Strain identifier

BacDive ID: 11123

Type strain: Yes

Species: Nocardioides dubius

Strain Designation: KSL-104

Strain history: CIP <- 2005, JCM <- J.H. Yoon, KRIBB, Taejon, Korea: strain KSL-104

NCBI tax ID(s): 317019 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7876

BacDive-ID: 11123

DSM-Number: 19084

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

description: Nocardioides dubius KSL-104 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from alkaline soil.

NCBI tax id

  • NCBI tax id: 317019
  • Matching level: species

strain history

@refhistory
7876<- JCM <- J.-H. Yoon, KSL-104
67770J.-H. Yoon KSL-104.
67771<- JH Yoon, KRIBB
118975CIP <- 2005, JCM <- J.H. Yoon, KRIBB, Taejon, Korea: strain KSL-104

doi: 10.13145/bacdive11123.20230509.8.1

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 dubius
  • full scientific name: Nocardioides dubius Yoon et al. 2005

@ref: 7876

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides dubius

full scientific name: Nocardioides dubius Yoon et al. 2005

strain designation: KSL-104

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31528positive2 µm0.9 µmrod-shapedyes
31636positiverod-shapedno
67771positive
118975positiverod-shapedno

pigmentation

@refproduction
31528yes
31636yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7876TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
118975CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7876positivegrowth28mesophilic
31528positivegrowth10-37
31636positivegrowth20-45
31528positiveoptimum30mesophilic
31636positiveoptimum20-45
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31636positivegrowth7
31528positivegrowth6.0-10.5alkaliphile
31636positiveoptimum7
31528positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31528aerobe
31636aerobe
67771aerobe

spore formation

@refspore formation
31528no
31636yes

halophily

  • @ref: 31528
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

@refobservation
31636aggregates in chains
31528aggregates in clumps
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3152817234glucose+carbon source
3152815361pyruvate+carbon source
3152817814salicin+carbon source
3152830031succinate+carbon source
3152817992sucrose+carbon source
3163622599arabinose+carbon source
3163617057cellobiose+carbon source
3163628757fructose+carbon source
3163617234glucose+carbon source
3163617754glycerol+carbon source
3163617306maltose+carbon source
3163629864mannitol+carbon source
3163617814salicin+carbon source
3163617992sucrose+carbon source
3163627082trehalose+carbon source
3163618222xylose+carbon source
315284853esculin+hydrolysis
3163617632nitrate+reduction

metabolite production

  • @ref: 31636
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31528acid phosphatase+3.1.3.2
31528alkaline phosphatase+3.1.3.1
31528catalase+1.11.1.6
31528gelatinase+
31528cytochrome oxidase+1.9.3.1
31636catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7876alkaline soilKwangchunRepublic of KoreaKORAsia
67770Alkaline soilKwangchunRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia
118975Environment, Alkaline soilKwangchunRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Alkaline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78761Risk group (German classification)
1189751Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7876
  • description: Nocardioides dubius 16S ribosomal RNA gene, partial sequence
  • accession: AY928902
  • length: 1473
  • database: ena
  • NCBI tax ID: 317019

GC content

@refGC-contentmethod
787670.6
3163667.5
6777070.6high performance liquid chromatography (HPLC)

External links

@ref: 7876

culture collection no.: DSM 19084, CIP 109028, JCM 13008, KCTC 9992

straininfo link

  • @ref: 80372
  • straininfo: 344061

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166734Nocardioides dubius sp. nov., isolated from an alkaline soil.Yoon JH, Lee CH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63748-02005Actinomycetales/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil MicrobiologyGenetics
Phylogeny21742819Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.Woo SG, Srinivasan S, Yang J, Jung YA, Kim MK, Lee MInt J Syst Evol Microbiol10.1099/ijs.0.033308-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Denitrification, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analysisGenetics
Phylogeny25893957Nocardioides solisilvae sp. nov., isolated from a forest soil.Sultanpuram VR, Mothe T, Mohammed FAntonie Van Leeuwenhoek10.1007/s10482-015-0455-x2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Forests, India, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny27411814Nocardioides gilvus sp. nov., isolated from Namtso Lake.Zhang HX, Wang K, Xu ZX, Chen GJ, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-016-0735-02016Actinomycetales/classification/*isolation & purification, Base Composition, DNA, Bacterial, Lakes/*microbiology, Molecular Typing, PhylogenyEnzymology
Phylogeny35482521Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste.Mitzscherling J, MacLean J, Lipus D, Bartholomaus A, Mangelsdorf K, Lipski A, Roddatis V, Liebner S, Wagner DInt J Syst Evol Microbiol10.1099/ijsem.0.0053192022*Actinomycetales, Alkanes, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Nocardioides, Phylogeny, Plastics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7876Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19084)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19084
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
31528Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2782228776041
31636Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2791928776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
80372Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID344061.1StrainInfo: A central database for resolving microbial strain identifiers
118975Curators of the CIPCollection of Institut Pasteur (CIP 109028)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109028