Strain identifier

BacDive ID: 1974

Type strain: Yes

Species: Burkholderia oklahomensis

Strain Designation: C6786

Strain history: CIP <- 2011, DSMZ <- LMG <- M.B. Glass, CDC, Atlanta, USA: strain C6786

NCBI tax ID(s): 342113 (species)

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General

@ref: 15939

BacDive-ID: 1974

DSM-Number: 21774

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

description: Burkholderia oklahomensis C6786 is an aerobe, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from 27-year-old male in farming accident, left thigh wound.

NCBI tax id

  • NCBI tax id: 342113
  • Matching level: species

strain history

@refhistory
15939<- LMG; LMG 23618 <- M. B. Glass, CDC, Atlanta; C6786 <- CDC, Atlanta;
121408CIP <- 2011, DSMZ <- LMG <- M.B. Glass, CDC, Atlanta, USA: strain C6786

doi: 10.13145/bacdive1974.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Burkholderia
  • species: Burkholderia oklahomensis
  • full scientific name: Burkholderia oklahomensis Glass et al. 2006

@ref: 15939

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia oklahomensis

full scientific name: Burkholderia oklahomensis Glass et al. 2006

strain designation: C6786

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23158negativerod-shapedyes
69480yes92.823
69480negative99.987
121408negativerod-shapedyes

colony morphology

  • @ref: 23158
  • colony color: white
  • colony shape: irregular
  • incubation period: 3 days
  • medium used: 5 % sheep blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15939TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
231585 % sheep blood agaryes
37596MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
15939COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
121408CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15939positivegrowth37mesophilic
23158positivegrowth25-37mesophilic
23158positivemaximum42thermophilic
37596positivegrowth37mesophilic
59160positivegrowth25-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23158aerobe
59160aerobe
121408obligate aerobe

spore formation

@refspore formationconfidence
69481no96
69480no99.993

halophily

  • @ref: 23158
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2315827897tryptophan-energy source
2315816136hydrogen sulfide-growth
2315865327D-xylose+assimilation
2315817234glucose+assimilation
2315817716lactose+assimilation
2315817306maltose+assimilation
2315829864mannitol+assimilation
2315817992sucrose+assimilation
2315817632nitrate+reduction
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
6836917632nitrate+reduction
12140817632nitrate+reduction
12140816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2315835581indoleno
12140835581indoleno

metabolite tests

  • @ref: 23158
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
15939catalase+1.11.1.6
15939cytochrome-c oxidase-1.9.3.1
23158arginine decarboxylase+4.1.1.19
23158arginine dihydrolase+3.5.3.6
23158catalase+1.11.1.6
23158cytochrome oxidase+1.9.3.1
23158lysine decarboxylase-4.1.1.18
23158ornithine decarboxylase-4.1.1.17
23158tryptophan deaminase-4.1.99.1
23158urease-3.5.1.5
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
121408oxidase+
121408catalase+1.11.1.6
121408urease-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
121408-+++++----++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15939+--+-++-+-+++-+++++++
15939++-+-++-+-+++-+++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
1593927-year-old male in farming accident, left thigh woundOklahomaUSAUSANorth America
59160Human wound,27-yr-old man,farming accidentOklahomaUSAUSANorth America1973
121408Human, Left thigh woundOklahomaUnited States of AmericaUSANorth America1973

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human#Female
#Host Body-Site#Other#Wound

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159392Risk group (German classification)
1214081Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia oklahomensis strain LMG 23618 16S ribosomal RNA gene, partial sequenceHQ8490921124ena342113
15939Burkholderia oklahomensis strain C6786 16S ribosomal RNA gene, partial sequenceDQ1083881499ena441162

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia oklahomensis C6786GCA_000959365completencbi441162
66792Burkholderia oklahomensis C6786GCA_001522135completencbi441162
66792Burkholderia oklahomensis LMG 23618GCA_900608545contigncbi342113
66792Burkholderia oklahomensis LMG 23618GCA_902829515scaffoldncbi342113
66792Burkholderia oklahomensis C6786GCA_000170375contigncbi441162
66792Burkholderia oklahomensis C6786441162.11completepatric441162
66792Burkholderia oklahomensis C6786441162.12wgspatric441162
66792Burkholderia oklahomensis C6786441162.10wgspatric441162
66792Burkholderia oklahomensis strain LMG 23618342113.5wgspatric342113
66792Burkholderia oklahomensis strain LMG 23618342113.7wgspatric342113
66792Burkholderia oklahomensis C6786641736121draftimg441162
66792Burkholderia oklahomensis C67862814123269completeimg441162
66792Burkholderia oklahomensis C67862627853643completeimg441162

GC content

  • @ref: 23158
  • GC-content: 66.0
  • method: Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileyes86.935yes
flagellatedno82.31no
gram-positiveno97.993no
anaerobicno98.015yes
aerobicyes85.561yes
halophileno92.115no
spore-formingno92.623no
glucose-utilyes92.474yes
thermophileno99.661no
glucose-fermentno88.773yes

External links

@ref: 15939

culture collection no.: DSM 21774, CCUG 51349, CIP 110344, LMG 23618, NCTC 13387, LMG 23678

straininfo link

  • @ref: 71619
  • straininfo: 297151

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957116Burkholderia oklahomensis sp. nov., a Burkholderia pseudomallei-like species formerly known as the Oklahoma strain of Pseudomonas pseudomallei.Glass MB, Steigerwalt AG, Jordan JG, Wilkins PP, Gee JEInt J Syst Evol Microbiol10.1099/ijs.0.63991-02006Burkholderia/classification/genetics/isolation & purification, Burkholderia pseudomallei/*classification/genetics, DNA, Bacterial/analysis, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/*analysis/geneticsPathogenicity
Phylogeny29721827Burkholderia alba sp. nov., isolated from a soil sample on Halla mountain in Jeju island.Lee JW, Kim YE, Park SJJ Microbiol10.1007/s12275-018-8034-22018Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/growth & development/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial/genetics, Hydrogen-Ion Concentration, Islands, Nucleic Acid Hybridization, Phenotype, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride, Soil, *Soil Microbiology, Species Specificity, TemperaturePhenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15939Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21774)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21774
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
23158Mindy B. Glass, Arnold G. Steigerwalt, Jean G. Jordan, Patricia P. Wilkins, Jay E. Gee10.1099/ijs.0.63991-0Burkholderia oklahomensis sp. nov., a Burkholderia pseudomallei-like species formerly known as the Oklahoma strain of Pseudomonas pseudomalleiIJSEM 56: 2171-2176 200616957116
37596Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8193
59160Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51349)https://www.ccug.se/strain?id=51349
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
68382Automatically annotated from API zym
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
71619Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297151.1StrainInfo: A central database for resolving microbial strain identifiers
121408Curators of the CIPCollection of Institut Pasteur (CIP 110344)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110344