Strain identifier
BacDive ID: 23277
Type strain: 
Species: Sphingomonas ginsengisoli
Strain history: <- S.-T. Lee, KAIST, Korean Advanced Institute of Science and Technology; Gsoil 634
NCBI tax ID(s): 363835 (species)
version 8.1 (current version)
General
@ref: 18850
BacDive-ID: 23277
DSM-Number: 18094
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Sphingomonas ginsengisoli DSM 18094 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.
NCBI tax id
- NCBI tax id: 363835
- Matching level: species
strain history
- @ref: 18850
- history: <- S.-T. Lee, KAIST, Korean Advanced Institute of Science and Technology; Gsoil 634
doi: 10.13145/bacdive23277.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingomonas
- species: Sphingomonas ginsengisoli
- full scientific name: Sphingomonas ginsengisoli An et al. 2013
@ref: 18850
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas ginsengisoli
full scientific name: Sphingomonas ginsengisoli An et al. 2013
type strain: yes
Morphology
cell morphology
- @ref: 30596
- gram stain: negative
- cell length: 1.3 µm
- cell width: 0.5 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 30596
- production: yes
Culture and growth conditions
culture medium
- @ref: 18850
- 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 |
|---|---|---|---|---|
| 18850 | positive | growth | 28 | mesophilic |
| 30596 | positive | optimum | 30 | mesophilic |
culture pH
- @ref: 30596
- ability: positive
- type: optimum
- pH: 7
Physiology and metabolism
oxygen tolerance
- @ref: 30596
- oxygen tolerance: aerobe
spore formation
- @ref: 30596
- spore formation: no
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30596 | 16808 | 2-dehydro-D-gluconate | + | carbon source |
| 30596 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
| 30596 | 17234 | glucose | + | carbon source |
| 30596 | 28087 | glycogen | + | carbon source |
| 30596 | 27570 | histidine | + | carbon source |
| 30596 | 17306 | maltose | + | carbon source |
| 30596 | 26271 | proline | + | carbon source |
| 30596 | 17822 | serine | + | carbon source |
| 30596 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30596 | acid phosphatase | + | 3.1.3.2 |
| 30596 | gelatinase | + |
Isolation, sampling and environmental information
isolation
- @ref: 18850
- sample type: soil of ginseng field
- geographic location: Pocheon province
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
Safety information
risk assessment
- @ref: 18850
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18850
- description: Sphingomonas ginsengisoli gene for 16S rRNA, partial sequence
- accession: AB245347
- length: 1436
- database: ena
- NCBI tax ID: 363835
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | 'Sphingomonas ginsengisoli' Hoang et al. 2012 KCTC 12630 | GCA_003332855 | contig | ncbi | 1706000 |
| 66792 | 'Sphingomonas ginsengisoli' Hoang et al. 2012 strain KCTC 12630 | 1706000.3 | wgs | patric | 1706000 |
| 66792 | Sphingomonas ginsengisoli KCTC 12630 | 2874729722 | draft | img | 1706000 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 18850 | 66.8 | high performance liquid chromatography (HPLC) |
| 30596 | 66.8 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 79.337 | yes |
| gram-positive | no | 96.793 | yes |
| anaerobic | no | 99.289 | yes |
| aerobic | yes | 93.31 | yes |
| halophile | no | 91.972 | no |
| spore-forming | no | 97.168 | no |
| thermophile | no | 95.692 | yes |
| glucose-util | yes | 84.527 | yes |
| flagellated | no | 97.594 | no |
| glucose-ferment | no | 91.536 | no |
External links
@ref: 18850
culture collection no.: DSM 18094, KCTC 12630, LMG 23739, Gsoil 634
straininfo link
- @ref: 87499
- straininfo: 401817
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22505600 | Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov. | An DS, Liu QM, Lee HG, Jung MS, Kim SC, Lee ST, Im WT | Int J Syst Evol Microbiol | 10.1099/ijs.0.039578-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Glycosphingolipids/analysis, Molecular Sequence Data, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analysis | Genetics |
| Phylogeny | 24449789 | Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir. | Huy H, Jin L, Lee KC, Kim SG, Lee JS, Ahn CY, Oh HM | Int J Syst Evol Microbiol | 10.1099/ijs.0.054510-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Eutrophication, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *Water Microbiology | Genetics |
| Phylogeny | 25985832 | Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond. | Kim JH, Kim SH, Kim KH, Lee PC | Int J Syst Evol Microbiol | 10.1099/ijs.0.000337 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycosides/biosynthesis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, *Ponds, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Xanthophylls/biosynthesis | Genetics |
| Phylogeny | 29388549 | Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus. | Yan ZF, Lin P, Won KH, Li CT, Park G, Chin B, Kook M, Wang QJ, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002566 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hibiscus/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
| Genetics | 30643871 | Draft Genome Sequence of KCTC 12630, the Type Strain of the Novel Species Sphingomonas ginsengisoli. | Li YQ, Zhang H, Narsing Rao MP, Dong ZY, Alkhalifah DHM, Hozzein WN, Xiao M, Li WJ | Microbiol Resour Announc | 10.1128/MRA.01032-18 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 18850 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18094) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18094 | |||
| 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 | |||
| 30596 | 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 | 26927 | 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) | |||
| 87499 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401817.1 | StrainInfo: A central database for resolving microbial strain identifiers |