Strain identifier
BacDive ID: 17455
Type strain: 
Species: Dyella ginsengisoli
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 363848 (species)
version 8.1 (current version)
General
@ref: 7368
BacDive-ID: 17455
DSM-Number: 18387
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Dyella ginsengisoli DSM 18387 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.
NCBI tax id
- NCBI tax id: 363848
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7368 | <- S.-T. Lee; Gsoil 3046 <- W.-T. Im |
| 67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive17455.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Rhodanobacteraceae
- genus: Dyella
- species: Dyella ginsengisoli
- full scientific name: Dyella ginsengisoli Jung et al. 2009
@ref: 7368
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Rhodanobacteraceae
genus: Dyella
species: Dyella ginsengisoli
full scientific name: Dyella ginsengisoli Jung et al. 2009
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility |
|---|---|---|---|---|---|
| 31846 | negative | 1.5-2.1 µm | 0.2-0.5 µm | rod-shaped | yes |
| 67771 | negative |
pigmentation
- @ref: 31846
- production: yes
Culture and growth conditions
culture medium
- @ref: 7368
- 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 |
|---|---|---|---|---|
| 7368 | positive | growth | 30 | mesophilic |
| 31846 | positive | growth | 15-42 | |
| 31846 | positive | optimum | 28.5 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31846 | positive | growth | 5.0-8.5 | alkaliphile |
| 31846 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 31846 | aerobe |
| 67771 | aerobe |
spore formation
- @ref: 31846
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31846 | NaCl | positive | growth | 0-2 % |
| 31846 | NaCl | positive | optimum | 1 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31846 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 31846 | 30089 | acetate | + | carbon source |
| 31846 | 17057 | cellobiose | + | carbon source |
| 31846 | 5291 | gelatin | + | carbon source |
| 31846 | 17234 | glucose | + | carbon source |
| 31846 | 29987 | glutamate | + | carbon source |
| 31846 | 28087 | glycogen | + | carbon source |
| 31846 | 17306 | maltose | + | carbon source |
| 31846 | 37684 | mannose | + | carbon source |
| 31846 | 506227 | N-acetylglucosamine | + | carbon source |
| 31846 | 27082 | trehalose | + | carbon source |
| 31846 | 31011 | valerate | + | carbon source |
| 31846 | 18222 | xylose | + | carbon source |
| 31846 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31846 | alkaline phosphatase | + | 3.1.3.1 |
| 31846 | alpha-galactosidase | + | 3.2.1.22 |
| 31846 | catalase | + | 1.11.1.6 |
| 31846 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7368 | soil of ginseng field | Pocheon Province | Republic of Korea | KOR | Asia |
| 67771 | From soil from a ginseng field in Pocheon Province | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
Safety information
risk assessment
- @ref: 7368
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7368
- description: Dyella ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 3046
- accession: AB245367
- length: 1491
- database: ena
- NCBI tax ID: 363848
GC content
- @ref: 7368
- GC-content: 66.6
External links
@ref: 7368
culture collection no.: DSM 18387, KCTC 12599, Gsoil 3046
straininfo link
- @ref: 86451
- straininfo: 291602
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19244422 | Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. | Jung HM, Ten LN, Kim KH, An DS, Im WT, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.64514-0 | 2009 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, *Panax/growth & development, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xanthomonadaceae/*classification/genetics/isolation & purification/physiology | Genetics |
| Phylogeny | 19542132 | Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil. | Weon HY, Anandham R, Kim BY, Hong SB, Jeon YA, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijs.0.004838-0 | 2009 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xanthomonadaceae/*classification/genetics/isolation & purification/physiology | Genetics |
| Phylogeny | 21296929 | Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field. | Wang L, An DS, Kim SG, Jin FX, Lee ST, Im WT | Int J Syst Evol Microbiol | 10.1099/ijs.0.025718-0 | 2011 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Ginsenosides/*metabolism, Molecular Sequence Data, Panax/growth & development/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/metabolism | Metabolism |
| Phylogeny | 25604344 | Rhodanobacter koreensis sp. nov., a bacterium isolated from tomato rhizosphere. | Won K, Singh H, Ngo HTT, Son H, Kook M, Kim KY, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.000077 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification | Genetics |
| Phylogeny | 27487774 | Dyella humi sp. nov., isolated from forest soil. | Chen MH, Lv YY, Wang J, Tang L, Qiu LH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001358 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7368 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18387) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18387 | |||
| 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 | |||
| 31846 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28110 | 28776041 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 86451 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID291602.1 | StrainInfo: A central database for resolving microbial strain identifiers |