Strain identifier

BacDive ID: 1987

Type strain: Yes

Species: Burkholderia seminalis

Strain Designation: AU0475

Strain history: <- CCUG <- E. Vanlaere, LMG <- J. J. LiPuma; AU0475

NCBI tax ID(s): 1108969 (strain), 488731 (species)

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General

@ref: 17254

BacDive-ID: 1987

DSM-Number: 23518

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

description: Burkholderia seminalis AU0475 is an aerobe, mesophilic, Gram-negative bacterium that has a yellow pigmentation and was isolated from human sputum from cystic fibrosis patient.

NCBI tax id

NCBI tax idMatching level
1108969strain
488731species

strain history

  • @ref: 17254
  • history: <- CCUG <- E. Vanlaere, LMG <- J. J. LiPuma; AU0475

doi: 10.13145/bacdive1987.20230509.8.1

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 seminalis
  • full scientific name: Burkholderia seminalis Vanlaere et al. 2008

@ref: 17254

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia seminalis

full scientific name: Burkholderia seminalis Vanlaere et al. 2008

strain designation: AU0475

type strain: yes

Morphology

cell morphology

  • @ref: 23365
  • gram stain: negative
  • cell shape: rod-shaped

colony morphology

  • @ref: 17254
  • type of hemolysis: gamma

pigmentation

  • @ref: 23365
  • production: yes
  • color: yellow

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17254COLUMBIA 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
17254R2A 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

culture temp

@refgrowthtypetemperaturerange
17254positivegrowth30mesophilic
23365positivegrowth30-37mesophilic
23365inconsistentgrowth42thermophilic
60238positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23365aerobe
60238aerobe

spore formation

  • @ref: 23365
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336517306maltose-assimilation
2336517632nitrate-reduction
2336517128adipate+assimilation
2336527689decanoate+assimilation
2336516947citrate+assimilation
233658391D-gluconate+assimilation
2336516899D-mannitol+assimilation
2336516024D-mannose+assimilation
2336517234glucose+assimilation
2336530849L-arabinose+assimilation
2336515589L-malate+assimilation
23365506227N-acetylglucosamine+assimilation
2336518401phenylacetate+assimilation
2336517992sucrose+assimilation
2336515963ribitol+builds acid from
2336517234glucose+builds acid from
2336517716lactose+builds acid from
2336517306maltose+builds acid from
2336518222xylose+builds acid from
233654853esculin+hydrolysis
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
17254catalase+1.11.1.6
17254cytochrome-c oxidase+1.9.3.1
23365arginine dihydrolase-3.5.3.6
23365beta-galactosidase+3.2.1.23
23365cytochrome oxidase+1.9.3.1
23365gelatinase+
23365lysine decarboxylase+4.1.1.18
23365ornithine decarboxylase+4.1.1.17
23365tryptophanase-4.1.99.1
23365urease-3.5.1.5
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
17254--+--++++++++-+++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
17254human sputum from cystic fibrosis patientUSAUSANorth America
233651998
60238Human sputum,cystic fibrosisUSAUSANorth America2004-06-03

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_198.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_18;97_18;98_21;99_198&stattab=map
  • Last taxonomy: Burkholderia
  • 16S sequence: AM747631
  • Sequence Identity:
  • Total samples: 5054
  • soil counts: 1055
  • aquatic counts: 564
  • animal counts: 1930
  • plant counts: 1505

Safety information

risk assessment

  • @ref: 17254
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17254
  • description: Burkholderia seminalis DSM 2351 partial 16S rRNA gene, type strain R-24196T
  • accession: AM747631
  • length: 1498
  • database: ena
  • NCBI tax ID: 1108969

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia seminalis LMG 24067GCA_902499165contigncbi488731
66792Burkholderia seminalis DSM 23518 LMG 24067GCA_902832885scaffoldncbi1108969
66792Burkholderia seminalis DSM 23518 strain LMG 240671108969.3wgspatric1108969
66792Burkholderia seminalis strain LMG 24067488731.17wgspatric488731

GC content

  • @ref: 23365
  • GC-content: 67.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno79.727no
gram-positiveno98.357yes
anaerobicno98.778yes
aerobicyes90.208no
halophileno91.061no
spore-formingno93.479yes
thermophileno99.603no
glucose-utilyes90.549yes
motileyes87.886no
glucose-fermentno85.267yes

External links

@ref: 17254

culture collection no.: DSM 23518, CCUG 54564, LMG 24067

straininfo link

  • @ref: 71634
  • straininfo: 137158

literature

  • topic: Phylogeny
  • Pubmed-ID: 18599699
  • title: Burkholderia latens sp. nov., Burkholderia diffusa sp. nov., Burkholderia arboris sp. nov., Burkholderia seminalis sp. nov. and Burkholderia metallica sp. nov., novel species within the Burkholderia cepacia complex.
  • authors: Vanlaere E, Lipuma JJ, Baldwin A, Henry D, De Brandt E, Mahenthiralingam E, Speert D, Dowson C, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65634-0
  • year: 2008
  • mesh: Base Sequence, Burkholderia/chemistry/*classification/genetics, Burkholderia cepacia complex/*classification, Genes, Bacterial/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17254Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23518)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23518
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
23365Elke Vanlaere, John J. LiPuma, Adam Baldwin, Deborah Henry, Evie De Brandt, Eshwar Mahenthiralingam, David Speert, Chris Dowson, Peter Vandamme10.1099/ijs.0.65634-0Burkholderia latens sp. nov., Burkholderia diffusa sp. nov., Burkholderia arboris sp. nov., Burkholderia seminalis sp. nov. and Burkholderia metallica sp. nov., novel species within the Burkholderia cepacia complexIJSEM 58: 1580-1590 200818599699
60238Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54564)https://www.ccug.se/strain?id=54564
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
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
71634Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137158.1StrainInfo: A central database for resolving microbial strain identifiers