Dokdonia pacifica (DSM 25597, CGMCC 1.12184, JCM 18216)

Name: Dokdonia pacifica (DSM 25597, CGMCC 1.12184, JCM 18216)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131369

Type strain

Strain Designation SW230

Culture col. no. DSM 25597 CGMCC 1.12184 JCM 18216 SW230 KCTC 52761

NCBI tax ID(s) 1627892

Special Collections DSMZ JCM KCTC

History <- X.-H. Zhang, Ocean Univ. China, Dept. of Marine Biology, Qingdao, P. R. China; sw230 X.-H. Zhang SW230.

Links

Dokdonia pacifica SW230 is a mesophilic prokaryote that was isolated from surface seawater seawater.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 407890

JCM 18216,DSM 25597

@ref 20215

Last LPSN update 2026-02-09 11:31:26

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Dokdonia

Species Dokdonia pacifica

Full scientific name Dokdonia pacifica Zhang et al. 2015

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	93
125438	97.981	negative
125439	98.8	negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22596	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22596	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		94.5

Observation

67770

Observationquinones: MK-6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	phenylmercury acetate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	gluconeogenesis	100	8 of 8
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	tryptophan metabolism	78.95	30 of 38
66794	heme metabolism	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	purine metabolism	76.6	72 of 94
66794	alanine metabolism	75.86	22 of 29
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	non-pathway related	71.05	27 of 38
66794	urea cycle	69.23	9 of 13
66794	flavin biosynthesis	66.67	10 of 15
66794	enterobactin biosynthesis	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	arginine metabolism	66.67	16 of 24
66794	lysine metabolism	66.67	28 of 42
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	glycine metabolism	60	6 of 10
66794	propionate fermentation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	vitamin B1 metabolism	53.85	7 of 13
66794	carotenoid biosynthesis	50	11 of 22
66794	sphingosine metabolism	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	arachidonic acid metabolism	50	9 of 18
66794	ethanol fermentation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	isoprenoid biosynthesis	50	13 of 26
66794	pantothenate biosynthesis	50	3 of 6
66794	oxidative phosphorylation	49.45	45 of 91
66794	degradation of pentoses	46.43	13 of 28
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	allantoin degradation	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	D-cycloserine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	chlorophyll metabolism	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	metabolism of disaccharids	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	phenol degradation	35	7 of 20
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	vitamin B12 metabolism	32.35	11 of 34
66794	coenzyme M biosynthesis	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude
22596	surface seawater seawater	South Pacific Gyre at station U1371 (45° 58' S 163° 11' W)	-45.9667	-163.183 -45.9667/-163.183
67770	Surface seawater of the South Pacific Gyre (45° 58' S 163° 11' W)		-45.9667	-163.183 -45.9667/-163.183

Taxonmaps

69479

Global distribution of 16S sequence KP862606 (>99% sequence identity) for Dokdonia pacifica subclade from Microbeatlas

Aquatic Samples	1748
Soil Samples	18
Animal Samples	169
Plant Samples	10
Total Samples	1945

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22596	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2724679821 annotated assembly for Dokdonia pacifica DSM 25597	scaffold	GCA_900188275	1627892.3	2724679821	1627892	72.98
66792	ASM1463668v1 assembly for Dokdonia pacifica CGMCC 1.12184	scaffold	GCA_014636685	1627892.4	8065389316	1627892	68.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22596	Dokdonia pacifica strain SW230 16S ribosomal RNA gene, partial sequence	KP862606	1484		1627892
67770	Krokinobacter sp. U1371-101202-SW230 16S ribosomal RNA gene, partial sequence	JQ082180	1420		1171541

GC content

@ref	GC-content (mol%)	Method
22596	36	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dokdonia pacifica CGMCC 1.12184
NCBI: GCA_014636685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.50	no
125439	motility	BacteriaNetⓘ	yes	52.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	83.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dokdonia pacifica CGMCC 1.12184
NCBI: GCA_014636685.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.98	no
125438	anaerobic	anaerobicⓘ	no	98.16	no
125438	aerobic	aerobicⓘ	yes	84.83	no
125438	spore-forming	spore-formingⓘ	no	89.82	no
125438	thermophilic	thermophileⓘ	no	96.76	yes
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dokdonia pacifica sp. nov., isolated from seawater.	Zhang Z, Gao X, Wang L, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijs.0.000252	2015

References

#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 )
#22596	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25597
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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

Dokdonia pacifica (DSM 25597, CGMCC 1.12184, JCM 18216)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900188275

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media