Strain identifier

BacDive ID: 11154

Type strain: Yes

Species: Nocardioides ginsengagri

Strain Designation: BX5-10

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 661493 (species)

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

@refhistory
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

@refgram staincell lengthcell widthcell shapemotility
30253positive1.5-2.8 µm0.4-0.7 µmrod-shapedno
67771positive

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

@refgrowthtypetemperaturerange
15652positivegrowth28mesophilic
30253positivegrowth10-37
30253positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30253positivegrowth5.5-9.5alkaliphile
30253positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30253aerobe
67771aerobe

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

@refvalueactivityec
30253acid phosphatase+3.1.3.2
30253catalase+1.11.1.6
30253cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15652soil of a ginseng fieldBaekdu MountainChinaCHNAsia
67771From soil of ginseng fieldBaekdu Mountain in Jilin districtRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#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

@refGC-contentmethod
1565270.3high performance liquid chromatography (HPLC)
3025370.3

External links

@ref: 15652

culture collection no.: DSM 21362, KCTC 19467, Gsoil BX5-10

straininfo link

  • @ref: 80403
  • straininfo: 403052

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21515700Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field.Lee SH, Liu QM, Lee ST, Kim SC, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.031823-02011Actinomycetales/*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/analysisGenetics
Phylogeny23264497Nocardioides marinquilinus sp. nov., isolated from coastal seawater.Cho Y, Jang GI, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.047902-02012Actinomycetales/*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/analysisGenetics
Phylogeny25951861Nocardioides antarcticus sp. nov., isolated from marine sediment.Deng S, Chang X, Zhang Y, Ren L, Jiang F, Qu Z, Peng FInt J Syst Evol Microbiol10.1099/ijs.0.0003092015Actinomycetales/*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/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15652Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21362)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21362
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30253Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2659528776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
80403Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403052.1StrainInfo: A central database for resolving microbial strain identifiers