Kocuria atrinae (DSM 23883, JCM 15914, KCTC 19594)

Name: Kocuria atrinae (DSM 23883, JCM 15914, KCTC 19594)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7665

Type strain

Strain Designation P30

Culture col. no. DSM 23883 JCM 15914 KCTC 19594 P30

NCBI tax ID(s) 592377

Special Collections DSMZ JCM KCTC Wink compendium Literature strains

History DSMZ <- KCTC <- KRIBB JCM <-- J.-W. Bae P30. KCTC <- JW Bae, KRIBB

Links

Kocuria atrinae P30 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from jeotgal, traditional fermented seafood.

Gram-positive coccus-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397153

KCTC 19594,JCM 15914,DSM 23883

@ref 20215

Last LPSN update 2026-05-29 08:26:42

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Kocuria

Species Kocuria atrinae

Full scientific name Kocuria atrinae Park et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Motility
29503	positive	1.25 µm	coccus-shaped
67771	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
21417	Ivory (1014)	10-14 days	ISP 2
21417		10-14 days	ISP 4
21417	Golden yellow (1004)	10-14 days	ISP 5
21417	Zinc yellow (1018)	10-14 days	ISP 7
21417	Golden yellow (1004)	10-14 days	Suter with tyrosine
21417	Zinc yellow (1018)	10-14 days	Suter without tyrosine

Multicellular morphology

@ref	Forms multicellular complex	Medium name
21417		ISP 2
21417		ISP 3
21417		ISP 4
21417		ISP 5
21417		ISP 6
21417		ISP 7
21417		Suter with tyrosine
21417		Suther without tyrosine

Pigmentation

29503

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17420	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
21417	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21417	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21417	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21417	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21417	Suter with tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21417	Suter without tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)
17420	positive	growth	28
29503	positive	growth	25-37
29503	positive	optimum	33.5
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
29503	positive	optimum	8.5
29503	positive	growth	07-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29503	aerobe
67771	aerobe
125439	obligate aerobe	96.668

Spore formation

@ref	Spore formation	Confidence
125439		97.53

Halophily

@ref	Salt	Growth	Tested relation	Concentration
21417	NaCl	positive	maximum	10 %
29503	NaCl	positive	growth	0-4 %
29503	NaCl	positive	optimum	1 %

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29503	28644 ChEBI	2-oxopentanoate	+	carbon source
29503	30089 ChEBI	acetate	+	carbon source
29503	22653 ChEBI	asparagine	+	carbon source
21417	62968 ChEBI	cellulose	-
68379	17634 ChEBI	D-glucose	+	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
29503	23652 ChEBI	dextrin	+	carbon source
29503	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
21417	28757 ChEBI	fructose	-
29503	28757 ChEBI	fructose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
29503	24265 ChEBI	gluconate	+	carbon source
21417	17234 ChEBI	glucose	+/-
29503	17234 ChEBI	glucose	+	carbon source
29503	29987 ChEBI	glutamate	+	carbon source
29503	17754 ChEBI	glycerol	+	carbon source
29503	17596 ChEBI	inosine	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
29503	25115 ChEBI	malate	+	carbon source
29503	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	+	fermentation	from API Coryne
21417	37684 ChEBI	mannose	-
29503	37684 ChEBI	mannose	+	carbon source
29503	51850 ChEBI	methyl pyruvate	+	carbon source
21417	17268 ChEBI	myo-inositol	-
29503	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
29503	17272 ChEBI	propionate	+	carbon source
29503	17148 ChEBI	putrescine	+	carbon source
29503	15361 ChEBI	pyruvate	+	carbon source
21417	16634 ChEBI	raffinose	-
21417	26546 ChEBI	rhamnose	+/-
29503	33942 ChEBI	ribose	+	carbon source
29503	30911 ChEBI	sorbitol	+	carbon source
29503	30031 ChEBI	succinate	+	carbon source
21417	17992 ChEBI	sucrose	+/-
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
29503	17748 ChEBI	thymidine	+	carbon source
29503	27082 ChEBI	trehalose	+	carbon source
29503	53423 ChEBI	tween 40	+	carbon source
29503	53426 ChEBI	tween 80	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
29503	16704 ChEBI	uridine	+	carbon source
29503	17151 ChEBI	xylitol	+	carbon source
21417	18222 ChEBI	xylose	+/-

Enzymes

@ref	Value	Activity	Ec
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
29503	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
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
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
29503	urease	+	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
21417	+	-	-	+	-	-	-	-	-	-	-	not determinedn.d.	+	+/-	+/-	-	+	-	+	+/-	not determinedn.d.

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
21417	+/-	+	+/-	+	-	+	-	-	-	-	+/-	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Seafood
#Engineered	#Food production	#Fermented

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
17420	jeotgal, traditional fermented seafood	Republic of Korea	KOR	Asia
67770	Korean traditional fermented seafood	Republic of Korea	KOR	Asia
67771	From Jeotgal, fermented shellfisg	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17420	1	Risk group (German classification) According to TRBA 466
21417	L1	German classification According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953142v1 assembly for Kocuria atrinae JCM 15914	scaffold	GCA_039531425	592377	62.66

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17420	Kocuria atrinae strain P30 16S ribosomal RNA gene, partial sequence	FJ607311	1472		592377

GC content

@ref	GC-content (mol%)	Method
17420	70.2
67770	70.2	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3953142v1 assembly for Kocuria atrinae JCM 15914
NCBI: GCA_039531425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.67	no
125439	gram_stain	BacteriaNetⓘ	positive	45.04	no
125439	motility	BacteriaNetⓘ	no	77.07	no
125439	spore_formation	BacteriaNetⓘ	no	97.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood.	Park EJ, Kim MS, Roh SW, Jung MJ, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.014506-0	2009

References

#17420	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23883
#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 )
#21417	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#25903	IJSEM 914 2010 ( DOI 10.1099/ijs.0.014506-0 , PubMed 19661502 )
#29503	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 #25903
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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

Kocuria atrinae (DSM 23883, JCM 15914, KCTC 19594)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039531425

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media