Strain identifier

BacDive ID: 2040

Type strain: Yes

Species: Cupriavidus numazuensis

Strain Designation: TE26

Strain history: CIP <- 2005, DSMZ, Wautersia numazuensis <- C. Kageyama, Shizuoka, Japan: strain TE26

NCBI tax ID(s): 1218073 (strain), 221992 (species)

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General

@ref: 6003

BacDive-ID: 2040

DSM-Number: 15562

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Cupriavidus numazuensis TE26 is an aerobe, mesophilic, motile bacterium that was isolated from pristine soil.

NCBI tax id

NCBI tax idMatching level
1218073strain
221992species

strain history

@refhistory
6003<- Ch. Kageyama; TE26
121371CIP <- 2005, DSMZ, Wautersia numazuensis <- C. Kageyama, Shizuoka, Japan: strain TE26

doi: 10.13145/bacdive2040.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Cupriavidus
  • species: Cupriavidus numazuensis
  • full scientific name: Cupriavidus numazuensis (Kageyama et al. 2005) Martínez-Aguilar et al. 2013

  • synonyms

    @refsynonym
    20215Wautersia numadzuensis
    20215Wautersia numazuensis

@ref: 6003

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus numazuensis

full scientific name: Cupriavidus numazuensis (Kageyama et al. 2005) Martínez-Aguilar et al. 2013

strain designation: TE26

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes92.391
69480100negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6003REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6003REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37397MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121371CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6003positivegrowth25mesophilic
37397positivegrowth25mesophilic
63132positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 63132
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30560581435-dehydro-D-gluconate+carbon source
3056017128adipate+carbon source
3056018403L-arabitol+carbon source
3056027689decanoate+carbon source
3056016947citrate+carbon source
3056033984fucose+carbon source
3056024265gluconate+carbon source
3056025115malate+carbon source
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30560urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6003+---+---+-----+++++++
6003+---+---------+++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6003pristine soilShizuoka prefectureJapanJPNAsia
63132Pristine soilJapanJPNAsia2005
121371Environment, Pristine soilJapanJPNAsia2001

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3685.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_409;97_464;98_534;99_3685&stattab=map
  • Last taxonomy: Cupriavidus
  • 16S sequence: AB104447
  • Sequence Identity:
  • Total samples: 6080
  • soil counts: 2258
  • aquatic counts: 1798
  • animal counts: 1650
  • plant counts: 374

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60031Risk group (German classification)
1213711Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6003
  • description: Wautersia numazuensis gene for 16S rRNA, complete sequence, strain: TE26
  • accession: AB104447
  • length: 1529
  • database: ena
  • NCBI tax ID: 221992

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cupriavidus numazuensis LMG 26411GCA_905397435contigncbi221992
66792Cupriavidus numazuensis strain LMG 26411221992.4wgspatric221992

GC content

  • @ref: 6003
  • GC-content: 64

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.24no
gram-positiveno98.687no
anaerobicno98.813yes
aerobicyes92.16yes
halophileno95.045no
spore-formingno93.81no
glucose-utilno60.166no
flagellatedno52.242no
thermophileno99.201yes
glucose-fermentno91.667yes

External links

@ref: 6003

culture collection no.: DSM 15562, CIP 108892, LMG 26411, CCUG 64483, NBRC 100056

straininfo link

  • @ref: 71687
  • straininfo: 200038

literature

  • topic: Phylogeny
  • Pubmed-ID: 22389284
  • title: Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov.
  • authors: Martinez-Aguilar L, Caballero-Mellado J, Estrada-de Los Santos P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.038729-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Cupriavidus/*classification/genetics, DNA, Bacterial/genetics, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6003Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15562)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15562
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
30560Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2689128776041
37397Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6573
63132Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 64483)https://www.ccug.se/strain?id=64483
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)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71687Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID200038.1StrainInfo: A central database for resolving microbial strain identifiers
121371Curators of the CIPCollection of Institut Pasteur (CIP 108892)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108892