Strain identifier

BacDive ID: 3852

Type strain: Yes

Species: Deinococcus radiodurans

Strain Designation: R1, R1

Strain history: CIP <- 1996, ATCC <- A.W. Anderson: strain R1 (smooth), Micrococcus radiodurans

NCBI tax ID(s): 1121384 (strain), 1408434 (strain), 1299 (species)

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General

@ref: 8768

BacDive-ID: 3852

DSM-Number: 20539

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

description: Deinococcus radiodurans R1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from irradiated ground pork and beef.

NCBI tax id

NCBI tax idMatching level
1121384strain
1408434strain
1299species

strain history

@refhistory
8768<- CCM <- R.G.E. Murray <- A.W. Anderson, R1
67770DSM 20539 <-- CCM 1700 <-- R. G. E. Murray <-- A. W. Anderson R1.
122123CIP <- 1996, ATCC <- A.W. Anderson: strain R1 (smooth), Micrococcus radiodurans

doi: 10.13145/bacdive3852.20230509.8.1

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 radiodurans
  • full scientific name: Deinococcus radiodurans (ex Raj et al. 1960) Brooks and Murray 1981

@ref: 8768

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus radiodurans

full scientific name: Deinococcus radiodurans (ex Raj et al. 1960) Brooks and Murray 1981

strain designation: R1, R1

type strain: yes

Morphology

cell morphology

  • @ref: 122123
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 122123

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_20539_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_20539_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_20539_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_20539_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_20539_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8768CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
37966MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122123CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122123CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8768positivegrowth30mesophilic
37966positivegrowth30mesophilic
67770positivegrowth30mesophilic
122123positivegrowth15-30
122123nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122123
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.947

compound production

  • @ref: 8768
  • compound: restriction endonuclease MraI

halophily

@refsaltgrowthtested relationconcentration
122123NaClpositivegrowth0 %
122123NaClnogrowth2 %
122123NaClnogrowth4 %
122123NaClnogrowth6 %
122123NaClnogrowth8 %
122123NaClnogrowth10 %

murein

  • @ref: 8768
  • murein short key: A21.01
  • type: A3ß L-Orn-Gly2-3

observation

  • @ref: 67770
  • observation: quinones: MK-8, a trace of MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122123nitrate-reduction17632
122123nitrite-reduction16301

metabolite production

  • @ref: 122123
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 122123
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122123oxidase+
122123beta-galactosidase-3.2.1.23
122123alcohol dehydrogenase-1.1.1.1
122123gelatinase+
122123amylase-
122123DNase+
122123caseinase+3.4.21.50
122123catalase+1.11.1.6
122123lecithinase-
122123lysine decarboxylase-4.1.1.18
122123ornithine decarboxylase-4.1.1.17
122123protease-
122123urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122123-+++-+-+-++----+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8768--------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122123-+-------++-----------------------------------------------+----------------+--+--------------------

Isolation, sampling and environmental information

isolation

@refsample type
8768irradiated ground pork and beef
48649Irradiated ground pork and beef
67770Irradiated ground pork and beef
122123Food, Irradiated ground pork and beef

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Meat
#Host#Mammals#Bovinae (Cow, Cattle)
#Host#Mammals#Suidae (Pig,Swine)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5554.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_493;97_3292;98_4142;99_5554&stattab=map
  • Last taxonomy: Deinococcus radiodurans subclade
  • 16S sequence: Y11332
  • Sequence Identity:
  • Total samples: 4981
  • soil counts: 213
  • aquatic counts: 639
  • animal counts: 3917
  • plant counts: 212

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87681Risk group (German classification)
1221231Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8768
  • description: D.radiodurans 16S rRNA gene
  • accession: Y11332
  • length: 1466
  • database: ena
  • NCBI tax ID: 1299

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539GCA_000008565completencbi243230
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539GCA_001638825completencbi243230
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ATCC 13939 substr. S1GCA_020546705completencbi243230
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ATCC 13939 substr. R2GCA_020547025completencbi243230
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ATCC 13939 substr. R1GCA_020546805completencbi243230
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ATCC 13939 substr. R6GCA_020547085completencbi243230
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ATCC 13939 substr. S2GCA_020546785completencbi243230
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539GCA_020546685completencbi243230
66792Deinococcus radiodurans ATCC 139391408434.3wgspatric1408434
66792Deinococcus radiodurans DSM 205391121384.3wgspatric1121384
66792Deinococcus radiodurans R1243230.69plasmidpatric243230
66792Deinococcus radiodurans R1243230.72plasmidpatric243230
66792Deinococcus radiodurans R1243230.55completepatric243230
66792Deinococcus radiodurans R1243230.70plasmidpatric243230
66792Deinococcus radiodurans R1243230.71plasmidpatric243230
66792Deinococcus radiodurans R1243230.17completepatric243230
66792Deinococcus radiodurans ATCC 139392556921628draftimg1408434
66792Deinococcus radiodurans DSM 205392563366733draftimg1121384
66792Deinococcus radiodurans R12687453506completeimg243230
67770Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539GCA_000687895contigncbi243230
67770Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539GCA_000685985contigncbi243230
66792Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539GCA_021378295completencbi243230
66792Deinococcus radiodurans ATCC 139391408434.30completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.27completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.26completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.25completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.28completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.29completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.18completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.17completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.13completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.16completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.15completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.14completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.22completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.24completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.23completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.21completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.20completepatric1408434
66792Deinococcus radiodurans ATCC 139391408434.19completepatric1408434

GC content

@refGC-contentmethod
876867.0
6777067thermal denaturation, midpoint method (Tm)
6777069thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.041no
gram-positiveyes79.501no
anaerobicno98.136no
aerobicyes86.144no
halophileno92.419no
spore-formingno93.965no
motileno89.837no
thermophileno88.069yes
glucose-utilyes84.694no
glucose-fermentno87.435no

External links

@ref: 8768

culture collection no.: CCUG 27074, DSM 20539, ATCC 13939, CCM 1700, JCM 16871, NCIB 9279, CIP 104750, HAMBI 1924, IFO 15346, LMG 4051, NBRC 15346, NCIMB 9279, UWO 288, VKM B-1422

straininfo link

  • @ref: 73362
  • straininfo: 2154

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism11948162Firm but slippery attachment of Deinococcus geothermalis.Kolari M, Schmidt U, Kuismanen E, Salkinoja-Salonen MSJ Bacteriol10.1128/JB.184.9.2473-2480.20022002*Bacterial Adhesion, Biofilms/*growth & development, Gram-Positive Cocci/metabolism/*physiology, Industrial Microbiology, Microscopy, Atomic ForceBiotechnology
Metabolism12399510Protein splicing of the Deinococcus radiodurans strain R1 Snf2 intein.Southworth MW, Perler FBJ Bacteriol10.1128/JB.184.22.6387-6388.20022002Cloning, Molecular, DNA-Binding Proteins/chemistry/*genetics/metabolism, Deinococcus/*genetics/metabolism, Molecular Sequence Data, *Nuclear Proteins, *Protein Splicing, Sequence Analysis, DNA, Transcription Factors/chemistry/*genetics/metabolismEnzymology
Genetics15503140Mismatch repair ensures fidelity of replication and recombination in the radioresistant organism Deinococcus radiodurans.Mennecier S, Coste G, Servant P, Bailone A, Sommer SMol Genet Genomics10.1007/s00438-004-1077-62004Amino Acid Sequence, Base Pair Mismatch/*genetics, Base Sequence, DNA Repair/*genetics, DNA Replication/*genetics, Deinococcus/*genetics/radiation effects, Escherichia coli Proteins/*genetics/metabolism, Gamma Rays, Mitomycin, Molecular Sequence Data, Multigene Family/genetics, Mutation/*genetics, Nucleic Acid Heteroduplexes/metabolism, Phosphoric Monoester Hydrolases/*genetics/metabolism, Pyrophosphatases, Sequence Alignment, Sequence Analysis, DNA, Transformation, Genetic, Ultraviolet RaysMetabolism
Metabolism19780959Effects of carotenoids from Deinococcus radiodurans on protein oxidation.Tian B, Sun Z, Shen S, Wang H, Jiao J, Wang L, Hu Y, Hua YLett Appl Microbiol10.1111/j.1472-765X.2009.02727.x2009Bacterial Proteins/metabolism, Biphenyl Compounds, Carotenoids/*chemistry, Deinococcus/*chemistry, Free Radical Scavengers/*chemistry, Lutein/chemistry, Lycopene, Oxidation-Reduction, *Oxidative Stress, Picrates, Protein Carbonylation
Phylogeny19801390Deinococcus wulumuqiensis sp. nov., and Deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil.Wang W, Mao J, Zhang Z, Tang Q, Xie Y, Zhu J, Zhang L, Liu Z, Shi Y, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.015917-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Deinococcus/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Soil Pollutants, Radioactive/*analysisMetabolism
Phylogeny25351880Deinococcus antarcticus sp. nov., isolated from soil.Dong N, Li HR, Yuan M, Zhang XH, Yu YInt J Syst Evol Microbiol10.1099/ijs.0.066324-02014Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Metabolism34685516Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses.Eugenie N, Zivanovic Y, Lelandais G, Coste G, Bouthier de la Tour C, Bentchikou E, Servant P, Confalonieri FCells10.3390/cells101025362021Bacterial Proteins/metabolism, DNA Damage/genetics, Deinococcus/genetics/*metabolism, Gene Expression Regulation, Bacterial/*physiology, Genomics, Regulon/*genetics/physiology, Transcription Factors/*metabolismGenetics
Pathogenicity36000901Culturomics of Bacteria from Radon-Saturated Water of the World's Oldest Radium Mine.Kapinusova G, Jani K, Smrhova T, Pajer P, Jarosova I, Suman J, Strejcek M, Uhlik OMicrobiol Spectr10.1128/spectrum.01995-222022Humans, Adolescent, *Radium, *Radon, Phylogeny, Water, *Uranium, Hydrogen Peroxide, Silver, Vitamin K 3, Bacteria, SulfurPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8768Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20539)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20539
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
37966Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16693
48649Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27074)https://www.ccug.se/strain?id=27074
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
73362Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2154.1StrainInfo: A central database for resolving microbial strain identifiers
122123Curators of the CIPCollection of Institut Pasteur (CIP 104750)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104750