Strain identifier

BacDive ID: 11143

Type strain: Yes

Species: Nocardioides dokdonensis

Strain Designation: FR1436

Strain history: <- CN Seong, Sunchon Natl. Univ.

NCBI tax ID(s): 450734 (species)

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General

@ref: 16096

BacDive-ID: 11143

DSM-Number: 22004

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

description: Nocardioides dokdonensis FR1436 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sand sediment from a beach.

NCBI tax id

  • NCBI tax id: 450734
  • Matching level: species

strain history

@refhistory
16096<- JCM/RIKEN <- C. N. Seong, Sunchon Natl. Univ., Korea; FR1436
67770C. N. Seong FR1436.
67771<- CN Seong, Sunchon Natl. Univ.

doi: 10.13145/bacdive11143.20230509.8.1

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 dokdonensis
  • full scientific name: Nocardioides dokdonensis Park et al. 2008

@ref: 16096

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides dokdonensis

full scientific name: Nocardioides dokdonensis Park et al. 2008 emend. Nouioui et al. 2018

strain designation: FR1436

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32644positive1.2-1.8 µm0.6-0.9 µmrod-shapedno
67771positive
69480no91.113
69480positive100

pigmentation

  • @ref: 32644
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16096TRYPTICASE 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
16096TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16096positivegrowth28mesophilic
32644positivegrowth04-30
32644positiveoptimum25mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32644positivegrowth05-10alkaliphile
32644positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32644aerobe
67771aerobe

spore formation

@refspore formationconfidence
32644no
69480no99.967

halophily

@refsaltgrowthtested relationconcentration
32644NaClpositivegrowth0-7 %
32644NaClpositiveoptimum0-3 %

observation

@refobservation
32644aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3264415963ribitol+carbon source
3264417754glycerol+carbon source
3264428053melibiose+carbon source
3264433942ribose+carbon source

enzymes

  • @ref: 32644
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16096sand sediment from a beachDokdo IslandRepublic of KoreaKORAsia
67770Sand sediment
67771From sand sedimentDokdoRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1800.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1021;97_1191;98_1423;99_1800&stattab=map
  • Last taxonomy: Nocardioides dokdonensis subclade
  • 16S sequence: EF633986
  • Sequence Identity:
  • Total samples: 166
  • soil counts: 41
  • aquatic counts: 24
  • animal counts: 71
  • plant counts: 30

Safety information

risk assessment

  • @ref: 16096
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16096
  • description: Nocardioides dokdonensis strain FR1436 16S ribosomal RNA gene, partial sequence
  • accession: EF633986
  • length: 1385
  • database: ena
  • NCBI tax ID: 450734

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides dokdonensis FR1436GCA_001653335completencbi1300347
66792Nocardioides dokdonensis FR14361300347.3completepatric1300347
66792Nocardioides dokdonensis FR14362751185838completeimg1300347

GC content

@refGC-contentmethod
1609669.1
6777069.1thermal denaturation, midpoint method (Tm)
6777072.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
flagellatedno98.535yes
gram-positiveyes90.772no
anaerobicno98.368yes
halophileno82.355no
spore-formingno89.776yes
glucose-utilyes88.252no
motileno96.166yes
aerobicyes85.954yes
thermophileno98.575no
glucose-fermentno91.071no

External links

@ref: 16096

culture collection no.: DSM 22004, JCM 14815, KCTC 19309

straininfo link

  • @ref: 80392
  • straininfo: 405763

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18984703Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment.Park SC, Baik KS, Kim MS, Chun J, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.65835-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, 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
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
Phylogeny22228655Nocardioides lianchengensis sp. nov., an actinomycete isolated from soil.Zhang J, Ma Y, Yu HInt J Syst Evol Microbiol10.1099/ijs.0.036723-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Genetics28770029Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436(T).Kwak MJ, Kwon SK, Kim JFStand Genomic Sci10.1186/s40793-017-0257-z2017

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16096Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22004)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22004
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
32644Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2885528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
80392Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405763.1StrainInfo: A central database for resolving microbial strain identifiers