Strain identifier
BacDive ID: 130230
Type strain:
Species: Paraburkholderia eburnea
Strain Designation: RR11
Strain history: S.-S. Lee RR11.
NCBI tax ID(s): 1189126 (species)
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
@ref | history |
---|---|
21541 | <- JCM <- S.-S. Lee; RR11 |
67770 | S.-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
@ref synonym 20215 Burkholderia eburnea 20215 Paraburkholderia 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
21541 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
21541 | catalase | + | 1.11.1.6 |
21541 | cytochrome-c oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21541 | - | - | - | - | - | - | - | + | + | +/- | + | + | + | +/- | + | + | - | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
21541 | peat soil near coal mine | Prokopyevsk, Kemerovo Oblast | Russia | RUS | Asia | 53.8808 | 86.7275 |
67770 | Peat soil (pH 4.5) near a coal mine at Prokopyevsk | Kemerovo Oblast | Russia | RUS |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paraburkholderia eburnea LMG 29537 | GCA_003003375 | scaffold | ncbi | 1189126 |
66792 | Paraburkholderia eburnea strain JCM 18070 | 1189126.3 | wgs | patric | 1189126 |
66792 | Paraburkholderia eburnea strain LMG 29537 | 1189126.4 | wgs | patric | 1189126 |
66792 | Paraburkholderia eburnea LMG 29537 | 2708743144 | draft | img | 1189126 |
66792 | Paraburkholderia eburnea JCM 18070 | 2708743145 | draft | img | 1189126 |
67770 | Paraburkholderia eburnea JCM 18070 | GCA_002917095 | scaffold | ncbi | 1189126 |
GC content
- @ref: 21541
- GC-content: 60.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 80.755 | no |
gram-positive | no | 98.089 | no |
anaerobic | no | 98.834 | no |
aerobic | yes | 88.653 | no |
halophile | no | 94.972 | no |
spore-forming | no | 93.47 | no |
glucose-util | yes | 93.307 | no |
thermophile | no | 99.301 | yes |
motile | yes | 84.975 | no |
glucose-ferment | no | 88.733 | yes |
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
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
21541 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29414 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29414) | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
88772 | Reimer, 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 identifiers | 10.60712/SI-ID399001.1 |