Strain identifier
BacDive ID: 11154
Type strain:
Species: Nocardioides ginsengagri
Strain Designation: BX5-10
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 661493 (species)
General
@ref: 15652
BacDive-ID: 11154
DSM-Number: 21362
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Nocardioides ginsengagri BX5-10 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil of a ginseng field.
NCBI tax id
- NCBI tax id: 661493
- Matching level: species
strain history
@ref | history |
---|---|
15652 | <- S. T. Lee <- W.-T. Im, KAIST; BX5-10 |
67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive11154.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Nocardioides
- species: Nocardioides ginsengagri
- full scientific name: Nocardioides ginsengagri Lee et al. 2012
@ref: 15652
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides ginsengagri
full scientific name: Nocardioides ginsengagri Lee et al. 2012
strain designation: BX5-10
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
30253 | positive | 1.5-2.8 µm | 0.4-0.7 µm | rod-shaped | no |
67771 | positive |
colony morphology
- @ref: 15652
- incubation period: 3-7 days
pigmentation
- @ref: 30253
- production: yes
Culture and growth conditions
culture medium
- @ref: 15652
- 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 |
---|---|---|---|---|
15652 | positive | growth | 28 | mesophilic |
30253 | positive | growth | 10-37 | |
30253 | positive | optimum | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30253 | positive | growth | 5.5-9.5 | alkaliphile |
30253 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30253 | aerobe |
67771 | aerobe |
spore formation
- @ref: 30253
- spore formation: no
halophily
- @ref: 30253
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <2 %
metabolite utilization
- @ref: 30253
- Chebi-ID: 22599
- metabolite: arabinose
- utilization activity: +
- kind of utilization tested: carbon source
enzymes
@ref | value | activity | ec |
---|---|---|---|
30253 | acid phosphatase | + | 3.1.3.2 |
30253 | catalase | + | 1.11.1.6 |
30253 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15652 | soil of a ginseng field | Baekdu Mountain | China | CHN | Asia |
67771 | From soil of ginseng field | Baekdu Mountain in Jilin district | 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: 15652
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15652
- description: Nocardioides ginsengagri strain BX5-10 16S ribosomal RNA gene, partial sequence
- accession: GQ339904
- length: 1424
- database: ena
- NCBI tax ID: 661493
GC content
@ref | GC-content | method |
---|---|---|
15652 | 70.3 | high performance liquid chromatography (HPLC) |
30253 | 70.3 |
External links
@ref: 15652
culture collection no.: DSM 21362, KCTC 19467, Gsoil BX5-10
straininfo link
- @ref: 80403
- straininfo: 403052
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21515700 | Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field. | Lee SH, Liu QM, Lee ST, Kim SC, Im WT | Int J Syst Evol Microbiol | 10.1099/ijs.0.031823-0 | 2011 | Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Panax/growth & development, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis | Genetics |
Phylogeny | 23264497 | Nocardioides marinquilinus sp. nov., isolated from coastal seawater. | Cho Y, Jang GI, Cho BC | Int J Syst Evol Microbiol | 10.1099/ijs.0.047902-0 | 2012 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Phylogeny | 25951861 | Nocardioides antarcticus sp. nov., isolated from marine sediment. | Deng S, Chang X, Zhang Y, Ren L, Jiang F, Qu Z, Peng F | Int J Syst Evol Microbiol | 10.1099/ijs.0.000309 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
15652 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21362) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21362 | |||
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 | |||
30253 | 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 | 26595 | 28776041 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
80403 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403052.1 | StrainInfo: A central database for resolving microbial strain identifiers |