Flavobacterium dankookense (DSM 25687, JCM 17065, KACC 14968)

Name: Flavobacterium dankookense (DSM 25687, JCM 17065, KACC 14968)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5587

Type strain

Strain Designation ARSA-19, ARSA-19(T)

Culture col. no. DSM 25687 JCM 17065 KACC 14968 KCTC 23179 ARSA-19 1 more

NCBI tax ID(s) 706186

Special Collections DSMZ JCM KCTC Literature strains

History <- KACC <- T.-Y. Ahn, Dankook Univ., Cheonan, Korea; ARSA-19 T.-Y. Ahn ARSA-19. <- TY Ahn, Dankook Univ.

Links

Flavobacterium dankookense ARSA-19 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater lake.

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

Name and taxonomic classification

SI-ID 406856

KCTC 23179,JCM 17065,DSM 25687

@ref 20215

Last LPSN update 2026-02-09 11:19:00

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium dankookense

Full scientific name Flavobacterium dankookense Lee et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30293	negative	1 µm	0.5 µm	rod-shaped
67771	negative
125438					93
125438	negative				97.955
125439	negative				99.8

Pigmentation

30293

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18084	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
18084	positive	growth	25
30293	positive	growth	04-37
30293	positive	optimum	25
67770	positive	growth	25
67771	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
30293	positive	optimum	7.75
30293	positive	growth	6.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30293	aerobe
67771	aerobe
125439	obligate aerobe	97.4

Spore formation

@ref	Spore formation	Confidence
125438		92.803
125439		99.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30293	NaCl	positive	growth	0-1 %

Observation

67770

Observationquinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30293	27689 ChEBI	decanoate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30293	acid phosphatase	+	3.1.3.2
30293	alkaline phosphatase	+	3.1.3.1
30293	catalase	+	1.11.1.6
30293	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	purine metabolism	67.02	63 of 94
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	flavin biosynthesis	66.67	10 of 15
66794	tryptophan metabolism	65.79	25 of 38
66794	histidine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	glycogen metabolism	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	glutathione metabolism	57.14	8 of 14
66794	tyrosine metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	d-xylose degradation	54.55	6 of 11
66794	methionine metabolism	53.85	14 of 26
66794	alanine metabolism	51.72	15 of 29
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	heme metabolism	50	7 of 14
66794	glutamate and glutamine metabolism	50	14 of 28
66794	quinate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	kanosamine biosynthesis II	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	Entner Doudoroff pathway	50	5 of 10
66794	isoleucine metabolism	50	4 of 8
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	proline metabolism	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	pentose phosphate pathway	45.45	5 of 11
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	myo-inositol biosynthesis	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	oxidative phosphorylation	39.56	36 of 91
66794	vitamin B1 metabolism	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	arginine metabolism	37.5	9 of 24
66794	carotenoid biosynthesis	36.36	8 of 22
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	formaldehyde oxidation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	octane oxidation	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of pentoses	32.14	9 of 28
66794	polyamine pathway	30.43	7 of 23
66794	metabolism of disaccharids	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	phenol degradation	25	5 of 20
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	urea cycle	23.08	3 of 13
66794	sulfate reduction	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	valine metabolism	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
18084	freshwater lake	Cheonan city, Cheon-ho reservoir at Dankook University (36° 49' N 127° 10' E)	Republic of Korea	KOR	Asia	36.8167	127.167 36.8167/127.167
67770	Freshwater reservoir in Cheonan		Republic of Korea	KOR	Asia
67771	From freshwater	Cheonan	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18084	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
67770	ASM436266v1 assembly for Flavobacterium dankookense DSM 25687	scaffold	GCA_004362665	706186.4	2695421041	706186	69.31

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18084	Flavobacterium dankookense strain ARSA-19 16S ribosomal RNA gene, partial sequence	GU295970	1406		706186

GC content

@ref	GC-content (mol%)	Method
18084	33.3	high performance liquid chromatography (HPLC)
30293	33.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium dankookense DSM 25687
NCBI: GCA_004362665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	no	66.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium dankookense strain DSM 25687
PATRIC: 706186.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.96	yes
125438	anaerobic	anaerobicⓘ	no	97.85	yes
125438	spore-forming	spore-formingⓘ	no	92.80	no
125438	aerobic	aerobicⓘ	yes	85.99	yes
125438	thermophilic	thermophileⓘ	no	97.68	yes
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium phycosphaerae sp. nov. isolated from the phycosphere of Microcystis aeruginosa.	Kim M, Lee BH, Lee KE, Park W	Int J Syst Evol Microbiol	10.1099/ijsem.0.004735	2021
Phylogeny	Flavobacterium silvisoli sp. nov., isolated from forest soil.	Chaudhary DK, Dahal RH, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003551	2019
Phylogeny	Flavobacterium paronense sp. nov., isolated from freshwater of an artificial vegetated island.	Joung Y, Kang H, Kim H, Kim TS, Han JH, Kim SB, Ahn TS, Joh K	Int J Syst Evol Microbiol	10.1099/ijsem.0.000727	2015
Phylogeny	Flavobacterium dankookense sp. nov., isolated from a freshwater reservoir, and emended descriptions of Flavobacterium cheonanense, F. chungnamense, F. koreense and F. aquatile.	Lee S, Weon HY, Han K, Ahn TY	Int J Syst Evol Microbiol	10.1099/ijs.0.032698-0	2011

References

#18084	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25687
#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 )
#26634	IJSEM 2378 2012 ( DOI 10.1099/ijs.0.032698-0 , PubMed 22140162 )
#30293	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 #26634
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Flavobacterium dankookense (DSM 25687, JCM 17065, KACC 14968)

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

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004362665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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