Polaribacter dokdonensis (DSM 17204, CIP 109304, DSW-5)

Name: Polaribacter dokdonensis (DSM 17204, CIP 109304, DSW-5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5627

Type strain

Strain Designation DSW-5

Culture col. no. DSM 17204 CIP 109304 DSW-5 KCTC 12392

NCBI tax ID(s) 326329

Special Collections DSMZ CIP Literature strains KCTC

Links

Polaribacter dokdonensis DSW-5 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 297296

DSM 17204,KCTC 12392,CIP 109304

@ref 20215

Last LPSN update 2025-12-16 09:48:06

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Polaribacter

Species Polaribacter dokdonensis

Full scientific name Polaribacter dokdonensis Yoon et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31566	negative	0.8-5 µm	0.4-0.6 µm	rod-shaped
118954	negative			rod-shaped
125439	negative				99.6
125438					94.5
125438	negative				98.585

Pigmentation

31566

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6814	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
32786	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118954	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6814	positive	growth	25	mesophilic
31566	positive	growth	04-33
31566	positive	optimum	25-28	mesophilic
32786	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
31566	positive	optimum	07-08
31566	positive	growth	5.5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31566	aerobe
125439	obligate aerobe	98.7

Spore formation

@ref	Spore formation	Confidence
31566
125439		94.3
125438		90.333

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31566	NaCl	positive	growth	02-05 %
31566	NaCl	positive	optimum	2 %

Observation

31566

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31566	28757 ChEBI	fructose	+	carbon source
118954	17632 ChEBI	nitrate	-	reduction
118954	16301 ChEBI	nitrite	-	reduction
31566	16634 ChEBI	raffinose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118954	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
31566	catalase	+	1.11.1.6
118954	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
31566	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
118954	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
118954	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
118954	-	+	+	+	+	+	+	+	+	-	+	+	-	-	-	-	-	-	-	-

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
6814	sea water	Dokdo	Republic of Korea	KOR	Asia
118954	Environment, Sea water	Dokdo Island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ004686 (>99% sequence identity) for Polaribacter from Microbeatlas

Aquatic Samples	2578
Soil Samples	78
Animal Samples	102
Plant Samples	15
Total Samples	2773

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6814	1	Risk group (German classification) According to TRBA 466
118954	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
124043	ASM2436234v1 assembly for Polaribacter dokdonensis KCTC 12392	complete	GCA_024362345	326329.5		326329	97.32
124043	ASM3802398v1 assembly for Polaribacter dokdonensis KCTC 12392	complete	GCA_038023985			326329	95.05
66792	DSW5v1 assembly for Polaribacter dokdonensis DSW-5	contig	GCA_001280865	1300348.6	2639762916	1300348	77.95
66792	IMG-taxon 2693430036 annotated assembly for Polaribacter dokdonensis DSW-5	scaffold	GCA_900106865	1300348.9	2693430036	1300348	77.36

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6814	Polaribacter dokdonensis strain DSW-5 16S ribosomal RNA gene, partial sequence	DQ004686	1475		1300348

GC content

31566

GC-content (mol%)30

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Polaribacter dokdonensis DSW-5
NCBI: GCA_900106865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.30	no
125439	motility	BacteriaNetⓘ	no	61.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Polaribacter dokdonensis DSW-5 DSW-5
NCBI: GCA_900106865.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.59	yes
125438	anaerobic	anaerobicⓘ	no	98.21	no
125438	aerobic	aerobicⓘ	yes	89.06	no
125438	spore-forming	spore-formingⓘ	no	90.33	yes
125438	thermophilic	thermophileⓘ	no	97.43	yes
125438	flagellated	motile2+ⓘ	no	94.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5.	Yoon K, Song JY, Kwak MJ, Kwon SK, Kim JF	J Microbiol	10.1007/s12275-017-6427-2	2017
Phylogeny	Polaribacter aquimarinus sp. nov., isolated from the surface of a marine red alga.	Xu W, Chen XY, Wei XT, Lu DC, Du ZJ.	Antonie Van Leeuwenhoek	10.1007/s10482-019-01350-z	2020
Phylogeny	Polaribacter litorisediminis sp. nov., isolated from a tidal flat.	Park S, Yoon SY, Ha MJ, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001919	2017
Phylogeny	Polaribacter haliotis sp. nov., isolated from the gut of abalone Haliotis discus hannai.	Kim YO, Park IS, Park S, Nam BH, Park JM, Kim DG, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001557	2016
Phylogeny	Polaribacter reichenbachii sp. nov.: a new marine bacterium associated with the green alga Ulva fenestrata.	Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV	Curr Microbiol	10.1007/s00284-012-0200-x	2012
Phylogeny	Polaribacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis, and emended descriptions of the genus Polaribacter and two Polaribacter species.	Fukui Y, Abe M, Kobayashi M, Saito H, Oikawa H, Yano Y, Satomi M	Int J Syst Evol Microbiol	10.1099/ijs.0.041434-0	2012
Phylogeny	Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.	Kim JH, Kim KY, Hahm YT, Kim BS, Chun J, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65346-0	2008
Phylogeny	Polaribacter dokdonensis sp. nov., isolated from seawater.	Yoon JH, Kang SJ, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63820-0	2006

References

#6814	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17204
#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 )
#31566	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 #27856 (see below)
#32786	; Curators of the CIP;
#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) .
#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 .
#118954	Collection of Institut Pasteur ; Curators of the CIP; CIP 109304
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Rate our new design

Content

About us

Polaribacter dokdonensis (DSM 17204, CIP 109304, DSW-5)

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_024362345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media