Strain identifier
BacDive ID: 24249
Type strain:
Species: Nocardioides ginsengisegetis
Strain history: KACC 14269 <-- W.-T. Im; Kyung Hee Univ., South Korea; Gsoil 485.
NCBI tax ID(s): 661491 (species)
General
@ref: 20682
BacDive-ID: 24249
DSM-Number: 21349
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Nocardioides ginsengisegetis DSM 21349 is a mesophilic, Gram-positive bacterium that was isolated from soil of a ginseng field.
NCBI tax id
- NCBI tax id: 661491
- Matching level: species
strain history
@ref | history |
---|---|
20682 | <- S. T. Lee, KAIST <- W.-T. Im; Gsoil 485 |
67770 | KACC 14269 <-- W.-T. Im; Kyung Hee Univ., South Korea; Gsoil 485. |
doi: 10.13145/bacdive24249.20230509.8.1
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 ginsengisegetis
- full scientific name: Nocardioides ginsengisegetis Im et al. 2011
@ref: 20682
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides ginsengisegetis
full scientific name: Nocardioides ginsengisegetis Im et al. 2011
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 20682
- 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 |
---|---|---|---|---|
20682 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.576
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
20682 | soil of a ginseng field | Pocheon Province | Republic of Korea | KOR | Asia |
67770 | Soil of a ginseng field of 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) |
taxonmaps
- @ref: 69479
- File name: preview.99_59859.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_20261;97_25200;98_42539;99_59859&stattab=map
- Last taxonomy: Nocardioides ginsengisegetis subclade
- 16S sequence: GQ339901
- Sequence Identity:
- Total samples: 6454
- soil counts: 4145
- aquatic counts: 520
- animal counts: 319
- plant counts: 1470
Safety information
risk assessment
- @ref: 20682
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20682
- description: Nocardioides ginsengisegetis strain Gsoil 485 16S ribosomal RNA gene, partial sequence
- accession: GQ339901
- length: 1426
- database: ena
- NCBI tax ID: 661491
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardioides ginsengisegetis DSM 21349 | GCA_014138045 | contig | ncbi | 661491 |
66792 | Nocardioides ginsengisegetis strain DSM 21349 | 661491.3 | wgs | patric | 661491 |
66792 | Nocardioides ginsengisegetis DSM 21349 | 2821005819 | draft | img | 661491 |
GC content
- @ref: 20682
- GC-content: 71.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 61 | no |
gram-positive | yes | 90.749 | no |
anaerobic | no | 98.725 | no |
halophile | no | 96.38 | no |
spore-forming | no | 88.28 | no |
glucose-util | yes | 87.091 | no |
thermophile | no | 97.124 | yes |
flagellated | no | 96.155 | no |
motile | no | 81.794 | no |
aerobic | yes | 93.15 | no |
glucose-ferment | no | 89.109 | no |
External links
@ref: 20682
culture collection no.: DSM 21349, KACC 14269, KCTC 19469, Gsoil 485, JCM 32750
straininfo link
- @ref: 88191
- straininfo: 400280
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21046340 | Nocardioides ginsengisegetis sp. nov., isolated from soil of a ginseng field. | Im WT, Kim SY, Liu QM, Yang JE, Lee ST, Yi TH | J Microbiol | 10.1007/s12275-010-0001-5 | 2010 | Actinomycetales/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Korea, Molecular Sequence Data, Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis | Genetics |
Phylogeny | 22707530 | Nocardioides perillae sp. nov., isolated from surface-sterilized roots of Perilla frutescens. | Du HJ, Wei YZ, Su J, Liu HY, Ma BP, Guo BL, Zhang YQ, Yu LY | Int J Syst Evol Microbiol | 10.1099/ijs.0.044982-0 | 2012 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Perilla frutescens/*microbiology, Phospholipids/analysis, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Phylogeny | 26443681 | Nocardioides ungokensis sp. nov., isolated from lake sediment. | Zhao Y, Liu Q, Kang MS, Jin F, Yu H, Im WT | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000657 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Enzymology |
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 | |
20682 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21349 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21349) | |
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 | |
88191 | 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-ID400280.1 |