Strain identifier

BacDive ID: 5505

Type strain: Yes

Species: Dokdonia donghaensis

Strain Designation: DSW-1

Strain history: CIP <- 2006, KCTC <- JH Yoon, KRIBB: strain DSW-1

NCBI tax ID(s): 326320 (species)

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

@ref: 6810

BacDive-ID: 5505

DSM-Number: 17200

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

description: Dokdonia donghaensis DSW-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 326320
  • Matching level: species

strain history

@refhistory
6810<- J.-H. Yoon; DSW-1
67771<- JH Yoon, KRIBB
118963CIP <- 2006, KCTC <- JH Yoon, KRIBB: strain DSW-1

doi: 10.13145/bacdive5505.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Dokdonia
  • species: Dokdonia donghaensis
  • full scientific name: Dokdonia donghaensis Yoon et al. 2005

@ref: 6810

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Dokdonia

species: Dokdonia donghaensis

full scientific name: Dokdonia donghaensis Yoon et al. 2005

strain designation: DSW-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31565negative13.25 µm0.45 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.996
118963negativerod-shapedno

pigmentation

  • @ref: 31565
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6810BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
118963CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6810positivegrowth30mesophilic
31565positivegrowth04-35
31565positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31565positivegrowth5.5-8.0
31565positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31565aerobe
67771aerobe

spore formation

@refspore formationconfidence
31565no
67771no
69481no100
69480no99.999
118963no

halophily

@refsaltgrowthtested relationconcentration
31565NaClpositivegrowth<7 %
31565NaClpositiveoptimum2 %

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3156553424tween 20+carbon source
3156553423tween 40+carbon source
3156553426tween 80+carbon source
315654853esculin+hydrolysis
11896317632nitrate-reduction
11896316301nitrite-reduction

metabolite production

  • @ref: 118963
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31565alkaline phosphatase+3.1.3.1
31565catalase+1.11.1.6
31565cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
118963oxidase+
118963catalase+1.11.1.6
118963urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118963-+++-++---++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6810sea waterDokdoRepublic of KoreaKORAsia
67771From seawaterDokdoRepublic of KoreaKORAsia
118963Environment, Sea waterDokdo IslandRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2807.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_277;97_306;98_2176;99_2807&stattab=map
  • Last taxonomy: Dokdonia
  • 16S sequence: DQ003276
  • Sequence Identity:
  • Total samples: 11394
  • soil counts: 263
  • aquatic counts: 10205
  • animal counts: 829
  • plant counts: 97

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68101Risk group (German classification)
1189631Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6810
  • description: Dokdonia donghaensis strain DSW-1 16S ribosomal RNA gene, partial sequence
  • accession: DQ003276
  • length: 1479
  • database: ena
  • NCBI tax ID: 326320

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dokdonia donghaensis DSW-1GCA_001653755completencbi1300343
66792Dokdonia donghaensis DSW-1GCA_000769435scaffoldncbi1300343
66792Dokdonia donghaensis DSW-11300343.5completepatric1300343
66792Dokdonia donghaensis DSW-11300343.3wgspatric1300343
66792Dokdonia donghaensis DSW-12627853639draftimg1300343

GC content

@refGC-content
681038
6777138.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno94.877yes
gram-positiveno98.191yes
anaerobicno99.472no
aerobicyes92.505yes
halophileyes60.176yes
spore-formingno95.079yes
glucose-utilyes85.906no
motileno88.888no
thermophileno99.147yes
glucose-fermentno90.201no

External links

@ref: 6810

culture collection no.: DSM 17200, KCTC 12391, CIP 109306

straininfo link

  • @ref: 74990
  • straininfo: 361675

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280490Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water.Yoon JH, Kang SJ, Lee CH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63817-02005DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Flavobacteriaceae/classification/cytology/*isolation & purification/physiology, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sodium Chloride/pharmacologyEnzymology
Phylogeny21984677Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005.Yoon JH, Kang SJ, Park S, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.035253-02011Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisTranscriptome
Metabolism26574687Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria.Gomez-Consarnau L, Gonzalez JM, Riedel T, Jaenicke S, Wagner-Dobler I, Sanudo-Wilhelmy SA, Fuhrman JAISME J10.1038/ismej.2015.1962015Flavobacteriaceae/*genetics/*metabolism, Gene Expression Regulation, Bacterial, Light, Phylogeny, Rhodopsins, Microbial/metabolism, Seawater/microbiology, Thiamine/*metabolism, Vitamins/metabolismPhylogeny
Genetics27491981Complete Genome Sequence of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia donghaensis DSW-1T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea).Kim K, Kwon SK, Yoon JH, Kim JFGenome Announc10.1128/genomeA.00804-162016Phylogeny
Phylogeny29570445Dokdonia aurantiaca sp. nov., isolated from seaweed Zostera marina.Choi S, Kang JW, Kim MS, Yoon JH, Seong CNInt J Syst Evol Microbiol10.1099/ijsem.0.0027302018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seaweed/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zosteraceae/*microbiologyTranscriptome
Phylogeny32228747Dokdonia sinensis sp. nov., a flavobacterium isolated from surface seawater.Zhou LY, Meng X, Zhong YL, Li GY, Du ZJ, Mu DSInt J Syst Evol Microbiol10.1099/ijsem.0.0039492020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/classification, Flavobacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6810Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17200)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17200
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
31565Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2785528776041
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
68382Automatically annotated from API zym
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
74990Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID361675.1StrainInfo: A central database for resolving microbial strain identifiers
118963Curators of the CIPCollection of Institut Pasteur (CIP 109306)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109306