Strain identifier

BacDive ID: 3861

Type strain: Yes

Species: Deinococcus radiopugnans

Strain history: DSM 12027 <-- ATCC 19172 <-- S. H. Hutner MIT 248 (Micrococcus roseus) <-- R. G. E. Murray <-- N. Davis et al. UWO 293.

NCBI tax ID(s): 585398 (strain), 57497 (species)

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General

@ref: 4580

BacDive-ID: 3861

DSM-Number: 12027

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Deinococcus radiopugnans DSM 12027 is a mesophilic bacterium that was isolated from irradiated haddock.

NCBI tax id

NCBI tax idMatching level
585398strain
57497species

strain history

@refhistory
4580<- ATCC <- S.H. Hutner, MIT 248 (Micrococcus roseus) <- R. Murray <- N. Davis et al.
67770DSM 12027 <-- ATCC 19172 <-- S. H. Hutner MIT 248 (Micrococcus roseus) <-- R. G. E. Murray <-- N. Davis et al. UWO 293.

doi: 10.13145/bacdive3861.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/deinococcota
  • domain: Bacteria
  • phylum: Deinococcota
  • class: Deinococci
  • order: Deinococcales
  • family: Deinococcaceae
  • genus: Deinococcus
  • species: Deinococcus radiopugnans
  • full scientific name: Deinococcus radiopugnans Brooks and Murray 1981

  • synonyms

    • @ref: 20215
    • synonym: Deinococcus swuensis

@ref: 4580

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus radiopugnans

full scientific name: Deinococcus radiopugnans Brooks and Murray 1981

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.733
6948099.999positive

Culture and growth conditions

culture medium

  • @ref: 4580
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
4580positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no97
69480no99.018

murein

  • @ref: 4580
  • murein short key: A21.01
  • type: A3ß L-Orn-Gly2-3

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4580irradiated haddockUSAUSANorth America
67770Irradiated haddock

isolation source categories

  • Cat1: #Host
  • Cat2: #Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_4680.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_2085;97_2512;98_3509;99_4680&stattab=map
  • Last taxonomy: Deinococcus
  • 16S sequence: Y11334
  • Sequence Identity:
  • Total samples: 1559
  • soil counts: 115
  • aquatic counts: 350
  • animal counts: 941
  • plant counts: 153

Safety information

risk assessment

  • @ref: 4580
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4580
  • description: D.radiopugnans 16S rRNA gene
  • accession: Y11334
  • length: 1469
  • database: ena
  • NCBI tax ID: 585398

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus radiopugnans ATCC 19172 DSM 12027GCA_014201625contigncbi585398
66792Deinococcus radiopugnans ATCC 19172585398.6wgspatric585398
66792Deinococcus radiopugnans ATCC 19172585398.4plasmidpatric585398
66792Deinococcus radiopugnans ATCC 19172 strain DSM 12027585398.8wgspatric585398
66792Deinococcus radiopugnans DSM 120272861237949draftimg585398
67770Deinococcus radiopugnans ATCC 19172GCA_006335125contigncbi585398

GC content

  • @ref: 67770
  • GC-content: 68
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
gram-positiveyes87.307no
anaerobicno98.486no
halophileno90.826no
spore-formingno91.335no
glucose-utilyes89.629no
thermophileno94.7yes
flagellatedno96.162no
aerobicyes91.439no
motileno88.691no
glucose-fermentno90.029no

External links

@ref: 4580

culture collection no.: DSM 12027, ATCC 19172, JCM 16872, UWO 293, MIT 248, CCM 2785, IFO 15348, JCM 21312, NBRC 15348, NCIMB 13155

straininfo link

  • @ref: 73371
  • straininfo: 46559

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics19504653Development of versatile shuttle vectors for Deinococcus grandis.Satoh K, Tu Z, Ohba H, Narumi IPlasmid10.1016/j.plasmid.2009.01.0052009Amino Acid Sequence, Base Sequence, Deinococcus/*genetics, *Genetic Techniques, Genetic Vectors/*genetics, Luciferases, Firefly/genetics, Molecular Sequence Data, Plasmids/chemistry/genetics, Sequence Alignment, Transformation, Genetic
Phylogeny22228662Deinococcus humi sp. nov., isolated from soil.Srinivasan S, Lee JJ, Lim S, Joe M, Kim MKInt J Syst Evol Microbiol10.1099/ijs.0.037234-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/isolation & purification, Fatty Acids/analysis, Gamma Rays, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny34236299Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans.Lakra P, Verma H, Talwar C, Singh DN, Singhvi N, Lal R, Gupta VInt J Syst Evol Microbiol10.1099/ijsem.0.0048792021Bacterial Typing Techniques, DNA, Bacterial/genetics, Deinococcus/*classification, Genomics, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitle
4580Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12027)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12027
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
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/
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73371Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46559.1StrainInfo: A central database for resolving microbial strain identifiers