Strain identifier

BacDive ID: 1964

Type strain: Yes

Species: Burkholderia ubonensis

Strain Designation: EY 3383

Strain history: CIP <- 2001, E. Yabuuchi, Gifu Univ., Japan, strain: EY 3383

NCBI tax ID(s): 101571 (species)

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General

@ref: 6890

BacDive-ID: 1964

DSM-Number: 17311

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

description: Burkholderia ubonensis EY 3383 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from road-side surface soil.

NCBI tax id

  • NCBI tax id: 101571
  • Matching level: species

strain history

@refhistory
6890<- CCUG <- CIP <- E. Yabuuchi, GIFU; EY 3383
396502001, E. Yabuuchi, Gifu University, Japan, strain: EY 3383
123706CIP <- 2001, E. Yabuuchi, Gifu Univ., Japan, strain: EY 3383

doi: 10.13145/bacdive1964.20230509.8.1

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 ubonensis
  • full scientific name: Burkholderia ubonensis corrig. Yabuuchi et al. 2000

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia uboniae

@ref: 6890

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia ubonensis

full scientific name: Burkholderia ubonensis Yabuuchi et al. 2000

strain designation: EY 3383

type strain: yes

Morphology

cell morphology

  • @ref: 123706
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 6890
  • incubation period: 2-3 days

pigmentation

  • @ref: 123706
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6890CASO 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
39650MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123706CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6890positivegrowth30mesophilic
39650positivegrowth30mesophilic
58360positivegrowth30-37mesophilic
123706positivegrowth25-41
123706nogrowth5psychrophilic
123706nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58360aerobe
123706obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
123706NaClpositivegrowth0-4 %
123706NaClnogrowth6 %
123706NaClnogrowth8 %
123706NaClnogrowth10 %

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
6836927897tryptophan-energy source
6836917632nitrate+reduction
12370616947citrate+carbon source
1237064853esculin-hydrolysis
12370617632nitrate+reduction
12370616301nitrite-reduction
12370617632nitrate-respiration

antibiotic resistance

  • @ref: 123706
  • 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
12370635581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
6890catalase+1.11.1.6
6890cytochrome-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
123706oxidase+
123706beta-galactosidase-3.2.1.23
123706alcohol dehydrogenase+1.1.1.1
123706gelatinase+
123706amylase-
123706DNase-
123706caseinase+3.4.21.50
123706catalase+1.11.1.6
123706tween esterase+
123706lecithinase+
123706lipase+
123706lysine decarboxylase-4.1.1.18
123706ornithine decarboxylase-4.1.1.17
123706protease+
123706tryptophan deaminase-
123706urease+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
123706-+++-+----++----++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6890+-++--+-+++++++++++++
6890+-+/-+--+-++++++++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123706+++++--++++----++-+++++-+-+----++++++----+-+++--++++-+++++-++++++--+---+++-+++-++--++-+-++++++---+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6890road-side surface soilUbon RatchathaniThailandTHAAsia
58360Soil,road-side surface soilUbon RatchataniThailandTHAAsia1989
123706Environment, Road-side, surface soilUbon RatchataniThailandTHAAsia1989

isolation source categories

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

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6890yes, in single cases1Risk group (German classification)
1237061Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia ubonensis strain CIP 107078 16S ribosomal RNA gene, partial sequenceEU0241791313ena101571
6890Burkholderia uboniae gene for 16S rRNA, partial sequenceAB0305841388ena101571

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia ubonensis LMG 20358GCA_902833085scaffoldncbi101571
66792Burkholderia ubonensis LMG 20358GCA_902499185contigncbi101571
66792Burkholderia ubonensis strain LMG 20358101571.350wgspatric101571
66792Burkholderia ubonensis strain LMG 20358101571.351wgspatric101571

GC content

  • @ref: 6890
  • GC-content: 69.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno86.05no
gram-positiveno97.957no
anaerobicno98.625yes
aerobicyes90.702yes
halophileno94.786no
spore-formingno91.169no
thermophileno99.272yes
glucose-utilyes92.057yes
motileyes86.641no
glucose-fermentno87.37no

External links

@ref: 6890

culture collection no.: DSM 17311, CCUG 48852, CIP 107078, NCTC 13147, LMG 20358

straininfo link

  • @ref: 71609
  • straininfo: 14631

literature

  • topic: Phylogeny
  • Pubmed-ID: 10832977
  • title: Burkholderia uboniae sp. nov., L-arabinose-assimilating but different from Burkholderia thailandensis and Burkholderia vietnamiensis.
  • authors: Yabuuchi E, Kawamura Y, Ezaki T, Ikedo M, Dejsirilert S, Fujiwara N, Naka T, Kobayashi K
  • journal: Microbiol Immunol
  • DOI: 10.1111/j.1348-0421.2000.tb02500.x
  • year: 2000
  • mesh: Anti-Bacterial Agents/pharmacology, Arabinose/*metabolism, Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/*genetics/physiology, DNA, Ribosomal/analysis/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6890Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17311)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17311
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
39650Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19279
58360Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48852)https://www.ccug.se/strain?id=48852
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
71609Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14631.1StrainInfo: A central database for resolving microbial strain identifiers
123706Curators of the CIPCollection of Institut Pasteur (CIP 107078)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107078