Microbacterium aquimaris (DSM 19713, CIP 110688, KCTC 19124)

Name: Microbacterium aquimaris (DSM 19713, CIP 110688, KCTC 19124)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7439

Type strain

Strain Designation JS54-2

Culture col. no. DSM 19713 CIP 110688 KCTC 19124 JS54-2 JCM 15625

NCBI tax ID(s) 459816

Special Collections DSMZ JCM KCTC CIP Wink compendium Literature strains

History DSMZ <- Jung-Sook Lee; JS54-2 JCM <-- KCTC 19124 <-- J.-S. Lee JS54-2. KCTC <- JS Lee, KRIBB CIP <- 2013, DSMZ <- J.S. Lee, Korea: strain JS54-2

Links

Microbacterium aquimaris JS54-2 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from seawater.

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

Name and taxonomic classification

SI-ID 399256

KCTC 19124,JCM 15625,DSM 19713,CIP 110688

@ref 20215

Last LPSN update 2026-05-29 08:26:39

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Microbacterium

Species Microbacterium aquimaris

Full scientific name Microbacterium aquimaris Kim et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32605	positive	1.25 µm	0.7 µm	rod-shaped
67771	positive
116460	positive			rod-shaped
125438					95

Colony morphology

@ref	Colony color	Incubation period	Medium used
19786	Rapeseed yellow (1021)	10-14 days	ISP 3
19786		10-14 days	ISP 4
19786		10-14 days	ISP 5
19786		10-14 days	ISP 6
19786		10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19786		ISP 3
19786		ISP 4
19786		ISP 5
19786		ISP 6
19786		ISP 7

Pigmentation

32605

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8042	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
19786	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19786	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
19786	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
19786	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19786	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
33591	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
116460	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
8042	positive	growth	28
19786	positive	optimum	28
32605	positive	growth	15-37
32605	positive	optimum	27.5
33591	positive	growth	30
67770	positive	growth	28
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
32605	positive	optimum	7.5
32605	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	96.444

Spore formation

@ref	Spore formation	Confidence
32605
125439		92.551

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32605	NaCl	positive	growth	10 %

Murein

@ref	Murein short key	Type
8042	B06	B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

Observation

67770

Observationquinones: MK-11, MK-12, MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32605	58143 ChEBI	5-dehydro-D-gluconate	+	carbon source
68379	17634 ChEBI	D-glucose	+	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	+	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
32605	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

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
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
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
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
32605	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
32605	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		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
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
19786	+	+	+	-	-	+	+	+	+	-	-	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
19786	not determinedn.d.	-	+	+	-	+	+	-	-	-	-	+	+	-	-	+	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8042	seawater	Jeju	Republic of Korea	KOR	Asia
67770	Seawater	Jeju	Republic of Korea	KOR	Asia
67771	From seawater	Jeju	Republic of Korea	KOR	Asia
116460	Environment, Seawater	Jeju Island	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8042	1	Risk group (German classification) According to TRBA 466
19786	1	Risk group (German classification) According to TRBA 466
116460	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
124043	ASM3453127v1 assembly for Microbacterium aquimaris KCTC 19124	scaffold	GCA_034531275	459816.10		459816	77.08
124043	ASM3953128v1 assembly for Microbacterium aquimaris JCM 15625	contig	GCA_039531285			459816	75.95
66792	ASM1527822v1 assembly for Microbacterium aquimaris JCM 15625	scaffold	GCA_015278225	459816.3	8069657581	459816	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8042	Microbacterium aquimaris partial 16S rRNA gene, type strain JS54-2T	AM778449	1431		459816

GC content

@ref	GC-content (mol%)	Method
8042	69.3
67770	69.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3453127v1 assembly for Microbacterium aquimaris KCTC 19124
NCBI: GCA_034531275

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.44	no
125439	gram_stain	BacteriaNetⓘ	positive	86.68	no
125439	motility	BacteriaNetⓘ	no	73.62	no
125439	spore_formation	BacteriaNetⓘ	no	92.55	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microbacterium aquimaris JCM 15625
NCBI: GCA_015278225.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.13	yes
125438	anaerobic	anaerobicⓘ	no	95.61	yes
125438	aerobic	aerobicⓘ	yes	83.34	yes
125438	spore-forming	spore-formingⓘ	no	68.86	yes
125438	thermophilic	thermophileⓘ	no	94.43	yes
125438	flagellated	motile2+ⓘ	no	95.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Microbacterium xanthum sp. nov. Isolated from Seaweed, with the Reclassification of Microbacterium ihumii Yacouba et al. 2023 as a Later Heterotypic Synonym of Microbacterium tenebrionis Lee and Kim 2023.	Lee SD, Yang HL, Kim IS.	Curr Microbiol	10.1007/s00284-025-04352-5	2025
Phylogeny	Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria.	Xie F, Niu S, Lin X, Pei S, Jiang L, Tian Y, Zhang G	J Microbiol	10.1007/s12275-021-1186-5	2021
Phylogeny	Microbacterium aquimaris sp. nov., isolated from seawater.	Kim KK, Lee KC, Oh HM, Lee JS	Int J Syst Evol Microbiol	10.1099/ijs.0.65763-0	2008

References

#8042	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19713
#19786	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#28818	IJSEM 1616 2008 ( DOI 10.1099/ijs.0.65763-0 , PubMed 18599704 )
#32605	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 #28818
#33591	; 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) .
#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 .
#116460	Collection of Institut Pasteur ; Curators of the CIP; CIP 110688
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Microbacterium aquimaris (DSM 19713, CIP 110688, KCTC 19124)

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

Murein

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_034531275

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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