Strain identifier
BacDive ID: 3778
Type strain: 
Species: Dyadobacter ginsengisoli
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 1121484 (strain), 363850 (species)
version 8.1 (current version)
General
@ref: 15427
BacDive-ID: 3778
DSM-Number: 21015
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Dyadobacter ginsengisoli DSM 21015 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil from ginseng field.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121484 | strain |
| 363850 | species |
strain history
| @ref | history |
|---|---|
| 15427 | <- KCTC/KRIBB <- S.-T. Lee, KAIST Daejeon |
| 67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive3778.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Dyadobacter
- species: Dyadobacter ginsengisoli
- full scientific name: Dyadobacter ginsengisoli Liu et al. 2006
@ref: 15427
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Spirosomaceae
genus: Dyadobacter
species: Dyadobacter ginsengisoli
full scientific name: Dyadobacter ginsengisoli Liu et al. 2006 emend. Hahnke et al. 2016
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility |
|---|---|---|---|---|---|
| 31804 | negative | 03-06 µm | 0.6-0.8 µm | rod-shaped | no |
| 67771 | rod-shaped | no | |||
| 67771 | negative |
pigmentation
- @ref: 31804
- production: yes
Culture and growth conditions
culture medium
- @ref: 15427
- name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1a
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) 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 |
|---|---|---|---|---|
| 15427 | positive | growth | 28 | mesophilic |
| 31804 | positive | growth | 04-30 | |
| 31804 | positive | optimum | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31804 | positive | growth | 5.5-8.5 | alkaliphile |
| 31804 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 31804 | aerobe |
| 67771 | aerobe |
spore formation
- @ref: 31804
- spore formation: no
halophily
- @ref: 31804
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
observation
| @ref | observation |
|---|---|
| 31804 | aggregates in chains |
| 67771 | quinones: MK-7 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31804 | 17716 | lactose | + | carbon source |
| 31804 | 17306 | maltose | + | carbon source |
| 31804 | 28053 | melibiose | + | carbon source |
| 31804 | 506227 | N-acetylglucosamine | + | carbon source |
| 31804 | 26546 | rhamnose | + | carbon source |
| 31804 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31804 | catalase | + | 1.11.1.6 |
| 31804 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 15427 | soil from ginseng field | Pocheon province | Republic of Korea | KOR | Asia |
| 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_132828.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_8223;97_43362;98_88813;99_132828&stattab=map
- Last taxonomy: Dyadobacter ginsengisoli subclade
- 16S sequence: AB245369
- Sequence Identity:
- Total samples: 480
- soil counts: 187
- aquatic counts: 18
- animal counts: 9
- plant counts: 266
Safety information
risk assessment
- @ref: 15427
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15427
- description: Dyadobacter ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 043
- accession: AB245369
- length: 1451
- database: ena
- NCBI tax ID: 363850
Genome sequences
- @ref: 66792
- description: Dyadobacter ginsengisoli DSM 21015
- accession: 2574179707
- assembly level: draft
- database: img
- NCBI tax ID: 1121484
GC content
| @ref | GC-content | method |
|---|---|---|
| 31804 | 48 | |
| 15427 | 49.0 | sequence analysis |
| 67771 | 48.0 |
External links
@ref: 15427
culture collection no.: DSM 21015, KCTC 12589, LMG 23409, Gsoil 043
straininfo link
- @ref: 73290
- straininfo: 289786
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16902034 | Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. | Liu QM, Im WT, Lee M, Yang DC, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.64322-0 | 2006 | Bacteroidetes/chemistry/*classification/genetics/isolation & purification, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, Vitamin K 2/analogs & derivatives | Genetics |
| Phylogeny | 19717578 | Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. | Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin R | Int J Syst Evol Microbiol | 10.1099/ijs.0.017236-0 | 2009 | Base Composition, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification/physiology | Genetics |
| Phylogeny | 20008109 | Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil. | Lee M, Woo SG, Park J, Yoo SA | Int J Syst Evol Microbiol | 10.1099/ijs.0.019653-0 | 2009 | Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Starch/*metabolism | Metabolism |
| Phylogeny | 22962334 | Dyadobacter jejuensis sp. nov., isolated from seawater. | Chun J, Kang JY, Joung Y, Kim H, Joh K, Jahng KY | Int J Syst Evol Microbiol | 10.1099/ijs.0.043620-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 34846279 | Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus. | Zhang Y, Peng X, Qin K, Liu J, Xu Q, Niu J, Zheng Y, Peng F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005103 | 2021 | Arctic Regions, Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Tundra, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15427 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21015) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21015 | |||
| 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 | |||
| 31804 | 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 | 28073 | 28776041 | |
| 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 | ||||
| 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 | |||
| 73290 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID289786.1 | StrainInfo: A central database for resolving microbial strain identifiers |