Strain identifier

BacDive ID: 3881

Type strain: Yes

Species: Deinococcus caeni

Strain Designation: Ho-08

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 569127 (species)

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General

@ref: 7438

BacDive-ID: 3881

DSM-Number: 18373

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

description: Deinococcus caeni Ho-08 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge, wastewater treatment plant.

NCBI tax id

  • NCBI tax id: 569127
  • Matching level: species

strain history

@refhistory
7438<- Sung Taik Lee; Ho08
67771<- ST Lee, KAIST

doi: 10.13145/bacdive3881.20230509.8.1

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 caeni
  • full scientific name: Deinococcus caeni Im et al. 2008

@ref: 7438

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus caeni

full scientific name: Deinococcus caeni Im et al. 2008

strain designation: Ho-08

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
31700negative02-03 µmcoccus-shaped
67771rod-shapedno
67771negative

pigmentation

  • @ref: 31700
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7438
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
7438positivegrowth28mesophilic
31700positivegrowth20-37
31700positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31700positivegrowth6-9.5alkaliphile
31700positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31700aerobe
67771aerobe

spore formation

@refspore formation
31700no
67771no

halophily

@refsaltgrowthtested relationconcentration
31700NaClpositivegrowth0-3 %
31700NaClpositiveoptimum0-3 %

observation

@refobservation
31700aggregates in chains
67771quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170017234glucose+carbon source
3170028087glycogen+carbon source
3170017306maltose+carbon source
31700506227N-acetylglucosamine+carbon source
3170026271proline+carbon source
3170017992sucrose+carbon source

enzymes

  • @ref: 31700
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7438activated sludge, wastewater treatment plantDaejeon CityRepublic of KoreaKORAsia
67771From activated sludge, wastewater-treatment plant that receives leachate from a landfill siteDaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_11955.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_228;97_2556;98_3167;99_11955&stattab=map
  • Last taxonomy: Deinococcus caeni
  • 16S sequence: DQ017709
  • Sequence Identity:
  • Total samples: 1788
  • soil counts: 73
  • aquatic counts: 580
  • animal counts: 1109
  • plant counts: 26

Safety information

risk assessment

  • @ref: 7438
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7438
  • description: Deinococcus caeni strain Ho-08 16S ribosomal RNA gene, partial sequence
  • accession: DQ017709
  • length: 1458
  • database: ena
  • NCBI tax ID: 569127

GC content

  • @ref: 7438
  • GC-content: 68.4

External links

@ref: 7438

culture collection no.: DSM 18373, KCTC 12553, NBRC 101312

straininfo link

  • @ref: 73391
  • straininfo: 292198

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842854Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge.Im WT, Jung HM, Ten LN, Kim MK, Bora N, Goodfellow M, Lim S, Jung J, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64082-02008Bacterial Typing Techniques, DNA, Bacterial/genetics, Deinococcus/chemistry/*classification/*genetics/isolation & purification/radiation effects, Fatty Acids/chemistry, Fresh Water/*microbiology, Gamma Rays, Genes, Bacterial, Genes, rRNA, Genotype, Microbial Viability, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Water MicrobiologyGenetics
Phylogeny20622051Deinococcus depolymerans sp. nov., a gamma- and UV-radiation-resistant bacterium, isolated from a naturally radioactive site.Asker D, Awad TS, McLandsborough L, Beppu T, Ueda KInt J Syst Evol Microbiol10.1099/ijs.0.013482-02010Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deinococcus/*classification/genetics/isolation & purification/*radiation effects, Fatty Acids/analysis, Fresh Water/*microbiology, *Gamma Rays, Glycolipids/analysis, Japan, Microbial Viability/radiation effects, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Ultraviolet RaysGenetics
Phylogeny21764979Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant.Srinivasan S, Kim MK, Lim S, Joe M, Lee MInt J Syst Evol Microbiol10.1099/ijs.0.033316-02011Base Composition, DNA, Bacterial/genetics, Deinococcus/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sewage/*microbiologyMetabolism
Phylogeny27480633Deinococcus seoulensis sp. nov., a bacterium isolated from sediment at Han River in Seoul, Republic of Korea.Lee JJ, Lee YH, Park SJ, Lim S, Jeong SW, Lee SY, Cho YJ, Kim MK, Jung HYJ Microbiol10.1007/s12275-016-6253-y2016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deinococcus/classification/genetics/*isolation & purification/metabolism, Fatty Acids/chemistry/metabolism, Geologic Sediments/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiologyMetabolism
Phylogeny28000055Deinococcus knuensis sp. nov., a bacterium isolated from river water.Lee JJ, Lee YH, Park SJ, Lee SY, Park S, Lee DS, Kang IK, Ten LN, Jung HYAntonie Van Leeuwenhoek10.1007/s10482-016-0813-32016Benzoquinones/analysis, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Deinococcus/*classification/genetics/*isolation & purification/radiation effects, Fatty Acids/analysis, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Phenotype, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sodium Chloride/metabolism, Species Specificity, Temperature, Vitamin K 2/analogs & derivatives/analysisPhenotype

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7438Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18373)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18373
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
31700Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2797728776041
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
73391Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292198.1StrainInfo: A central database for resolving microbial strain identifiers