Strain identifier

BacDive ID: 5394

Type strain: Yes

Species: Erythrobacter donghaensis

Strain Designation: SW-132

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 267135 (species)

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General

@ref: 6335

BacDive-ID: 5394

DSM-Number: 16220

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

description: Erythrobacter donghaensis SW-132 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea water of tidal flat.

NCBI tax id

  • NCBI tax id: 267135
  • Matching level: species

strain history

@refhistory
6335<- J.-H. Yoon; SW-132
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive5394.20230509.8.1

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 donghaensis
  • full scientific name: Erythrobacter donghaensis (Yoon et al. 2004) Xu et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Porphyrobacter donghaensis

@ref: 6335

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Porphyrobacter

species: Porphyrobacter donghaensis

full scientific name: Porphyrobacter donghaensis Yoon et al. 2004

strain designation: SW-132

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidence
31290negative1.7 µm0.7 µmno
67771negative
69480negative99.995

Culture and growth conditions

culture medium

  • @ref: 6335
  • 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
6335positivegrowth30mesophilic
31290positivegrowth10-45
31290positiveoptimum33.5mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31290positivegrowth05-08
31290positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31290aerobe
67771aerobe

spore formation

@refspore formationconfidence
31290no
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
31290NaClpositivegrowth0-7 %
31290NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3129017057cellobiose+carbon source
3129017234glucose+carbon source
3129025115malate+carbon source
3129017306maltose+carbon source
3129015361pyruvate+carbon source
3129030031succinate+carbon source
3129018222xylose+carbon source
312904853esculin+hydrolysis

enzymes

@refvalueactivityec
31290catalase+1.11.1.6
31290cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6335sea water of tidal flatHwajinpo beachRepublic of KoreaKORAsia
67771From seawaterthe east seaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_6830.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_1392;98_1691;99_6830&stattab=map
  • Last taxonomy: Erythrobacter
  • 16S sequence: AY559428
  • Sequence Identity:
  • Total samples: 693
  • soil counts: 38
  • aquatic counts: 585
  • animal counts: 55
  • plant counts: 15

Safety information

risk assessment

  • @ref: 6335
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6335
  • description: Porphyrobacter donghaensis strain SW-132 16S ribosomal RNA gene, partial sequence
  • accession: AY559428
  • length: 1440
  • database: ena
  • NCBI tax ID: 267135

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erythrobacter donghaensis DSM 16220GCA_002155425contigncbi267135
66792Porphyrobacter donghaensis strain DSM 16220267135.40wgspatric267135
66792Porphyrobacter donghaensis DSM 162202840396641draftimg267135

GC content

  • @ref: 31290
  • GC-content: 66.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno50yes
gram-positiveno97.924yes
anaerobicno99.371yes
aerobicyes94.818yes
halophileno85.302no
spore-formingno94.969yes
glucose-utilyes85.535no
flagellatedno86.575no
thermophileno93.958yes
glucose-fermentno91.919no

External links

@ref: 6335

culture collection no.: DSM 16220, KCTC 12229

straininfo link

  • @ref: 74884
  • straininfo: 134455

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6335Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16220)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16220
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
31290Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2760928776041
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
74884Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134455.1StrainInfo: A central database for resolving microbial strain identifiers