Strain identifier
BacDive ID: 1975
Type strain: 
Species: Paraburkholderia ginsengisoli
Strain Designation: KMY03
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 1218078 (strain), 311231 (species)
version 8.1 (current version)
General
@ref: 15853
BacDive-ID: 1975
DSM-Number: 21638
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Paraburkholderia ginsengisoli KMY03 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil from a ginseng field.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 311231 | species |
| 1218078 | strain |
strain history
| @ref | history |
|---|---|
| 15853 | <- KCTC <- S.-T. Lee, KAIST |
| 67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive1975.20230509.8.1
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 ginsengisoli
- full scientific name: Paraburkholderia ginsengisoli (Kim et al. 2006) Sawana et al. 2015
synonyms
- @ref: 20215
- synonym: Burkholderia ginsengisoli
@ref: 15853
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Paraburkholderia
species: Paraburkholderia ginsengisoli
full scientific name: Paraburkholderia ginsengisoli (Kim et al. 2006) Sawana et al. 2015
strain designation: KMY03
type strain: yes
Morphology
cell morphology
- @ref: 67771
- gram stain: negative
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 15853 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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 |
| 15853 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15853 | positive | growth | 28 | mesophilic |
| 60245 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 60245 | aerobe |
| 67771 | aerobe |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 27689 | decanoate | + | assimilation |
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 17306 | maltose | - | 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 |
|---|---|---|---|
| 68369 | cytochrome 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 | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 15853 | - | - | - | - | - | + | - | + | + | + | + | + | + | - | + | + | +/- | + | - | + | - |
| 15853 | - | - | - | - | - | + | - | + | + | +/- | + | + | + | - | + | + | +/- | + | - | + | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|
| 15853 | soil from a ginseng field | Republic of Korea | KOR | Asia | |
| 60245 | Soil,ginseng field | 2006 | |||
| 67771 | From forest soil | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_6599.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_173;97_187;98_2245;99_6599&stattab=map
- Last taxonomy: Paraburkholderia
- 16S sequence: AB681301
- Sequence Identity:
- Total samples: 404
- soil counts: 253
- aquatic counts: 62
- animal counts: 69
- plant counts: 20
Safety information
risk assessment
- @ref: 15853
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Burkholderia ginsengisoli gene for 16S rRNA, partial sequence, strain: NBRC 100965 | AB681301 | 1460 | ena | 311231 |
| 15853 | Burkholderia ginsengisoli gene for 16S rRNA, partial sequence, strain: KMY03 | AB201286 | 1462 | ena | 311231 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paraburkholderia ginsengisoli NBRC 100965 | GCA_000739735 | contig | ncbi | 1218078 |
| 66792 | Burkholderia ginsengisoli NBRC 100965 | 1218078.3 | wgs | patric | 1218078 |
| 66792 | Paraburkholderia ginsengisoli NBRC 100965 | 2600255070 | draft | img | 1218078 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 91.38 | no |
| gram-positive | no | 98.343 | yes |
| anaerobic | no | 98.546 | no |
| aerobic | yes | 90.061 | yes |
| halophile | no | 92.993 | no |
| spore-forming | no | 93.89 | no |
| glucose-util | yes | 92.428 | no |
| flagellated | no | 79.357 | no |
| thermophile | no | 99.642 | yes |
| glucose-ferment | no | 90.074 | yes |
External links
@ref: 15853
culture collection no.: DSM 21638, CCUG 54571, KCTC 12389, LMG 24044, NBRC 100965
straininfo link
- @ref: 71620
- straininfo: 290457
literature
- topic: Phylogeny
- Pubmed-ID: 17082385
- title: Burkholderia ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.
- authors: Kim HB, Park MJ, Yang HC, An DS, Jin HZ, Yang DC
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64387-0
- year: 2006
- mesh: Bacterial Typing Techniques, Burkholderia/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flagella, Genes, rRNA, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, *Panax, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, beta-Glucosidase/*biosynthesis
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 15853 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21638) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21638 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 60245 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54571) | https://www.ccug.se/strain?id=54571 | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 68369 | Automatically annotated from API 20NE | |||||
| 69479 | João 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 | |||
| 71620 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID290457.1 | StrainInfo: A central database for resolving microbial strain identifiers |