Strain identifier

BacDive ID: 1947

Type strain: Yes

Species: Burkholderia dolosa

Strain Designation: AU0645, R-5670

Strain history: CIP <- 2004, CCUG <- 2003, LMG <- T. Coenye, Gent, Belgium <- J. LiPuma, Philadelphia, USA

NCBI tax ID(s): 152500 (species)

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General

@ref: 6284

BacDive-ID: 1947

DSM-Number: 16088

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

description: Burkholderia dolosa AU0645 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sputum of cystic fibrosis patient.

NCBI tax id

  • NCBI tax id: 152500
  • Matching level: species

strain history

@refhistory
6284<- LMG <- T. Coenye, Univ. Ghent, Belgium; R-5670 <- J. J. LiPuma, Philadelphia USA; AU0645
118960CIP <- 2004, CCUG <- 2003, LMG <- T. Coenye, Gent, Belgium <- J. LiPuma, Philadelphia, USA

doi: 10.13145/bacdive1947.20250331.9.3

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 dolosa
  • full scientific name: Burkholderia dolosa Vermis et al. 2004

@ref: 6284

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia dolosa

full scientific name: Burkholderia dolosa Vermis et al. 2004

strain designation: AU0645, R-5670

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
30053negative2 µmrod-shapedyes
118960negativerod-shapedyes
125438negative97.5

colony morphology

  • @ref: 6284
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6284CASO 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
36729MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118960CIP Medium 339yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=339
118960CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
6284positivegrowth28
36729positivegrowth30
57842positivegrowth37
118960positivegrowth30-41
118960nogrowth5
118960nogrowth10

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30053aerobe
57842aerobe
118960obligate aerobe
125439obligate aerobe99.5

halophily

@refsaltgrowthtested relationconcentration
118960NaClpositivegrowth0-4 %
118960NaClnogrowth6 %
118960NaClnogrowth8 %
118960NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3005322599arabinose+carbon source
1189604853esculin-hydrolysis
11896017632nitrate+reduction
11896016301nitrite-reduction
11896017632nitrate-respiration
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

antibiotic resistance

  • @ref: 118960
  • 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
11896035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
6284catalase+1.11.1.6
6284cytochrome-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
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
118960oxidase+
118960beta-galactosidase+3.2.1.23
118960alcohol dehydrogenase-1.1.1.1
118960gelatinase-
118960amylase-
118960DNase-
118960caseinase-3.4.21.50
118960catalase+1.11.1.6
118960tween esterase+
118960lecithinase-
118960lipase-
118960lysine decarboxylase-4.1.1.18
118960ornithine decarboxylase-4.1.1.17
118960protease+
118960tryptophan deaminase-
118960urease-3.5.1.5
68369gelatinase-
68369urease-3.5.1.5
68382beta-glucosidase-3.2.1.21
68369cytochrome oxidase+1.9.3.1
68369beta-glucosidase-3.2.1.21
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    57842C14:04.114
    57842C15:00.415
    57842C16:027.216
    57842C17:00.217
    57842C18:00.418
    57842C12:0 ALDE ?0.210.915
    57842C13:1 at 12-130.512.931
    57842C14:0 2OH0.815.205
    57842C14:0 3OH/C16:1 ISO I5.715.485
    57842C16:0 2OH317.233
    57842C16:0 3OH4.917.52
    57842C16:1 2OH0.917.047
    57842C16:1 ω5c0.615.908
    57842C16:1 ω7c615.819
    57842C17:0 CYCLO24.116.888
    57842C18:1 2OH1.219.088
    57842C18:1 ω7c /12t/9t6.117.824
    57842C19:0 CYCLO ω8c12.118.9
    57842Unidentified0.316.091
    57842Unidentified0.317.748
    57842Unidentified0.618.139
    57842unknown 18.4450.418.445
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118960-+++++----++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6284+------++++++-+++++++
6284+------++++++-++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118960+++++--------+-----+++--+-++-+++++--++-+---++--+++++-++++--++++++------+++--++-+++--+-+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6284sputum of cystic fibrosis patientUSAUSANorth America
57842Human sputum,cystic fibrosisUSAUSANorth America
118960Human, Sputum, cystic fibrosisUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Disease#Cystic fibrosis
#Infection#Patient
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62842Risk group (German classification)
1189601Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia dolosa strain LMG 18943 16S ribosomal RNA gene, partial sequenceHQ8490791124nuccore152500
20218Burkholderia dolosa strain LMG 18943 16S ribosomal RNA gene, partial sequenceJX9869701485nuccore152500

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia dolosa LMG 18943GCA_902499135contigncbi152500
66792Burkholderia dolosa strain FDAARGOS_1463152500.30completepatric152500
66792Burkholderia dolosa strain LMG 18943152500.12wgspatric152500
66792Burkholderia dolosa strain FDAARGOS_1463152500.66completepatric152500
66792Burkholderia dolosa strain FDAARGOS_1463152500.52completepatric152500
66792Burkholderia dolosa strain FDAARGOS_1463152500.41completepatric152500

GC content

  • @ref: 30053
  • GC-content: 67.3

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.532yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.482no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.565no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5no
125438motile2+flagellatedAbility to perform flagellated movementyes79.53no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno86.7
125439BacteriaNetmotilityAbility to perform movementyes69.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative78.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.5

External links

@ref: 6284

culture collection no.: DSM 16088, CCUG 47727, LMG 18943, CIP 108406

straininfo link

  • @ref: 71592
  • straininfo: 13005

literature

  • topic: Phylogeny
  • Pubmed-ID: 15143009
  • title: Proposal to accommodate Burkholderia cepacia genomovar VI as Burkholderia dolosa sp. nov.
  • authors: Vermis K, Coenye T, LiPuma JJ, Mahenthiralingam E, Nelis HJ, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02888-0
  • year: 2004
  • mesh: Base Sequence, Burkholderia/*classification/genetics/metabolism, Burkholderia cepacia/*classification/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6284Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16088)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16088
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
30053Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126414
36729Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6025
57842Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47727)https://www.ccug.se/strain?id=47727
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
71592Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13005.1StrainInfo: A central database for resolving microbial strain identifiers
118960Curators of the CIPCollection of Institut Pasteur (CIP 108406)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108406
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1