Microbacterium marinilacus (DSM 18904, CIP 109810, JCM 16546)

Name: Microbacterium marinilacus (DSM 18904, CIP 109810, JCM 16546)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7436

Type strain

Strain Designation YM11-607

Culture col. no. DSM 18904 CIP 109810 JCM 16546 MBIC 07778 YM11-607 1 more

NCBI tax ID(s) 415209

Special Collections DSMZ JCM CIP Wink compendium Literature strains

History DSMZ <- Hiroaki Kasai <- Y. Matsuo, YM11-607 JCM <-- DSM 18904 <-- H. Kasai <-- Y. Matsuo YM11-607. CIP <- 2008, DSMZ <- Hiroaki Kasai <- Y. Matsuo, Heita, Marine Biotech. Inst., Iwate, Japan: strain YM11-607

Links

Microbacterium marinilacus YM11-607 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from hydra.

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

Name and taxonomic classification

SI-ID 310974

DSM 18905,JCM 15577,DSM 18904,CIP 109810,JCM 16546,CIP 109809

@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 marinilacus

Full scientific name Microbacterium marinilacus Kageyama et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
32148	positive	0.75 µm	0.5 µm	rod-shaped
120805	positive			rod-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
19772	Beige (1001)	10-14 days	ISP 2
19772		10-14 days	ISP 3
19772	Beige	10-14 days	ISP 4
19772	Pale yellow	10-14 days	ISP 5
19772	Pale yellow	10-14 days	ISP 6
19772	Beige	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19772		ISP 2
19772		ISP 3
19772		ISP 4
19772		ISP 5
19772		ISP 6
19772		ISP 7

Pigmentation

32148

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7613	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
19772	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
19772	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:
19772	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
19772	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
19772	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
19772	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
37849	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120805	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7613	positive	growth	28
19772	positive	optimum	28
32148	positive	growth	12-38
32148	positive	optimum	25
37849	positive	growth	20
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32148	positive	optimum	9
32148	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32148	aerobe
120805	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32148	NaCl	positive	growth	<8 %
32148	NaCl	positive	optimum	4 %

Observation

67770

Observationquinones: MK-11, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
32148	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
32148	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
32148	17234 ChEBI	glucose	+	carbon source
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
32148	17306 ChEBI	maltose	+	carbon source
32148	29864 ChEBI	mannitol	+	carbon source
32148	37684 ChEBI	mannose	+	carbon source
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
32148	506227 ChEBI	N-acetylglucosamine	+	carbon source
120805	17632 ChEBI	nitrate	-	reduction
120805	16301 ChEBI	nitrite	-	reduction
32148	18257 ChEBI	ornithine	+	carbon source
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
32148	26546 ChEBI	rhamnose	+	carbon source
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
32148	27082 ChEBI	trehalose	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
32148	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120805	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
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
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-galactosidase	-	3.2.1.23	from API zym
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
32148	catalase	+	1.11.1.6
120805	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	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
120805	oxidase	+
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
120805	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne

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
19772	not determinedn.d.	+	-	-	-	-	+	+	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	-	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
19772	not determinedn.d.	-	+	-	-	-	+	-	+	-	+	-	-	-	-	+	+	+	-	+
120805	-	+	-	-	-	+	-	-	+	+	+	+	-	-	-	+	+	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
7613	-	-	-	-	+	-	-	-	-	-	+	+	+	+	-	+	-	-	+	-	-	-	+	-	-	+	-	+	+	-	-	+	+	+	+	+	+	+	-	+	+	-	-	-	-	-	-	+	-	+
120805	not determinedn.d.	+/-	-	-	+/-	-	+/-	-	-	-	+/-	+/-	+/-	+/-	-	+/-	-	-	+/-	-	-	-	-	-	-	+/-	-	+/-	+/-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	+/-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Cnidaria (Corals)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7613	hydra	Sano Marine Lake	Palau	PLW	Australia and Oceania
67770	Unidentified hydroid collected from the Sano Marine Lake		Palau	PLW	Australia and Oceania
120805	Environment, Hydra, marine lake		Palau	PLW	Australia and Oceania

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7613	1	Risk group (German classification) According to TRBA 466
19772	1	Risk group (German classification) According to TRBA 466
120805	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	ASM1975376v1 assembly for Microbacterium marinilacus YM11-607	scaffold	GCA_019753765	415209.3	8069628081	415209	69.33
124043	ASM3953656v1 assembly for Microbacterium marinilacus JCM 16546	scaffold	GCA_039536565			415209	66.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7613	Microbacterium marinilacus gene for 16S rRNA, partial sequence	AB286020	1465		415209

GC content

@ref	GC-content (mol%)	Method
7613	71.6
67770	71.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microbacterium marinilacus YM11-607
NCBI: GCA_019753765.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	84.34	yes
125438	anaerobic	anaerobicⓘ	no	95.25	yes
125438	aerobic	aerobicⓘ	yes	83.71	yes
125438	spore-forming	spore-formingⓘ	no	73.97	no
125438	thermophilic	thermophileⓘ	no	95.47	yes
125438	flagellated	motile2+ⓘ	no	76.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbacterium stercoris sp. nov., an indole acetic acid-producing actinobacterium isolated from cow dung.	Zhang L, Jiao Y, Ling L, Wang H, Song W, Zhao T, Guo L, Xiang W, Zhao J, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.005099	2021
Phylogeny	Microbacterium album sp. nov. and Microbacterium deserti sp. nov., two halotolerant actinobacteria isolated from desert soil.	Yang ZW, Salam N, Mohany M, Chinnathambi A, Alharbi SA, Xiao M, Hozzein WN, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002485	2017
Phylogeny	Microbacterium lacusdiani sp. nov., a phosphate-solubilizing novel actinobacterium isolated from mucilaginous sheath of Microcystis.	Zhang BH, Salam N, Cheng J, Li HQ, Yang JY, Zha DM, Guo QG, Li WJ	J Antibiot (Tokyo)	10.1038/ja.2016.125	2016
Phylogeny	Microbacterium sediminicola sp. nov. and Microbacterium marinilacus sp. nov., isolated from marine environments.	Kageyama A, Takahashi Y, Matsuo Y, Kasai H, Shizuri Y, Omura S	Int J Syst Evol Microbiol	10.1099/ijs.0.65038-0	2007

References

#7613	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18904
#19772	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 )
#28391	IJSEM 2355 2007 ( DOI 10.1099/ijs.0.65038-0 , PubMed 17911310 )
#32148	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 #28391
#37849	; 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;
#68371	Automatically annotated from API 50CH acid .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#120805	Collection of Institut Pasteur ; Curators of the CIP; CIP 109810
#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 )
#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

Microbacterium marinilacus (DSM 18904, CIP 109810, JCM 16546)

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

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_019753765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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