Dokdonia donghaensis (DSM 17200, KCTC 12391, DSW-1)

Name: Dokdonia donghaensis (DSM 17200, KCTC 12391, DSW-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5505

Type strain

Strain Designation DSW-1

Culture col. no. DSM 17200 KCTC 12391 DSW-1 CIP 109306

NCBI tax ID(s) 326320

Special Collections DSMZ KCTC CIP Literature strains

Links

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

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 361675

KCTC12391,DSM 17200,CIP 109306

@ref 20215

Last LPSN update 2025-12-16 09:48:05

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Dokdonia

Species Dokdonia donghaensis

Full scientific name Dokdonia donghaensis Yoon et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31565	negative	13.25 µm	0.45 µm	rod-shaped
67771				rod-shaped
67771	negative
118963	negative			rod-shaped
125438					92.5
125438	negative				96.45
125439	negative				90.1

Pigmentation

31565

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6810	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	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
118963	CIP Medium 13		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6810	positive	growth	30	mesophilic
31565	positive	growth	04-35
31565	positive	optimum	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31565	positive	optimum	7.5
31565	positive	growth	5.5-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31565	aerobe
67771	aerobe
125439	obligate aerobe	92.1

Spore formation

@ref	Spore formation	Confidence
31565
67771
118963
125439		95.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31565	NaCl	positive	growth	<7 %
31565	NaCl	positive	optimum	2 %

Observation

67771

Observationquinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31565	4853 ChEBI	esculin	+	hydrolysis
118963	17632 ChEBI	nitrate	-	reduction
118963	16301 ChEBI	nitrite	-	reduction
31565	53424 ChEBI	tween 20	+	carbon source
31565	53423 ChEBI	tween 40	+	carbon source
31565	53426 ChEBI	tween 80	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118963	35581 ChEBI	indole

Enzymes

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

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118963	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6810	sea water	Dokdo	Republic of Korea	KOR	Asia
67771	From seawater	Dokdo	Republic of Korea	KOR	Asia
118963	Environment, Sea water	Dokdo Island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ003276 (>99% sequence identity) for Dokdonia from Microbeatlas

Aquatic Samples	10205
Soil Samples	263
Animal Samples	829
Plant Samples	97
Total Samples	11394

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6810	1	Risk group (German classification) According to TRBA 466
118963	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM165375v1 assembly for Dokdonia donghaensis DSW-1	complete	GCA_001653755	1300343.5		1300343	98.2
66792	ASM76943v1 assembly for Dokdonia donghaensis DSW-1	scaffold	GCA_000769435	1300343.3	2627853639	1300343	76.17

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6810	Dokdonia donghaensis strain DSW-1 16S ribosomal RNA gene, partial sequence	DQ003276	1479		326320

GC content

@ref	GC-content (mol%)
6810	38
67771	38.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dokdonia donghaensis DSW-1
PATRIC: 1300343.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.80	no
125439	motility	BacteriaNetⓘ	yes	56.30	no
125439	gram_stain	BacteriaNetⓘ	negative	90.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dokdonia donghaensis DSW-1 DSW-1
NCBI: GCA_001653755.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.45	no
125438	anaerobic	anaerobicⓘ	no	97.82	yes
125438	aerobic	aerobicⓘ	yes	88.48	yes
125438	spore-forming	spore-formingⓘ	no	89.71	no
125438	thermophilic	thermophileⓘ	no	96.27	yes
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete 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 JF	Genome Announc	10.1128/genomeA.00804-16	2016
Metabolism	Proteorhodopsin 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 JA	ISME J	10.1038/ismej.2015.196	2015
Phylogeny	Reclassification 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 TK	Int J Syst Evol Microbiol	10.1099/ijs.0.035253-0	2011
Phylogeny	Dokdonia sinensis sp. nov., a flavobacterium isolated from surface seawater.	Zhou LY, Meng X, Zhong YL, Li GY, Du ZJ, Mu DS	Int J Syst Evol Microbiol	10.1099/ijsem.0.003949	2020
Phylogeny	Dokdonia aurantiaca sp. nov., isolated from seaweed Zostera marina.	Choi S, Kang JW, Kim MS, Yoon JH, Seong CN	Int J Syst Evol Microbiol	10.1099/ijsem.0.002730	2018
Phylogeny	Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water.	Yoon JH, Kang SJ, Lee CH, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63817-0	2005

References

#6810	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17200
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#31565	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27855 (see below)
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68382	Automatically annotated from API zym .
#69479	João 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.: MicrobeAtlas 1.0 beta .
#118963	Collection of Institut Pasteur ; Curators of the CIP; CIP 109306
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Dokdonia donghaensis (DSM 17200, KCTC 12391, DSW-1)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001653755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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