Strain identifier

BacDive ID: 5396

Type strain: Yes

Species: Erythrobacter dokdonensis

Strain Designation: DSW-74

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 328225 (species)

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General

@ref: 6721

BacDive-ID: 5396

DSM-Number: 17193

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

description: Erythrobacter dokdonensis DSW-74 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 328225
  • Matching level: species

strain history

@refhistory
6721<- J.-H. Yoon; DSW74
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive5396.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Erythrobacter
  • species: Erythrobacter dokdonensis
  • full scientific name: Erythrobacter dokdonensis (Yoon et al. 2006) Xu et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Porphyrobacter dokdonensis

@ref: 6721

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Porphyrobacter

species: Porphyrobacter dokdonensis

full scientific name: Porphyrobacter dokdonensis Yoon et al. 2006

strain designation: DSW-74

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31578negative0.5-2.5 µm0.4-0.6 µmovoid-shapedno
67771negative
69480negative99.997

pigmentation

  • @ref: 31578
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6721
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6721positivegrowth30mesophilic
31578positivegrowth10-43
31578positiveoptimum35-37mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31578positivegrowth5.5-8
31578positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31578aerobe
67771aerobe

spore formation

@refspore formationconfidence
31578no
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
31578NaClpositivegrowth0-7 %
31578NaClpositiveoptimum2 %

observation

  • @ref: 31578
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3157817057cellobiose+carbon source
3157825115malate+carbon source
3157817306maltose+carbon source
3157815361pyruvate+carbon source
3157830031succinate+carbon source
315784853esculin+hydrolysis

enzymes

@refvalueactivityec
31578catalase+1.11.1.6
31578cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6721sea waterDokdoRepublic of KoreaKORAsia
67771From seawaterDokdoRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_57975.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_1392;98_1691;99_57975&stattab=map
  • Last taxonomy: Erythrobacter
  • 16S sequence: DQ011529
  • Sequence Identity:
  • Total samples: 549
  • soil counts: 34
  • aquatic counts: 448
  • animal counts: 34
  • plant counts: 33

Safety information

risk assessment

  • @ref: 6721
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6721
  • description: Porphyrobacter dokdonensis strain DSW-74 16S ribosomal RNA gene, partial sequence
  • accession: DQ011529
  • length: 1440
  • database: ena
  • NCBI tax ID: 328225

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erythrobacter dokdonensis DSM 17193GCA_002155305contigncbi328225
66792Erythrobacter dokdonensis DSW-74GCA_001677335contigncbi1300349
66792Porphyrobacter dokdonensis strain DSM 17193328225.4wgspatric328225
66792Erythrobacter dokdonensis DSW-742842993287draftimg1300349

GC content

@refGC-contentmethod
672165.8high performance liquid chromatography (HPLC)
3157865.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.817no
anaerobicno99.392yes
halophileno76.055no
spore-formingno94.983yes
glucose-utilyes86.245no
motileyes54.104yes
flagellatedno83.576yes
aerobicyes93.482yes
thermophileno88.387yes
glucose-fermentno92.958no

External links

@ref: 6721

culture collection no.: DSM 17193, KCTC 12395, DSW 74

straininfo link

  • @ref: 74886
  • straininfo: 291134

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6721Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17193)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17193
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
31578Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2786728776041
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)
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
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
74886Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID291134.1StrainInfo: A central database for resolving microbial strain identifiers