Strain identifier

BacDive ID: 11130

Type strain: Yes

Species: Nocardioides terrigena

Strain Designation: DS-17

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 424797 (species)

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General

@ref: 15789

BacDive-ID: 11130

DSM-Number: 21550

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

description: Nocardioides terrigena DS-17 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 424797
  • Matching level: species

strain history

@refhistory
15789<- JCM <- J.-H. Yoon; DS-17
67770J.-H. Yoon DS-17.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive11130.20230509.8.1

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 terrigena
  • full scientific name: Nocardioides terrigena Yoon et al. 2007

@ref: 15789

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides terrigena

full scientific name: Nocardioides terrigena Yoon et al. 2007

strain designation: DS-17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32177positive1.35 µm0.55 µmrod-shapedno
67771positive

pigmentation

  • @ref: 32177
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15789R2A 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
15789TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf

culture temp

@refgrowthtypetemperaturerange
15789positivegrowth28mesophilic
32177positivegrowth04-35
32177positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 32177
  • ability: positive
  • type: optimum
  • pH: 8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32177aerobe
67771aerobe

spore formation

  • @ref: 32177
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32177NaClpositivegrowth0-3 %
32177NaClpositiveoptimum0.75 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3217717128adipate+carbon source
3217728260galactose+carbon source
3217724265gluconate+carbon source
3217717716lactose+carbon source
3217725115malate+carbon source
3217729864mannitol+carbon source
3217728053melibiose+carbon source
3217726546rhamnose+carbon source
3217753424tween 20+carbon source
3217753423tween 40+carbon source
3217753425tween 60+carbon source
3217753426tween 80+carbon source

enzymes

@refvalueactivityec
32177alkaline phosphatase+3.1.3.1
32177cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15789soilDokdoRepublic of KoreaKORAsia
67770Soil
67771From soilDokdoRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1486.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_851;97_993;98_1172;99_1486&stattab=map
  • Last taxonomy: Nocardioides
  • 16S sequence: EF363712
  • Sequence Identity:
  • Total samples: 3058
  • soil counts: 1379
  • aquatic counts: 486
  • animal counts: 701
  • plant counts: 492

Safety information

risk assessment

  • @ref: 15789
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15789
  • description: Nocardioides terrigena strain DS-17 16S ribosomal RNA gene, partial sequence
  • accession: EF363712
  • length: 1470
  • database: ena
  • NCBI tax ID: 424797

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides terrigena strain KCTC 19217424797.3wgspatric424797
67770Nocardioides terrigena KCTC 19217GCA_003047265contigncbi424797

GC content

@refGC-contentmethod
1578971.5
6777071.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes91.39no
anaerobicno99.223no
halophileno92.127yes
spore-formingno87.588yes
glucose-utilyes88.543no
aerobicyes94.917yes
flagellatedno98.355no
thermophileno99.348yes
motileno95.868no
glucose-fermentno92.547no

External links

@ref: 15789

culture collection no.: DSM 21550, JCM 14582, KCTC 19217

straininfo link

  • @ref: 80379
  • straininfo: 319385

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978202Nocardioides terrigena sp. nov., isolated from soil.Yoon JH, Kang SJ, Lee SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65079-02007Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny18842843Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65566-02008Actinomycetales/chemistry/*classification/*genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny19126721Nocardioides basaltis sp. nov., isolated from black beach sand.Kim KH, Roh SW, Chang HW, Nam YD, Yoon JH, Jeon CO, Oh HM, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65785-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Silicon Dioxide, Species SpecificityPhenotype
Phylogeny19196766Nocardioides sediminis sp. nov., isolated from a sediment sample.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.002162-02009Actinomycetales/*classification/genetics/isolation & purification/ultrastructure, Geologic Sediments/*microbiology, Korea, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny29927366Nocardioides allogilvus sp. nov., a novel actinobacterium isolated from a karst cave.Zhang LY, Ming H, Zhao ZL, Ji WL, Salam N, Jiao JY, Fang BZ, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0028632018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny30547859Nocardioides gansuensis sp. nov., isolated from geopark soil.Wu S, Xia X, Zhou Z, Wang D, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0031572018Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15789Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21550)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21550
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
32177Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2841928776041
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
80379Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID319385.1StrainInfo: A central database for resolving microbial strain identifiers