Strain identifier

BacDive ID: 24249

Type strain: Yes

Species: Nocardioides ginsengisegetis

Strain history: KACC 14269 <-- W.-T. Im; Kyung Hee Univ., South Korea; Gsoil 485.

NCBI tax ID(s): 661491 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
20682<- S. T. Lee, KAIST <- W.-T. Im; Gsoil 485
67770KACC 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

@refgrowthtypetemperaturerange
20682positivegrowth28mesophilic
67770positivegrowth28mesophilic

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

@refsample typegeographic locationcountryorigin.countrycontinent
20682soil of a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67770Soil of a ginseng field of Pocheon ProvinceRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides ginsengisegetis DSM 21349GCA_014138045contigncbi661491
66792Nocardioides ginsengisegetis strain DSM 21349661491.3wgspatric661491
66792Nocardioides ginsengisegetis DSM 213492821005819draftimg661491

GC content

  • @ref: 20682
  • GC-content: 71.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno61no
gram-positiveyes90.749no
anaerobicno98.725no
halophileno96.38no
spore-formingno88.28no
glucose-utilyes87.091no
thermophileno97.124yes
flagellatedno96.155no
motileno81.794no
aerobicyes93.15no
glucose-fermentno89.109no

External links

@ref: 20682

culture collection no.: DSM 21349, KACC 14269, KCTC 19469, Gsoil 485, JCM 32750

straininfo link

  • @ref: 88191
  • straininfo: 400280

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21046340Nocardioides ginsengisegetis sp. nov., isolated from soil of a ginseng field.Im WT, Kim SY, Liu QM, Yang JE, Lee ST, Yi THJ Microbiol10.1007/s12275-010-0001-52010Actinomycetales/*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/analysisGenetics
Phylogeny22707530Nocardioides 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 LYInt J Syst Evol Microbiol10.1099/ijs.0.044982-02012Actinomycetales/*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/analysisGenetics
Phylogeny26443681Nocardioides ungokensis sp. nov., isolated from lake sediment.Zhao Y, Liu Q, Kang MS, Jin F, Yu H, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0006572015Actinomycetales/*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/chemistryEnzymology

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
20682Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-21349Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21349)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
88191Reimer, 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 identifiers10.60712/SI-ID400280.1