Strain identifier
BacDive ID: 3018
Type strain: 
Species: Variovorax ginsengisoli
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 363844 (species)
version 8.1 (current version)
General
@ref: 17930
BacDive-ID: 3018
DSM-Number: 25185
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Variovorax ginsengisoli DSM 25185 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.
NCBI tax id
- NCBI tax id: 363844
- Matching level: species
strain history
| @ref | history |
|---|---|
| 17930 | <- KCTC <- S. T. Lee, KAIST |
| 67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive3018.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Variovorax
- species: Variovorax ginsengisoli
- full scientific name: Variovorax ginsengisoli Im et al. 2010
@ref: 17930
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Variovorax
species: Variovorax ginsengisoli
full scientific name: Variovorax ginsengisoli Im et al. 2010
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility |
|---|---|---|---|---|---|
| 23101 | negative | 1.5-3.0 µm | 0.3-0.5 µm | rod-shaped | yes |
| 67771 | negative |
colony morphology
- @ref: 23101
- colony size: 2.0-5.0 mm
- colony color: yellowish
- incubation period: 3 days
- medium used: R2A agar (Difco)
multimedia
- @ref: 17930
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25185.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 17930 | 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 |
| 23101 | R2A agar (Difco) | yes |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17930 | positive | growth | 28 | mesophilic |
| 23101 | positive | growth | 4.0-30.0 | |
| 23101 | no | growth | 37.0 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 23101
- ability: positive
- type: growth
- pH: 5.0-8.5
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 23101 | aerobe |
| 23101 | facultative anaerobe |
| 67771 | aerobe |
spore formation
- @ref: 23101
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 23101 | NaCl | positive | growth | 0.0 %(w/v) |
| 23101 | NaCl | positive | growth | 1.0 %(w/v) |
| 23101 | NaCl | no | growth | 2 .0 %(w/v) |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23101 | 17128 | adipate | - | carbon source |
| 23101 | 16947 | citrate | - | carbon source |
| 23101 | 15824 | D-fructose | - | carbon source |
| 23101 | 28847 | D-fucose | - | carbon source |
| 23101 | 17634 | D-glucose | - | carbon source |
| 23101 | 16988 | D-ribose | - | carbon source |
| 23101 | 17924 | D-sorbitol | - | carbon source |
| 23101 | 24265 | gluconate | - | carbon source |
| 23101 | 17268 | myo-inositol | - | carbon source |
| 23101 | 17240 | itaconate | - | carbon source |
| 23101 | 62345 | L-rhamnose | - | carbon source |
| 23101 | 17266 | L-sorbose | - | carbon source |
| 23101 | 18300 | maleic acid | - | carbon source |
| 23101 | 25115 | malate | - | carbon source |
| 23101 | 506227 | N-acetylglucosamine | - | carbon source |
| 23101 | 17814 | salicin | - | carbon source |
| 23101 | 17822 | serine | - | carbon source |
| 23101 | 62968 | cellulose | - | degradation |
| 23101 | 17029 | chitin | - | degradation |
| 23101 | 16991 | dna | - | degradation |
| 23101 | olive oil | - | degradation | |
| 23101 | skimmed milk | - | degradation | |
| 23101 | 37166 | xylan | - | degradation |
| 23101 | 16193 | 3-hydroxybenzoate | + | carbon source |
| 23101 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 23101 | 17879 | 4-hydroxybenzoate | + | carbon source |
| 23101 | 30089 | acetate | + | carbon source |
| 23101 | 16449 | alanine | + | carbon source |
| 23101 | 16899 | D-mannitol | + | carbon source |
| 23101 | 16024 | D-mannose | + | carbon source |
| 23101 | 27570 | histidine | + | carbon source |
| 23101 | 30849 | L-arabinose | + | carbon source |
| 23101 | 24996 | lactate | + | carbon source |
| 23101 | 15792 | malonate | + | carbon source |
| 23101 | 18401 | phenylacetate | + | carbon source |
| 23101 | 26271 | proline | + | carbon source |
| 23101 | 17272 | propionate | + | carbon source |
| 23101 | 9300 | suberic acid | + | carbon source |
| 23101 | 31011 | valerate | + | carbon source |
| 23101 | 17632 | nitrate | + | reduction |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. | is sensitive | sensitivity conc. |
|---|---|---|---|---|---|---|---|
| 23101 | 6472 | lincomycin | yes | yes | 15 µg | ||
| 23101 | 28971 | ampicillin | yes | yes | 20 µg | ||
| 23101 | 17833 | gentamicin | yes | yes | 30 µg | ||
| 23101 | 28368 | novobiocin | yes | yes | 5 µg | ||
| 23101 | 18208 | penicillin g | yes | yes | 20 Unit | ||
| 23101 | 17698 | chloramphenicol | yes | yes | 100 µg | ||
| 23101 | 16869 | oleandomycin | yes | yes | 15 µg | ||
| 23101 | 48923 | erythromycin | yes | yes | 25 µg | ||
| 23101 | 6104 | kanamycin | yes | yes | 30 µg | ||
| 23101 | 7507 | neomycin | yes | yes | 30 µg | ||
| 23101 | 27902 | tetracycline | yes | yes | 30 µg | ||
| 23101 | 17076 | streptomycin | yes | yes | 50 µg |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 23101 | acid phosphatase | + | 3.1.3.2 |
| 23101 | alpha-glucosidase | + | 3.2.1.20 |
| 23101 | naphthol-AS-BI-phosphohydrolase | - | |
| 23101 | urease | - | 3.5.1.5 |
| 23101 | valine arylamidase | +/- |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
|---|---|---|---|---|---|---|---|---|---|
| 17930 | soil of ginseng field | Pocheon Province | Republic of Korea | KOR | Asia | ||||
| 23101 | one-fifth-strength modified R2A agar plates | per litre distilled water: 0.25 g tryptone, 0.25 g peptone, 0.25 g yeast extract, 0.125 g malt extract, 0.125 g beef extract, 0.25 g Casamino acids, 0.25 g soytone, 0.5 g glucose, 0.3 g soluble starch, 0.2 g xylan, 0.3 g sodium pyruvate, 0.5 g KNO3 , 0.3 g K2HPO4 , 0.05 g MgSO4 , 0.05 g CaCl2 and 15 g agar | 30 days | 25.0 | |||||
| 67771 | From soil of the ginseng field | 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_9161.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_308;97_342;98_387;99_9161&stattab=map
- Last taxonomy: Variovorax
- 16S sequence: AB245358
- Sequence Identity:
- Total samples: 16187
- soil counts: 4721
- aquatic counts: 6392
- animal counts: 2284
- plant counts: 2790
Safety information
risk assessment
- @ref: 17930
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17930
- description: Variovorax ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 3165
- accession: AB245358
- length: 1492
- database: ena
- NCBI tax ID: 363844
GC content
- @ref: 17930
- GC-content: 66.0
- method: high performance liquid chromatography (HPLC)
External links
@ref: 17930
culture collection no.: DSM 25185, CCUG 52469, KCTC 12583, LMG 23392, Gsoil 3165
straininfo link
- @ref: 72540
- straininfo: 370251
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19684323 | Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field. | Im WT, Liu QM, Lee KJ, Kim SY, Lee ST, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.014514-0 | 2009 | Base Composition, Base Sequence, Comamonadaceae/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Panax/*microbiology, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Genetics |
| Phylogeny | 21948092 | Variovorax defluvii sp. nov., isolated from sewage. | Jin L, Kim KK, Ahn CY, Oh HM | Int J Syst Evol Microbiol | 10.1099/ijs.0.035295-0 | 2011 | Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/microbiology, Sequence Analysis, DNA, Sewage/*microbiology | Genetics |
| Phylogeny | 25504533 | Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere. | Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JG | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0304-3 | 2014 | Bacterial Typing Techniques, Base Composition, Carbon-Carbon Lyases/*metabolism, China, Cluster Analysis, Comamonadaceae/*classification/enzymology/genetics/*isolation & purification, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Musa, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology | Enzymology |
| Phylogeny | 29948826 | Proposal of three novel species of soil bacteria, Variovorax ureilyticus, Variovorax rhizosphaerae, and Variovorax robiniae, in the family Comamonadaceae. | Nguyen TM, Trinh NH, Kim J | J Microbiol | 10.1007/s12275-018-8025-3 | 2018 | Bacterial Typing Techniques, Base Composition, Comamonadaceae/chemistry/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysis | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17930 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25185) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25185 | |||
| 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 | |||
| 23101 | Wan-Taek Im,Qing-Mei Liu,Kang-Jin Lee,Se-Young Kim,Sung-Taik Lee,Tae-Hoo Yi | 10.1099/ijs.0.014514-0 | Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field | IJSEM 60: 1565-1569 2010 | 19684323 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 72540 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID370251.1 | StrainInfo: A central database for resolving microbial strain identifiers |