Strain identifier

BacDive ID: 3886

Type strain: Yes

Species: Deinococcus yunweiensis

Strain history: <- WJ Li, Yunnan Institute of Microbiology, China

NCBI tax ID(s): 367282 (species)

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General

@ref: 6685

BacDive-ID: 3886

DSM-Number: 17005

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

description: Deinococcus yunweiensis DSM 17005 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from contaminated agar plate.

NCBI tax id

  • NCBI tax id: 367282
  • Matching level: species

strain history

@refhistory
6685<- W.-J. Li; YIM 007
67771<- WJ Li, Yunnan Institute of Microbiology, China

doi: 10.13145/bacdive3886.20241212.9.2

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 yunweiensis
  • full scientific name: Deinococcus yunweiensis Zhang et al. 2007

@ref: 6685

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus yunweiensis

full scientific name: Deinococcus yunweiensis Zhang et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31791negativerod-shapedno
67771rod-shapedno
67771negative

pigmentation

  • @ref: 31791
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6685GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
6685GLYCEROL-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
6685positivegrowth28
31791positivegrowth10-50
31791positiveoptimum30
67771positivegrowth28

culture pH

@refabilitytypepHPH range
31791positivegrowth06-09alkaliphile
31791positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31791aerobe
67771aerobe

spore formation

@refspore formation
31791no
67771no

halophily

  • @ref: 31791
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0-1 %

observation

  • @ref: 67771
  • observation: quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3179122599arabinose+carbon source
3179124175galacturonate+carbon source
3179117234glucose+carbon source
3179115792malonate+carbon source
3179117306maltose+carbon source
3179129864mannitol+carbon source
3179128053melibiose+carbon source
3179126546rhamnose+carbon source
3179117814salicin+carbon source
3179130911sorbitol+carbon source
3179117992sucrose+carbon source

enzymes

@refvalueactivityec
31791alpha-galactosidase+3.2.1.22
31791catalase+1.11.1.6
31791cytochrome oxidase+1.9.3.1
31791urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6685contaminated agar plateYunnan ProvinceChinaCHNAsia
67771From contaminated plateYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Laboratory#Lab enrichment

taxonmaps

  • @ref: 69479
  • File name: preview.99_17405.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_8928;97_10736;98_13175;99_17405&stattab=map
  • Last taxonomy: Deinococcus yunweiensis subclade
  • 16S sequence: DQ344634
  • Sequence Identity:
  • Total samples: 2412
  • soil counts: 512
  • aquatic counts: 841
  • animal counts: 649
  • plant counts: 410

Safety information

risk assessment

  • @ref: 6685
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6685
  • description: Deinococcus yunweiensis strain YIM 007 16S ribosomal RNA gene, partial sequence
  • accession: DQ344634
  • length: 1459
  • database: nuccore
  • NCBI tax ID: 367282

GC content

  • @ref: 6685
  • GC-content: 64.1

External links

@ref: 6685

culture collection no.: DSM 17005, KCTC 3962, YIM 007, KCTC 3955

straininfo link

  • @ref: 73396
  • straininfo: 232161

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267981Deinococcus yunweiensis sp. nov., a gamma- and UV-radiation-resistant bacterium from China.Zhang YQ, Sun CH, Li WJ, Yu LY, Zhou JQ, Zhang YQ, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.64292-02007Bacteria, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deinococcus/*classification/*isolation & purification/physiology/radiation effects, Fatty Acids/analysis/chemistry, *Gamma Rays, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Movement, Ornithine/analysis, Peptidoglycan/chemistry, Phospholipids/analysis/chemistry, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Spores, Bacterial, Temperature, *Ultraviolet RaysGenetics
Phylogeny29080938Description of Deinococcus populi sp. nov. from the trunk surface of a Japanese aspen tree.Li J, Kudo C, Tonouchi AArch Microbiol10.1007/s00203-017-1443-52017Bacterial Typing Techniques, Base Composition/genetics, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Glycolipids/analysis, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Plant Bark/*microbiology, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisTranscriptome
Phylogeny29561256Deinococcus rufus sp. nov., isolated from soil near an iron factory.Wang Q, Song Y, Choi L, Liu H, Wang G, Li MInt J Syst Evol Microbiol10.1099/ijsem.0.0027242018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/isolation & purification, Extraction and Processing Industry, Fatty Acids/chemistry, Glycolipids/chemistry, Iron, Nucleic Acid Hybridization, Parabens, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6685Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17005)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17005
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
31791Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2806228776041
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
73396Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232161.1StrainInfo: A central database for resolving microbial strain identifiers