Strain identifier
BacDive ID: 134422
Type strain: 
Species: Sphingomonas ginsenosidimutans
Strain history: CIP <- 2012, JCM <- 2010, W.T. Im: strain Gsoil 1429
NCBI tax ID(s): 862134 (species)
version 8.1 (current version)
General
@ref: 32732
BacDive-ID: 134422
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Sphingomonas ginsenosidimutans CIP 110393 is a mesophilic, Gram-negative bacterium of the family Sphingomonadaceae.
NCBI tax id
- NCBI tax id: 862134
- Matching level: species
strain history
| @ref | history |
|---|---|
| 67770 | W.-T. Im Gsoil 1429. |
| 32732 | CIP <- 2012, JCM <- 2010, W.T. Im: strain Gsoil 1429 |
doi: 10.13145/bacdive134422.20230509.8.1
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 ginsenosidimutans
- full scientific name: Sphingomonas ginsenosidimutans Choi et al. 2011
@ref: 32732
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas ginsenosidimutans
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | cell shape | motility |
|---|---|---|---|---|
| 69480 | negative | 99.979 | ||
| 32732 | negative | rod-shaped | no |
Culture and growth conditions
culture medium
| @ref | name | growth | composition | link |
|---|---|---|---|---|
| 32732 | MEDIUM 464 - for Citricoccus muralis | yes | Distilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(20.000 g);Peptone (10.000 g);Beef extract (10.000 g) | |
| 32732 | CIP Medium 464 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=464 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 32732 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.999
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | geographic location | country | origin.country | continent | sample type |
|---|---|---|---|---|---|
| 32732 | Pocheon province | Republic of Korea | KOR | Asia | |
| 67770 | Republic of Korea | KOR | Asia | Soil of a ginseng cultivating field of Pocheon Province | |
| 32732 | Pocheon | Republic of Korea | KOR | Asia | Environment, Soil of a ginseng cultivating field |
taxonmaps
- @ref: 69479
- File name: preview.99_7051.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_761;97_887;98_5182;99_7051&stattab=map
- Last taxonomy: Sphingomonas
- 16S sequence: HM204925
- Sequence Identity:
- Total samples: 341
- soil counts: 19
- aquatic counts: 67
- animal counts: 216
- plant counts: 39
Safety information
risk assessment
- @ref: 32732
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
- @ref: 67770
- description: Sphingomonas ginsenosidimutans strain Gsoil 1429 16S ribosomal RNA gene, partial sequence
- accession: HM204925
- length: 1439
- database: ena
- NCBI tax ID: 862134
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingomonas ginsenosidimutans strain KACC 14949 | 862134.4 | wgs | patric | 862134 |
| 66792 | Sphingomonas ginsenosidimutans KACC 14949 | 2903810532 | draft | img | 862134 |
| 67770 | Sphingomonas ginsenosidimutans KACC 14949 | GCA_002374835 | contig | ncbi | 862134 |
GC content
- @ref: 67770
- GC-content: 65.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 83 | no |
| motile | yes | 71.993 | no |
| flagellated | no | 86.762 | no |
| gram-positive | no | 96.402 | no |
| anaerobic | no | 99.053 | no |
| halophile | no | 91.567 | no |
| spore-forming | no | 94.12 | no |
| glucose-util | yes | 88.403 | no |
| aerobic | yes | 93.506 | no |
| thermophile | no | 97.963 | yes |
| glucose-ferment | no | 91.45 | no |
External links
@ref: 32732
culture collection no.: CIP 110393, JCM 17074, KACC 14949, LMG 25799, Gsoil 1429
straininfo link
- @ref: 91948
- straininfo: 369866
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21221931 | Sphingomonas ginsenosidimutans sp. nov., with ginsenoside converting activity. | Choi TE, Liu QM, Yang JE, Sun S, Kim SY, Yi TH, Im WT | J Microbiol | 10.1007/s12275-010-0469-z | 2011 | Base Composition, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/isolation & purification/*metabolism/physiology, Temperature, beta-Glucosidase/metabolism | Metabolism |
| Phylogeny | 31140971 | Sphingomonas aracearum sp. nov., isolated from rhizospheric soil of Araceae plants. | Wang Z, Zeng Q, Fang Z, Zhu D, Xu D, Wang G, Zheng S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003477 | 2019 | Araceae/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 31418668 | Sphingomonas gilva sp. nov., isolated from mountain soil. | Zhu D, Niu Y, Liu D, Wang G, Zheng S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003645 | 2019 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 32732 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110393 | Collection of Institut Pasteur (CIP 110393) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 91948 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID369866.1 |