgia, Sapelo islandUSAUSANorth America
121244Environment, Salt marsh mudSapelo Island, GeorgiaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
4311Risk group (German classification)
1212442Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio natriegens 16S ribosomal RNA gene, partial sequenceDQ0689381470nuccore1219067
20218Vibrio natriegens 16S ribosomal RNA gene, partial sequenceHM7713431471nuccore1219067
20218V.natrigens 16S ribosomal RNAX565811483nuccore1219067
20218V.natriegens (ATCC 14048T) gene for 16S ribosomal RNAX747141466nuccore1219067
20218Vibrio natriegens 16S rRNAD11211214nuccore691
20218Vibrio natriegens 16S rRNAD11260214nuccore691
20218Vibrio natriegens 16S rRNAD11309192nuccore691
20218Vibrio natriegens gene for 16S rRNA, partial sequence, strain: NBRC 15636AB6809221478nuccore1219067

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759GCA_001456255completencbi1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759GCA_001680025completencbi1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759GCA_001591085contigncbi1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759GCA_000417905contigncbi1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759GCA_000438785scaffoldncbi1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 7591219067.6wgspatric1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 7591219067.11wgspatric1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 7591219067.7wgspatric1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 7591219067.12completepatric1219067
66792Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 strain ATCC 140481219067.16completepatric1219067
66792Vibrio natriegens ATCC 140482811995373completeimg1219067
66792Vibrio natriegens ATCC 140482811995319completeimg1219067

GC content

  • @ref: 431
  • GC-content: 46.4

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96
125439BacteriaNetgram_stainReaction to gram-stainingnegative93.7
125439BacteriaNetmotilityAbility to perform movementyes68.7
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.7
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.706no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no57.809no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.228no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes90.101no

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

topicPubmed-IDtitleauthorsjournalDOIyearmesh
Genetics23929482Draft Genome Sequence of the Fast-Growing Marine Bacterium Vibrio natriegens Strain ATCC 14048.Wang Z, Lin B, Hervey WJ 4th, Vora GJGenome Announc10.1128/genomeA.00589-132013
Pathogenicity28659560Environmental Impact of Tributyltin-Resistant Marine Bacteria in the Indigenous Microbial Population of Tributyltin-Polluted Surface Sediments.Mimura H, Yagi M, Yoshida KBiocontrol Sci10.4265/bio.22.892017DNA, Ribosomal, *Drug Resistance, Microbial, Geologic Sediments/*microbiology, Photobacterium/*drug effects/growth & development, Trialkyltin Compounds/*pharmacology, Water Microbiology, Water Pollutants, Chemical/pharmacology
31253674Generation 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 JAppl Environ Microbiol10.1128/AEM.00853-192019*DNA Damage, *Osmotic Pressure, Prophages/*physiology, Vibrio/*physiology/virology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
431Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 759)https://www.dsmz.de/collection/catalogue/details/culture/DSM-759
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
37063Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14963
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
68369Automatically annotated from API 20NE
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
86264Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92285.1StrainInfo: A central database for resolving microbial strain identifiers
121244Curators of the CIPCollection of Institut Pasteur (CIP 103193)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103193
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1