Strain identifier

BacDive ID: 1955

Type strain: Yes

Species: Paraburkholderia caledonica

Strain Designation: W50D

Strain history: CIP <- 2001, CCUG <- 1999, T. Coeyne and P. Vandamme, LMG, Belgium, strain W50D

NCBI tax ID(s): 1218115 (strain), 134536 (species)

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General

@ref: 6731

BacDive-ID: 1955

DSM-Number: 17062

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

description: Paraburkholderia caledonica W50D is an obligate aerobe, mesophilic, motile bacterium that was isolated from rhizosphere soil.

NCBI tax id

NCBI tax idMatching level
134536species
1218115strain

strain history

@refhistory
6731<- CCUG <- T. Coenye and P. Vandamme, Ghent
67770IAM 15100 <-- LMG 19076 <-- T. Coenye R-4200 <-- J. Govan W50D.
117101CIP <- 2001, CCUG <- 1999, T. Coeyne and P. Vandamme, LMG, Belgium, strain W50D

doi: 10.13145/bacdive1955.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Paraburkholderia
  • species: Paraburkholderia caledonica
  • full scientific name: Paraburkholderia caledonica (Coenye et al. 2001) Sawana et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia caledonica

@ref: 6731

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia caledonica

full scientific name: Paraburkholderia caledonica (Coenye et al. 2001) Sawana et al. 2015

strain designation: W50D

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.728
6948099.991negative
117101yesnegativerod-shaped

colony morphology

  • @ref: 6731
  • type of hemolysis: gamma

pigmentation

  • @ref: 117101
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6731R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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
6731CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
41959MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117101CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6731positivegrowth30mesophilic
41959positivegrowth30mesophilic
67770positivegrowth28mesophilic
117101positivegrowth10-37
117101nogrowth5psychrophilic
117101nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117101
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
117101NaClpositivegrowth0-4 %
117101NaClnogrowth6 %
117101NaClnogrowth8 %
117101NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+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
11710116947citrate+carbon source
1171014853esculin-hydrolysis
11710117632nitrate-reduction
11710116301nitrite-reduction
11710117632nitrate-respiration

antibiotic resistance

  • @ref: 117101
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11710135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
6731catalase+1.11.1.6
6731cytochrome-c oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
117101oxidase+
117101beta-galactosidase+3.2.1.23
117101alcohol dehydrogenase-1.1.1.1
117101gelatinase-
117101amylase-
117101DNase-
117101caseinase-3.4.21.50
117101catalase+1.11.1.6
117101tween esterase-
117101lecithinase-
117101lipase-
117101lysine decarboxylase-4.1.1.18
117101ornithine decarboxylase-4.1.1.17
117101protease-
117101tryptophan deaminase-
117101urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117101--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6731-------++++++-++-+-++
6731-------++++++-+++/-+-++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
117101+++++------+++-++--+++-++-++---+++--++-+---+++++++++-++++--++++++--+---+-+-+++-++++++-+-++++-++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6731rhizosphere soilEdinburghUnited KingdomGBREurope
55371Soil rhizosphereEdinburghUnited KingdomGBREurope
67770Soil rhizosphereEdinburghUnited KingdomGBREurope
117101Environment, Soil rhizosphereUnited KingdomGBREurope1999

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host Body-Site#Plant#Rhizosphere
#Host#Plants

taxonmaps

  • @ref: 69479
  • File name: preview.99_7623.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_173;97_187;98_381;99_7623&stattab=map
  • Last taxonomy: Paraburkholderia caledonica
  • 16S sequence: HQ849076
  • Sequence Identity:
  • Total samples: 6100
  • soil counts: 3308
  • aquatic counts: 930
  • animal counts: 719
  • plant counts: 1143

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67311Risk group (German classification)
1171011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia caledonica strain CIP 107098 16S ribosomal RNA gene, partial sequenceEU0241571315ena134536
20218Burkholderia caledonica strain LMG 19076 16S ribosomal RNA gene, partial sequenceHQ8490761126ena134536
6731Burkholderia sp. LMG 19076 16S ribosomal RNA, partial sequenceAF2157041476ena134536
67770Burkholderia caledonica gene for 16S rRNA, partial sequence, strain: NBRC 102488AB6818271460ena134536

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia caledonica LMG 19076GCA_902833635scaffoldncbi134536
66792Burkholderia caledonica NBRC 1024881218115.9wgspatric1218115
66792Paraburkholderia caledonica strain LMG 19076134536.51wgspatric134536
66792Paraburkholderia caledonica NBRC 1024882579779093draftimg1218115
67770Paraburkholderia caledonica NBRC 102488GCA_000685095contigncbi1218115

GC content

  • @ref: 67770
  • GC-content: 62.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes87.807no
gram-positiveno98.323no
anaerobicno98.877no
aerobicyes88.322no
halophileno94.939no
spore-formingno93.754no
thermophileno99.192yes
glucose-utilyes90.765no
flagellatedno83.68no
glucose-fermentno89.733no

External links

@ref: 6731

culture collection no.: DSM 17062, ATCC BAA 462, CCM 7150, CCUG 42236, CIP 107098, LMG 19076, JCM 21561, IAM 15100, JCM 13458, KCTC 12919, NBRC 102488, NCIMB 13884, VTT E-022246

straininfo link

  • @ref: 71600
  • straininfo: 12999

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11411678Burkholderia fungorum sp. nov. and Burkholderia caledonica sp. nov., two new species isolated from the environment, animals and human clinical samples.Coenye T, Laevens S, Willems A, Ohlen M, Hannant W, Govan JR, Gillis M, Falsen E, Vandamme PInt J Syst Evol Microbiol10.1099/00207713-51-3-10992001Animals, Bacterial Proteins/analysis, Base Composition, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Humans, Molecular Sequence Data, Nitrates/metabolism, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Trehalose/metabolism, Triticum/microbiology, Zea mays/microbiologyPathogenicity
Phylogeny17082385Burkholderia ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Kim HB, Park MJ, Yang HC, An DS, Jin HZ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64387-02006Bacterial Typing Techniques, Burkholderia/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flagella, Genes, rRNA, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, *Panax, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, beta-Glucosidase/*biosynthesisGenetics
Phylogeny23710046Burkholderia rhynchosiae sp. nov., isolated from Rhynchosia ferulifolia root nodules.De Meyer SE, Cnockaert M, Ardley JK, Trengove RD, Garau G, Howieson JG, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.048751-02013Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, South Africa, Ubiquinone/chemistryGenetics
Phylogeny26410793Burkholderia dipogonis sp. nov., isolated from root nodules of Dipogon lignosus in New Zealand and Western Australia.Sheu SY, Chen MH, Liu WYY, Andrews M, James EK, Ardley JK, De Meyer SE, James TK, Howieson JG, Coutinho BG, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0006392015Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Introduced Species, Molecular Sequence Data, New Zealand, Nitrogen Fixation, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, Western AustraliaGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6731Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17062)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17062
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
41959Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19301
55371Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42236)https://www.ccug.se/strain?id=42236
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
68382Automatically annotated from API zym
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
71600Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12999.1StrainInfo: A central database for resolving microbial strain identifiers
117101Curators of the CIPCollection of Institut Pasteur (CIP 107098)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107098