Dyadobacter koreensis (DSM 19938, KCTC 12537, NBRC 101116)

Name: Dyadobacter koreensis (DSM 19938, KCTC 12537, NBRC 101116)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3779

Type strain

Strain Designation WPCB 159

Culture col. no. DSM 19938 KCTC 12537 NBRC 101116 WPCB 159

NCBI tax ID(s) 408657

Special Collections DSMZ KCTC Literature strains

Links

Dyadobacter koreensis WPCB 159 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from fresh water.

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

Name and taxonomic classification

SI-ID 406258

KCTC 12537,NBRC 101116,DSM 19938

@ref 20215

Last LPSN update 2025-12-16 09:47:39

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Dyadobacter

Species Dyadobacter koreensis

Full scientific name Dyadobacter koreensis Baik et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape
32063	negative	rod-shaped
67771		rod-shaped
67771	negative
125438	negative
125439	negative

Pigmentation

32063

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15419	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15419	positive	growth	25	mesophilic
32063	positive	growth	04-30
32063	positive	optimum	25	mesophilic
67771	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
32063	positive	optimum	7
32063	positive	growth	05-11

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32063	aerobe
67771	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		93.4

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32063	22599 ChEBI	arabinose	+	carbon source
32063	28757 ChEBI	fructose	+	carbon source
32063	28260 ChEBI	galactose	+	carbon source
32063	17234 ChEBI	glucose	+	carbon source
32063	37684 ChEBI	mannose	+	carbon source
32063	28053 ChEBI	melibiose	+	carbon source
32063	17814 ChEBI	salicin	+	carbon source
32063	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32063	catalase	+	1.11.1.6
32063	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	starch degradation	100	10 of 10
66794	kanosamine biosynthesis II	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	quinate degradation	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cellulose degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	purine metabolism	81.91	77 of 94
66794	glycogen metabolism	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	lipid metabolism	77.42	24 of 31
66794	leucine metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	coenzyme A metabolism	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	glutamate and glutamine metabolism	75	21 of 28
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	pyrimidine metabolism	73.33	33 of 45
66794	metabolism of disaccharids	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	myo-inositol biosynthesis	70	7 of 10
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	degradation of pentoses	67.86	19 of 28
66794	IAA biosynthesis	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	acetoin degradation	66.67	2 of 3
66794	lipid A biosynthesis	66.67	6 of 9
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	methionine metabolism	65.38	17 of 26
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	degradation of hexoses	61.11	11 of 18
66794	degradation of sugar acids	60	15 of 25
66794	arachidonate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	tryptophan metabolism	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	non-pathway related	55.26	21 of 38
66794	carotenoid biosynthesis	54.55	12 of 22
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	biotin biosynthesis	50	2 of 4
66794	ascorbate metabolism	50	11 of 22
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	coenzyme M biosynthesis	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	urea cycle	46.15	6 of 13
66794	phenol degradation	45	9 of 20
66794	nitrate assimilation	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	tyrosine metabolism	42.86	6 of 14
66794	oxidative phosphorylation	41.76	38 of 91
66794	vitamin B12 metabolism	41.18	14 of 34
66794	3-chlorocatechol degradation	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	sulfoquinovose degradation	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	chlorophyll metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15419	fresh water	Woopo wetland	Republic of Korea	KOR	Asia
67771	From freshwater	Woopo wetland	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB681383 (>99% sequence identity) for Dyadobacter koreensis subclade from Microbeatlas

Aquatic Samples	3
Soil Samples	4
Animal Samples	3
Plant Samples	3
Total Samples	13

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15419	1	Risk group (German 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	IMG-taxon 2622736476 annotated assembly for Dyadobacter koreensis DSM 19938	scaffold	GCA_900108855	408657.4	2622736476	408657	70.38

Genome browser: GCA_900108855

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Dyadobacter koreensis gene for 16S rRNA, partial sequence, strain: NBRC 101116	AB681383	1433		408657
15419	Dyadobacter koreensis strain KCTC 12537 16S ribosomal RNA gene, partial sequence	EF017660	1412		408657

GC content

@ref	GC-content (mol%)
32063	44
67771	44.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dyadobacter koreensis DSM 19938
NCBI: GCA_900108855

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.40	no
125439	motility	BacteriaNetⓘ	no	64.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dyadobacter koreensis DSM 19938
NCBI: GCA_900108855.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.87	yes
125438	anaerobic	anaerobicⓘ	no	98.75	yes
125438	aerobic	aerobicⓘ	yes	88.52	yes
125438	spore-forming	spore-formingⓘ	no	85.08	no
125438	thermophilic	thermophileⓘ	no	97.85	yes
125438	flagellated	motile2+ⓘ	no	86.25	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil.	Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin R	Int J Syst Evol Microbiol	10.1099/ijs.0.017236-0	2009
Phylogeny	Dyadobacter koreensis sp. nov., isolated from fresh water.	Baik KS, Kim MS, Kim EM, Kim HR, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.64902-0	2007
Phylogeny	Dyadobacter diqingensis sp. nov., isolated from Baima snow mountain of Diqing Tibetan Autonomous Prefecture in Yunnan province, south-west China.	Ran L, Peng M, Wang WQ, Feng YZ, Wang J, Wang Y, Li CY, Liu XX, Chunyu WX, Tang SK	Arch Microbiol	10.1007/s00203-022-03192-2	2022

References

#15419	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19938
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#32063	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 #28310 (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) .
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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

Dyadobacter koreensis (DSM 19938, KCTC 12537, NBRC 101116)

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

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900108855

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media