Strain identifier

BacDive ID: 130230

Type strain: Yes

Species: Paraburkholderia eburnea

Strain Designation: RR11

Strain history: S.-S. Lee RR11.

NCBI tax ID(s): 1189126 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 21541

BacDive-ID: 130230

DSM-Number: 29414

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Paraburkholderia eburnea RR11 is a mesophilic, Gram-negative bacterium that was isolated from peat soil near coal mine.

NCBI tax id

  • NCBI tax id: 1189126
  • Matching level: species

strain history

@refhistory
21541<- JCM <- S.-S. Lee; RR11
67770S.-S. Lee RR11.

doi: 10.13145/bacdive130230.20230509.8.1

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 eburnea
  • full scientific name: Paraburkholderia eburnea corrig. (Kang et al. 2014) Sawana et al. 2015
  • synonyms

    @refsynonym
    20215Burkholderia eburnea
    20215Paraburkholderia eburne

@ref: 21541

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia eburnea

full scientific name: Paraburkholderia eburnea (Kang et al. 2014) Sawana et al. 2015

strain designation: RR11

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.976

colony morphology

  • @ref: 21541
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 21541
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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
21541positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+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
21541catalase+1.11.1.6
21541cytochrome-c 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21541-------+++/-++++/-++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
21541peat soil near coal mineProkopyevsk, Kemerovo OblastRussiaRUSAsia53.880886.7275
67770Peat soil (pH 4.5) near a coal mine at ProkopyevskKemerovo OblastRussiaRUS

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)

Safety information

risk assessment

  • @ref: 21541
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21541
  • description: Burkholderia eburnea strain RR11 from Russia 16S ribosomal RNA gene, partial sequence
  • accession: JQ692176
  • length: 1446
  • database: ena
  • NCBI tax ID: 1189126

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia eburnea LMG 29537GCA_003003375scaffoldncbi1189126
66792Paraburkholderia eburnea strain JCM 180701189126.3wgspatric1189126
66792Paraburkholderia eburnea strain LMG 295371189126.4wgspatric1189126
66792Paraburkholderia eburnea LMG 295372708743144draftimg1189126
66792Paraburkholderia eburnea JCM 180702708743145draftimg1189126
67770Paraburkholderia eburnea JCM 18070GCA_002917095scaffoldncbi1189126

GC content

  • @ref: 21541
  • GC-content: 60.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno80.755no
gram-positiveno98.089no
anaerobicno98.834no
aerobicyes88.653no
halophileno94.972no
spore-formingno93.47no
glucose-utilyes93.307no
thermophileno99.301yes
motileyes84.975no
glucose-fermentno88.733yes

External links

@ref: 21541

culture collection no.: DSM 29414, JCM 18070, KEMC 7302-065, LMG 29537

straininfo link

  • @ref: 88772
  • straininfo: 399001

literature

  • topic: Phylogeny
  • Pubmed-ID: 24363296
  • title: Burkholderia eburnea sp. nov., isolated from peat soil.
  • authors: Kang SR, Srinivasan S, Lee SS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.051078-0
  • year: 2013
  • mesh: Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21541Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29414Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29414)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88772Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399001.1