Name: Kocuria marina DSM 16420
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7657

Type strain:

Species: Kocuria marina

Culture col. no.: DSM 16420, KCTC 9943, KMM 3905, CCUG 51442, JCM 13363, NBRC 110801

Strain history: <- SB Kim <- OI Nedashkovskaya, KMM, Russia

NCBI tax ID(s): 223184 (species)

SI-ID 99594

KCTC 9943, DSM 16420, JCM 13363, CCUG 51442

Special Collections

Other strains from Kocuria marina

Section

Kocuria marina DSM 16420 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from marine sediment.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Micrococcaceae*
	Genus	*Kocuria*
	Species	**Kocuria marina**
	Full Scientific Name (LPSN)	Kocuria marina Kim et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #29957]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %90.941

[Ref.: #29957]	Cell shape	coccus-shaped

[Ref.: #29957]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.5

[Ref.: #69279]	Colony color	Colourless
[Ref.: #69279]	Cultivation medium used	ISP 4

[Ref.: #69279]	Colony color	Honey yellow (1005)
[Ref.: #69279]	Cultivation medium used	ISP 2

[Ref.: #69279]	Colony color	Lemon yellow (1012)
[Ref.: #69279]	Cultivation medium used	ISP 3

[Ref.: #69279]	Colony color	Lemon yellow (1012)
[Ref.: #69279]	Cultivation medium used	suter without tyrosine

[Ref.: #69279]	Colony color	Sand yellow (1002)
[Ref.: #69279]	Cultivation medium used	suter with tyrosine

[Ref.: #69279]	Colony color	Sand yellow (1002), zinc yellow (1018)
[Ref.: #69279]	Cultivation medium used	ISP 7

[Ref.: #69279]	Colony color	Sufur yellow (1016)
[Ref.: #69279]	Cultivation medium used	ISP 6

[Ref.: #69279]	Colony color	Sulfur yellow (1016)
[Ref.: #69279]	Cultivation medium used	ISP 5

[Ref.: #69279]	Pigment production	yes
[Ref.: #69279]	Pigment name	Melanin
[Ref.: #69279]	Pigment production	yes
[Ref.: #69279]	Pigmentation color	Maize yellow (1006), olive brown (8008), sand yellow (1002)
[Ref.: #69279]	Pigment name	soluble pigment

[Ref.: #69279]	Multicellular complex forming ability	no
[Ref.: #69279]	Multicellular complex name	Aerial mycelium
[Ref.: #69279]	Medium Name (multicellularity)	ISP 2

[Ref.: #69279]	Multicellular complex forming ability	no
[Ref.: #69279]	Multicellular complex name	Aerial mycelium
[Ref.: #69279]	Medium Name (multicellularity)	ISP 3

[Ref.: #69279]	Multicellular complex forming ability	no
[Ref.: #69279]	Multicellular complex name	Aerial mycelium
[Ref.: #69279]	Medium Name (multicellularity)	ISP 4

[Ref.: #69279]	Multicellular complex forming ability	no
[Ref.: #69279]	Multicellular complex name	Aerial mycelium
[Ref.: #69279]	Medium Name (multicellularity)	ISP 5

[Ref.: #69279]	Multicellular complex forming ability	no
[Ref.: #69279]	Multicellular complex name	Aerial mycelium
[Ref.: #69279]	Medium Name (multicellularity)	ISP 6

[Ref.: #69279]	Multicellular complex forming ability	no
[Ref.: #69279]	Multicellular complex name	Aerial mycelium
[Ref.: #69279]	Medium Name (multicellularity)	ISP 7

[Ref.: #69279]	Multicellular complex forming ability	no
[Ref.: #69279]	Multicellular complex name	Aerial mycelium
[Ref.: #69279]	Medium Name (multicellularity)	suter with tyrosine

[Ref.: #69279]	Multicellular complex forming ability	no
[Ref.: #69279]	Multicellular complex name	Aerial mycelium
[Ref.: #69279]	Medium Name (multicellularity)	suter without tyrosine

Multimedia content

[Ref.: #69279]

Caption:

Plates (514, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69279]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

[Ref.: #69279]

Caption:

Plates (514, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69279]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

[Ref.: #69279]

Caption:

(ISP6, ISP7, SSM+T, SSM-T)

[Ref.: #69279]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

[Ref.: #69279]

Caption:

(ISP6, ISP7, SSM+T, SSM-T)

[Ref.: #69279]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6441]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #6441]

Culture medium growth

[Ref.: #6441]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6441]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6441]	growth	28 °C
[Ref.: #29957]	growth	04-43 °C
[Ref.: #29957]	optimum	23.5 °C
[Ref.: #59189]	growth	30-37 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29957]	Oxygen tolerance	aerobe
[Ref.: #59189]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29957]

Ability of spore formation

	Salt		Salt conc.
[Ref.: #29957]	NaCl	growth	0-15	%
[Ref.: #29957]	NaCl	optimum	7.5	%
[Ref.: #69279]	NaCl	growth	0-7.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69279]	arabinose ChEBI	-	growth
[Ref.: #69279]	cellulose ChEBI	-	growth
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #69279]	fructose ChEBI	+	growth
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #29957]	glucose ChEBI	+	carbon source
[Ref.: #69279]	glucose ChEBI	+	growth
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #69279]	inositol ChEBI	+	growth
[Ref.: #29957]	lactose ChEBI	+	carbon source
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29957]	mannose ChEBI	+	carbon source
[Ref.: #69279]	mannose ChEBI	+/-	growth
[Ref.: #29957]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #69279]	raffinose ChEBI	-	growth
[Ref.: #69279]	rhamnose ChEBI	+/-	growth
[Ref.: #29957]	sucrose ChEBI	+	carbon source
[Ref.: #69279]	sucrose ChEBI	+	growth
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #69279]	xylose ChEBI	-	growth
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym, API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #29957]	catalase	+	1.11.1.6
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #29957]	gelatinase	+
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #68379]	pyrazinamidase	+	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #29957]	urease	+	3.5.1.5
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #69279]	3773	+	+	+	+	-	+	+	-	-	+	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #69279]	5957	not determinedn.d.	+	+/-	+	+	+	+	+/-	-	-	-	+/-	-	+	-	+	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6441]	Sample type/isolated from	marine sediment
[Ref.: #6441]	Geographic location (country and/or sea, region)	East Sea, Gulf of Peter the Great, Troitsa Bay
[Ref.: #6441]	Country	Russia
[Ref.: #6441]	Country ISO 3 Code	RUS
[Ref.: #6441]	Continent	Europe

[Ref.: #59189]	Sample type/isolated from	Marine sediment

[Ref.: #67770]	Sample type/isolated from	Marine sediment from the Troitsa Bay of the Gulf of Peter the Great
[Ref.: #67770]	Geographic location (country and/or sea, region)	East Siberian Sea

[Ref.: #67771]	Sample type/isolated from	From marine sediment
[Ref.: #67771]	Country	Russia
[Ref.: #67771]	Country ISO 3 Code	RUS
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY211385 (>99% sequence identity) for Kocuria from Microbeatlas

Aquatic Samples	184
Soil Samples	229
Animal Samples	4324
Plant Samples	45
Total Samples	4782

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6441]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6441]	Kocuria marina 16S ribosomal RNA gene, partial sequence	AY211385	1440	GenBank ENA	223184 tax ID
[Ref.: #20218]	Kocuria marina partial 16S rRNA gene, isolate OS-69.b	AM237369	1209	GenBank ENA	223184 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Kocuria marina strain KCTC 9943	223184.20	wgs	PATRIC	223184 tax ID	*

[Ref.: #6441]	GC-content	60 mol%
[Ref.: #67771]	GC-content	60.0 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Kocuria marina strain KCTC 9943 PATRIC: 223184.20
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.941	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.958	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	77.696	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	83.038	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	91.5	no

Availability in culture collections External links

[Ref.: #6441]

Culture collection no.

DSM 16420, KCTC 9943, KMM 3905, CCUG 51442, JCM 13363, NBRC 110801

[Ref.: #77101]

SI-ID 99594

Literature:

Only first 10 entries are displayed. Click here to see all.

	Title	Authors	Journal	DOI	Year
Phylogeny	Kocuria tytonis sp. nov., isolated from the uropygial gland of an American barn owl (Tyto furcata).	Braun MS, Wang E, Zimmermann S, Wagner H, Wink M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003170	2019	*
Phylogeny	Isolation, purification, structural elucidation and antimicrobial activities of kocumarin, a novel antibiotic isolated from actinobacterium Kocuria marina CMG S2 associated with the brown seaweed Pelvetia canaliculata.	Uzair B, Menaa F, Khan BA, Mohammad FV, Ahmad VU, Djeribi R, Menaa B	Microbiol Res	10.1016/j.micres.2017.10.007	2017	*
Phylogeny	Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove.	Hamada M, Shibata C, Tamura T, Nurkanto A, Ratnakomala S, Lisdiyanti P, Suzuki KI	Int J Syst Evol Microbiol	10.1099/ijsem.0.001186	2016	*
Phylogeny	Kocuria indica sp. nov., isolated from a sediment sample.	Dastager SG, Tang SK, Srinivasan K, Lee JC, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.052548-0	2013	*
Phylogeny	Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment.	Kim SB, Nedashkovskaya OI, Mikhailov VV, Han SK, Kim KO, Rhee MS, Bae KS	Int J Syst Evol Microbiol	10.1099/ijs.0.02742-0	2004	*
	Headspace/GC-MS Analysis and Investigation of Antibacterial, Antioxidant and Cytotoxic Activity of Essential Oils and Hydrolates from Rosmarinus officinalis L. and Lavandula angustifolia Miller.	Garzoli S, Laghezza Masci V, Franceschi S, Tiezzi A, Giacomello P, Ovidi E	Foods	10.3390/foods10081768	2021	*
	Laurus nobilis, Salvia sclarea and Salvia officinalis Essential Oils and Hydrolates: Evaluation of Liquid and Vapor Phase Chemical Composition and Biological Activities.	Ovidi E, Laghezza Masci V, Zambelli M, Tiezzi A, Vitalini S, Garzoli S	Plants (Basel)	10.3390/plants10040707	2021	*

References

#6441

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16420

#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 )

#29957

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 #26326 (see below)

#59189 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 51442

#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) .

#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 .

#69279

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#77101

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID99594.1 )

#26326

IJSEM 1617 2004 ( DOI 10.1099/ijs.0.02742-0 , PubMed 15388718 )

* These data were automatically processed and therefore are not curated

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Kocuria marina strain KCTC 9943

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