Strain identifier

BacDive ID: 11133

Type strain: Yes

Species: Nocardioides hankookensis

Strain Designation: DS-30

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 443157 (species)

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General

@ref: 15730

BacDive-ID: 11133

DSM-Number: 21479

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Nocardioides hankookensis DS-30 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 443157
  • Matching level: species

strain history

@refhistory
15730<- CCUG <- J. H. Yoon, KRIBB, Taejon, South Korea; DS-30
67770CCUG 54522 <-- J.-H. Yoon DS-30.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive11133.20230509.8.1

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 hankookensis
  • full scientific name: Nocardioides hankookensis Yoon et al. 2008

@ref: 15730

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides hankookensis

full scientific name: Nocardioides hankookensis Yoon et al. 2008

strain designation: DS-30

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32290positive5.75 µm0.6 µmrod-shapedno
67771positive

colony morphology

  • @ref: 60212
  • incubation period: 27 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15730R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
15730TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf

culture temp

@refgrowthtypetemperaturerange
15730positivegrowth28mesophilic
32290positivegrowth10-34
60212positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
32290positivegrowth5.5-8
32290positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32290aerobe
60212aerobe
67771aerobe

spore formation

  • @ref: 32290
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32290NaClpositivegrowth0-2 %
32290NaClpositiveoptimum0.25 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3229017128adipate+carbon source
3229022599arabinose+carbon source
3229028260galactose+carbon source
3229024265gluconate+carbon source
3229025115malate+carbon source
3229029864mannitol+carbon source
3229028053melibiose+carbon source
3229026546rhamnose+carbon source

enzymes

@refvalueactivityec
32290alkaline phosphatase+3.1.3.1
32290cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15730soilDokdoRepublic of KoreaKORAsia
60212SoilDokdoRepublic of KoreaKORAsia2004-05-01
67770Soil
67771From soilDokdoRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6625.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1465;97_3844;98_4885;99_6625&stattab=map
  • Last taxonomy: Nocardioides hankookensis
  • 16S sequence: EF555584
  • Sequence Identity:
  • Total samples: 2425
  • soil counts: 1533
  • aquatic counts: 164
  • animal counts: 673
  • plant counts: 55

Safety information

risk assessment

  • @ref: 15730
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15730
  • description: Nocardioides hankookensis strain DS-30 16S ribosomal RNA gene, partial sequence
  • accession: EF555584
  • length: 1447
  • database: ena
  • NCBI tax ID: 443157

GC content

@refGC-contentmethod
1573071.3
6777071.3high performance liquid chromatography (HPLC)

External links

@ref: 15730

culture collection no.: DSM 21479, CCUG 54522, KCTC 19246, JCM 15302

straininfo link

  • @ref: 80382
  • straininfo: 323980

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18218945Nocardioides hankookensis sp. nov., isolated from soil.Yoon JH, Kang SJ, Lee MH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65267-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny20173009Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.Song GC, Yasir M, Bibi F, Chung EJ, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.019919-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cyperaceae/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, TemperatureGenetics
Phylogeny23990649Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots.Han JH, Kim TS, Joung Y, Kim MN, Shin KS, Bae T, Kim SBInt J Syst Evol Microbiol10.1099/ijs.0.054619-02013Actinomycetales/*classification/genetics/isolation & purification, Artemisia/microbiology, Bacterial Typing Techniques, Base Composition, Conyza/microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny24651303Nocardioides soli sp. nov., a carbendazim-degrading bacterium isolated from soil under the long-term application of carbendazim.Sun LN, Zhang J, Gong FF, Wang X, Hu G, Li SP, Hong QInt J Syst Evol Microbiol10.1099/ijs.0.057935-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Benzimidazoles/*metabolism, Carbamates/*metabolism, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fungicides, Industrial/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/metabolism, Vitamin K 2/analogs & derivatives/chemistryMetabolism
Phylogeny27381405Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu.Huang MJ, Huang HQ, Salam N, Xiao M, Duan YQ, Kim CJ, Li QQ, Chen W, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0012742016Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Caryophyllaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15730Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21479)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21479
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
32290Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2853028776041
60212Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54522)https://www.ccug.se/strain?id=54522
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
80382Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323980.1StrainInfo: A central database for resolving microbial strain identifiers