Strain identifier

BacDive ID: 3890

Type strain: Yes

Species: Deinococcus roseus

Strain Designation: TDMA-uv51

Strain history: D. Asker et al. TDMA-uv51.

NCBI tax ID(s): 392414 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16189

BacDive-ID: 3890

DSM-Number: 22367

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

description: Deinococcus roseus TDMA-uv51 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Fresh water.

NCBI tax id

  • NCBI tax id: 392414
  • Matching level: species

strain history

@refhistory
16189<- CCUG; CCUG 53611 <- D. Asker, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; TDMA-uv51
67770D. Asker et al. TDMA-uv51.

doi: 10.13145/bacdive3890.20240510.9

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 roseus
  • full scientific name: Deinococcus roseus Asker et al. 2008

@ref: 16189

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus roseus

full scientific name: Deinococcus roseus Asker et al. 2008

strain designation: TDMA-uv51

type strain: yes

Morphology

cell morphology

  • @ref: 32604
  • gram stain: positive
  • cell length: 1.65 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 59944
  • incubation period: 2-3 days

pigmentation

  • @ref: 32604
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16189R2A 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
16189NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
16189GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)yeshttps://mediadive.dsmz.de/medium/1484Name: Glycerol-Yeast extract-Peptone Medium (DSMZ Medium 1484) Composition: Agar 15.0 g/l Yeast extract 5.0 g/l Bacto peptone 3.0 g/l Betaine 1.25 g/l Sodium pyruvate 1.25 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Pyridoxine hydrochloride 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l (DL)-alpha-Lipoic acid 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine HCl 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Glycerol Distilled water

culture temp

@refgrowthtypetemperature
16189positivegrowth28
32604positivegrowth20-40
32604positiveoptimum37
59944positivegrowth30
67770positivegrowth30

culture pH

@refabilitytypepHPH range
32604positivegrowth05-09alkaliphile
32604positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32604aerobe
59944aerobe

spore formation

@refspore formationconfidence
32604no
69481no100

halophily

@refsaltgrowthtested relationconcentration
32604NaClpositivegrowth<1 %
32604NaClpositiveoptimum0.25 %

observation

@refobservation
32604aggregates in chains
67770quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3260422599arabinose+carbon source
326045291gelatin+carbon source
3260417234glucose+carbon source
3260417306maltose+carbon source
3260429864mannitol+carbon source
3260437684mannose+carbon source
3260453426tween 80+carbon source
326044853esculin+hydrolysis

enzymes

@refvalueactivityec
32604catalase+1.11.1.6
32604cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16189Fresh waterTottori, Misasa (radioactive site)JapanJPNAsia
59944Fresh waterMisasa (a radioactive site)JapanJPNAsia2005-09-01
67770Freshwater sample collected at MisasaTottori Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_12649.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_653;96_3530;97_4335;98_5549;99_12649&stattab=map
  • Last taxonomy: Deinococcus roseus
  • 16S sequence: AB264136
  • Sequence Identity:
  • Total samples: 35
  • soil counts: 12
  • aquatic counts: 14
  • animal counts: 8
  • plant counts: 1

Safety information

risk assessment

  • @ref: 16189
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16189
  • description: Deinococcus roseus gene for 16S rRNA, partial sequence
  • accession: AB264136
  • length: 1402
  • database: nuccore
  • NCBI tax ID: 392414

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus roseus JCM 14370GCA_014646895scaffoldncbi392414
66792Deinococcus roseus strain JCM 14370392414.3wgspatric392414

GC content

@refGC-contentmethod
1618957.4
3260469.1
6777057.1-57.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno93.932yes
gram-positiveyes80.73yes
anaerobicno99.091no
aerobicyes90.87no
halophileno94.091no
spore-formingno89.253yes
thermophileno89.896no
glucose-utilyes90.206yes
motileno85.959yes
glucose-fermentno80.751no

External links

@ref: 16189

culture collection no.: DSM 22367, CCUG 53611, JCM 14370, NBRC 102117

straininfo link

  • @ref: 73400
  • straininfo: 397839

literature

  • topic: Phylogeny
  • Pubmed-ID: 18096345
  • title: Deinococcus misasensis and Deinococcus roseus, novel members of the genus Deinococcus, isolated from a radioactive site in Japan.
  • authors: Asker D, Awad TS, Beppu T, Ueda K
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2007.10.002
  • year: 2007
  • mesh: Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deinococcus/*classification/genetics/*isolation & purification/radiation effects, Fatty Acids/analysis, Gamma Rays, Genes, rRNA, Japan, Molecular Sequence Data, Oxidoreductases/metabolism, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Ultraviolet Rays, *Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16189Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22367)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22367
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
32604Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2881728776041
59944Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53611)https://www.ccug.se/strain?id=53611
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
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
73400Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397839.1StrainInfo: A central database for resolving microbial strain identifiers