Strain identifier

BacDive ID: 23887

Type strain: Yes

Species: Deinococcus wulumuqiensis

Strain Designation: R12

Strain history: CIP <- 2010, NBRC <- J. Mao and W. Wang, Xinjiang Academy Agric. Sciences, Xinjiang, China: strain R12

NCBI tax ID(s): 1288484 (strain), 980427 (species)

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General

@ref: 20523

BacDive-ID: 23887

DSM-Number: 28115

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

description: Deinococcus wulumuqiensis R12 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
980427species
1288484strain

strain history

@refhistory
20523<- NBRC <- CGMCC 1.8884 <- J. Mao and W. Wang, Xinjiang Acd. Agri. Sci., China; R12
123965CIP <- 2010, NBRC <- J. Mao and W. Wang, Xinjiang Academy Agric. Sciences, Xinjiang, China: strain R12

doi: 10.13145/bacdive23887.20230509.8.1

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 wulumuqiensis
  • full scientific name: Deinococcus wulumuqiensis Wang et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Deinococcus xibeiensis

@ref: 20523

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus wulumuqiensis

full scientific name: Deinococcus wulumuqiensis Wang et al. 2010 emend. Hong et al. 2015

strain designation: R12

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29562positivecoccus-shapedno
69480no90.477
69480positive95.283
123965positivecoccus-shapedno

pigmentation

  • @ref: 29562
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20523R2A 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
40421MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
20523PP-MEDIUM (DSMZ Medium 513)yeshttps://mediadive.dsmz.de/medium/513Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water
123965CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
123965CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20523positivegrowth28mesophilic
29562positivegrowth10-55
29562positiveoptimum37mesophilic
40421positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29562positivegrowth05-12alkaliphile
29562positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29562aerobe
123965facultative anaerobe

spore formation

@refspore formationconfidence
29562no
69481no98
69480no99.463

observation

  • @ref: 29562
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2956228757fructose+carbon source
2956224996lactate+carbon source
2956225017leucine+carbon source
2956226271proline+carbon source
2956226986threonine+carbon source
2956216296D-tryptophan+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12396517632nitrate-reduction
12396516301nitrite-reduction

metabolite production

  • @ref: 123965
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29562catalase+1.11.1.6
29562cytochrome oxidase+1.9.3.1
123965oxidase+
123965catalase+1.11.1.6
123965urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123965-+-+-+----+----+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123965+/----------+/-+/---------+/-------+/---+/-+/----+/-+/---+/----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20523soilXinjiang Uigur autonomous regionChinaCHNAsia
123965Environment, Radiotion polluted soilNorthwesternChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_813.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_493;97_562;98_647;99_813&stattab=map
  • Last taxonomy: Deinococcus wulumuqiensis subclade
  • 16S sequence: KJ784486
  • Sequence Identity:
  • Total samples: 14686
  • soil counts: 1239
  • aquatic counts: 3949
  • animal counts: 8916
  • plant counts: 582

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
205231Risk group (German classification)
1239651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20523Deinococcus wulumuqiensis strain R12 16S ribosomal RNA gene, partial sequenceEU0250281459ena1288484
20523Deinococcus wulumuqiensis strain DSM 28115 16S ribosomal RNA gene, partial sequenceKJ7844861469ena1288484

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus wulumuqiensis R12GCA_011067105completencbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875815contigncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875845contigncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875855scaffoldncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875785scaffoldncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875735scaffoldncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875745scaffoldncbi1288484
66792Deinococcus wulumuqiensis R12 R12GCA_014875965scaffoldncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875975contigncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875875scaffoldncbi1288484
66792Deinococcus wulumuqiensis R12GCA_000348665contigncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875835scaffoldncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875905scaffoldncbi1288484
66792Deinococcus wulumuqiensis R12GCA_014875925contigncbi1288484
66792Deinococcus wulumuqiensis R121288484.9wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.8wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.16wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.15wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.17wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.7completepatric1288484
66792Deinococcus wulumuqiensis R121288484.20wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.13wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.18wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.10wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.11wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.19wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.12wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.14wgspatric1288484
66792Deinococcus wulumuqiensis R121288484.3wgspatric1288484
66792Deinococcus wulumuqiensis strain CGMCC 1.8884980427.6wgspatric980427
66792Deinococcus wulumuqiensis R122551306669draftimg1288484
66792Deinococcus wulumuqiensis R12GCA_014875755scaffoldncbi1288484
66792Deinococcus wulumuqiensis CGMCC 1.8884GCA_014645575scaffoldncbi980427

GC content

  • @ref: 20523
  • GC-content: 66.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno89.247yes
flagellatedno95.174yes
gram-positiveyes81.65no
anaerobicno98.646yes
aerobicyes89.76no
halophileno92.917no
spore-formingno92.809yes
thermophileno78.751yes
glucose-utilyes83.96no
glucose-fermentno90.719no

External links

@ref: 20523

culture collection no.: DSM 28115, CGMCC 1.8884, CIP 110212, NBRC 105665

straininfo link

  • @ref: 87897
  • straininfo: 370644

literature

  • topic: Phylogeny
  • Pubmed-ID: 19801390
  • title: Deinococcus wulumuqiensis sp. nov., and Deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil.
  • authors: Wang W, Mao J, Zhang Z, Tang Q, Xie Y, Zhu J, Zhang L, Liu Z, Shi Y, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.015917-0
  • year: 2009
  • mesh: DNA, 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/*analysis
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20523Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28115Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28115)
29562Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172595728776041
40421Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8046
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87897Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID370644.1
123965Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110212Collection of Institut Pasteur (CIP 110212)