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Strain identifier

BacDive ID: 2037

Type strain: Yes

Species: Cupriavidus oxalaticus

Strain Designation: Ox1

Strain history: LMG 2235 <-- W. Harder <-- J. Quale.

NCBI tax ID(s): 1349762 (strain), 96344 (species)

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General

@ref: 554

BacDive-ID: 2037

DSM-Number: 1105

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

description: Cupriavidus oxalaticus Ox1 is a mesophilic bacterium that was isolated from garden soil.

NCBI tax id

NCBI tax idMatching level
96344species
1349762strain

strain history

doi: 10.13145/bacdive2037.20221219.7.1

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 oxalaticus
  • full scientific name: Cupriavidus oxalaticus (Sahin et al. 2000) Vandamme and Coenye 2004

  • synonyms

    @refsynonym
    20215Wautersia oxalatica
    20215Ralstonia oxalaticus
    20215Ralstonia oxalatica

@ref: 554

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus oxalaticus

full scientific name: Cupriavidus oxalaticus (Sahin et al. 2000) Vandamme and Coenye 2004

strain designation: Ox1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes50
6948099.103negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
554R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
554NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
554CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium220.pdf
554TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
40709MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
554positivegrowth28mesophilic
40709positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 94.35

compound production

  • @ref: 554
  • compound: polyhydroxyalkanoic acids

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 96.821

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

metabolite production

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

metabolite tests

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

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
554+-------------+++++++
554+-------------+++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
554garden soil
44481Indian earthworm,intestinal tractIndiaINDAsia
67770Alimentary tract of an Indian earthworm

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

  • @ref: 554
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Cupriavidus oxalaticus partial 16S rRNA gene, type strain CCUG 2086TFN5976101392ena96344
20218Cupriavidus oxalaticus strain CIP 107389 16S ribosomal RNA gene, partial sequenceEU0241561316ena96344
20218Ralstonia oxalatica 16S ribosomal RNA gene, complete sequenceAF1555671469ena96344
20218Wautersia oxalatica 16S rRNA gene, 23S rRNA gene and ITS1, specimen voucher LMG2235AJ783980895ena96344
20218Wautersia oxalatica 16S rRNA gene, 23S rRNA gene and ITS1, specimen voucher LMG2235AJ783981714ena96344
20218Cupriavidus oxalaticus gene for 16S rRNA, partial sequence, strain: NBRC 13593AB6804531459ena96344

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cupriavidus oxalaticus Ox1GCA_016894385completencbi96344
66792Cupriavidus oxalaticus Cupriavidus oxalaticus LMG 2235GCA_900249725chromosomencbi96344
66792Cupriavidus oxalaticus NBRC 135931349762.5wgspatric1349762
66792Cupriavidus oxalaticus strain Cupriavidus oxalaticus LMG 223596344.7wgspatric96344
66792Cupriavidus oxalaticus NBRC 135932731957685draftimg1349762
67770Cupriavidus oxalaticus NBRC 13593 NBRC 13593GCA_001592245contigncbi1349762
67770Cupriavidus oxalaticus isolate Cupriavidus oxalaticus LMG 2235 genome assembly, chromosome: CO2235, whole genome shotgun sequenceLT978515ena96344
66792Enterococcus casseliflavus J2GCA_017356325scaffoldpatric37734
66792Brucella melitensis 1GCA_900236435completepatric29459

GC content

  • @ref: 67770
  • GC-content: 68
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 554

culture collection no.: CCUG 2086, LMG 2235, LMG 5121, DSM 1105, ATCC 11883, NCIB 8642, JCM 11285, IFO 13593, NBRC 13593, NCIMB 8642

straininfo link

@refpassport
20218http://www.straininfo.net/strains/6866
20218http://www.straininfo.net/strains/6863
20218http://www.straininfo.net/strains/6869

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10930072Taxonomic position of "Pseudomonas oxalaticus" strain ox14T (DSM 1105T) (Khambata and Bhat, 1953) and its description in the genus Ralstonia as Ralstonia oxalatica comb. nov.Sahin N, Isik K, Tamer AU, Goodfellow MSyst Appl Microbiol10.1016/s0723-2020(00)80006-52000Bacterial Typing Techniques, DNA, Ribosomal/genetics, Gram-Negative Aerobic Rods and Cocci/*classification, Molecular Sequence Data, Oxalates/metabolism, Pseudomonas/*classification, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny15545472Taxonomy of the genus Cupriavidus: a tale of lost and found.Vandamme P, Coenye TInt J Syst Evol Microbiol10.1099/ijs.0.63247-02004Bacterial Proteins/analysis/isolation & purification, Base Composition, Burkholderiaceae/*classification/genetics/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Proteome/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Metabolism16821716Identification of oxalotrophic bacteria by neural network analysis of numerical phenetic data.Sahin N, Aydin SFolia Microbiol (Praha)10.1007/BF029321612006Gram-Negative Aerobic Bacteria/*classification/metabolism, *Neural Networks, Computer, Oxalates/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
554Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1105)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1105
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
40709Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4819
44481Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2086)https://www.ccug.se/strain?id=2086
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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)