Cognatiyoonia koreensis (DSM 17925, CIP 109899, KACC 11519)

Name: Cognatiyoonia koreensis (DSM 17925, CIP 109899, KACC 11519)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13677

Type strain

Strain Designation GA2-M3

Culture col. no. DSM 17925 CIP 109899 KACC 11519 GA2-M3

NCBI tax ID(s) 364200

Special Collections DSMZ CIP

History DSMZ <- S.-W. Kwon, KACC; GA2-M3 <- B.-Y. Kim CIP <- 2008, DSMZ <- KACC <- B.Y. Kim, RDA, Suwon, Korea: strain GA2-M3

Links

Cognatiyoonia koreensis GA2-M3 is a facultative anaerobe, Gram-negative, oval-shaped bacterium that was isolated from sea sand.

Gram-negative oval-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 292323

DSM 17925,KACC 11519,CIP 109899

@ref 20215

Last LPSN update 2026-05-29 08:28:06

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Cognatiyoonia

Species Cognatiyoonia koreensis

Full scientific name Cognatiyoonia koreensis (Weon et al. 2006) Wirth and Whitman 2018

Synonyms (1)

Loktanella koreensis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125439	negative		98.214
125438	negative		97.5
120474	negative	oval-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7251	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
34592	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120474	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7251	positive	growth	25
34592	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
120474	facultative anaerobe
125439	obligate aerobe	94.37

Spore formation

@ref	Spore formation	Confidence
125439		99.735

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120474	17632 ChEBI	nitrate	+	reduction
120474	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120474	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
120474	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
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
120474	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
120474	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	Entner Doudoroff pathway	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	IAA biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	pyrimidine metabolism	86.67	39 of 45
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	purine metabolism	84.04	79 of 94
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B12 metabolism	82.35	28 of 34
66794	flavin biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	degradation of sugar acids	80	20 of 25
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	arginine metabolism	75	18 of 24
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	starch degradation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	degradation of sugar alcohols	68.75	11 of 16
66794	lipid metabolism	67.74	21 of 31
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	chlorophyll metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	non-pathway related	63.16	24 of 38
66794	oxidative phosphorylation	62.64	57 of 91
66794	lysine metabolism	61.9	26 of 42
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	degradation of pentoses	60.71	17 of 28
66794	glycogen metabolism	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	phenol degradation	60	12 of 20
66794	gallate degradation	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	vitamin B6 metabolism	54.55	6 of 11
66794	sulfopterin metabolism	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	carnitine metabolism	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	arachidonic acid metabolism	50	9 of 18
66794	phenylmercury acetate degradation	50	1 of 2
66794	acetate fermentation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	androgen and estrogen metabolism	50	8 of 16
66794	tyrosine metabolism	50	7 of 14
66794	polyamine pathway	47.83	11 of 23
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	vitamin B1 metabolism	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	ascorbate metabolism	40.91	9 of 22
66794	hydrogen production	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	ginsenoside metabolism	31.25	5 of 16
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	mevalonate metabolism	28.57	2 of 7
66794	alginate biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	daunorubicin biosynthesis	22.22	2 of 9

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
120474	-	-	+	+	-	+	-	-	-	-	-	-	-	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Sandy

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7251	sea sand	Pohang City, Homi cape	Republic of Korea	KOR	Asia
120474	Environment, Sea sand	Homi cape, Pohang city	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ344498 (>99% sequence identity) for Cognatiyoonia koreensis subclade from Microbeatlas

Aquatic Samples	49
Soil Samples	0
Animal Samples	3
Plant Samples	0
Total Samples	52

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7251	1	Risk group (German classification) According to TRBA 466
120474	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	IMG-taxon 2619619643 annotated assembly for Cognatiyoonia koreensis DSM 17925	contig	GCA_900109295	364200.6	2619619643	364200	78.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7251	Loktanella koreensis strain GA2-M3 16S ribosomal RNA gene, partial sequence	DQ344498	1395		364200

GC content

7251

GC-content (mol%)60.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2619619643 annotated assembly for Cognatiyoonia koreensis DSM 17925
NCBI: GCA_900109295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.37	no
125439	motility	BacteriaNetⓘ	yes	56.89	no
125439	gram_stain	BacteriaNetⓘ	negative	98.21	no
125439	spore_formation	BacteriaNetⓘ	no	99.74	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cognatiyoonia koreensis strain DSM 17925
PATRIC: 364200.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	93.35	yes
125438	spore-forming	spore-formingⓘ	no	86.11	no
125438	aerobic	aerobicⓘ	yes	86.41	no
125438	thermophilic	thermophileⓘ	no	96.11	yes
125438	flagellated	motile2+ⓘ	no	61.32	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Loktanella koreensis sp. nov., isolated from sea sand in Korea.	Weon HY, Kim BY, Yoo SH, Kim JS, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64276-0	2006

References

#7251	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17925
#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 )
#34592	; 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) .
#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 )
#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 .
#120474	Collection of Institut Pasteur ; Curators of the CIP; CIP 109899
#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 )

Content

About us

Cognatiyoonia koreensis (DSM 17925, CIP 109899, KACC 11519)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900109295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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