Name: Microbacterium marinilacus YM11-607
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7436

Type strain:

Species: Microbacterium marinilacus

Strain Designation: YM11-607

Culture col. no.: DSM 18904, CIP 109810, JCM 16546, MBIC 07778, NBRC 104188

Strain history: CIP <- 2008, DSMZ <- Hiroaki Kasai <- Y. Matsuo, Heita, Marine Biotech. Inst., Iwate, Japan: strain YM11-607

NCBI tax ID(s): 415209 (species)

SI-ID 310974

DSM 18904, CIP 109810, JCM 16546, CIP 109809

Special Collections

Section

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

Gram-positive
rod-shaped
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	*Microbacteriaceae*
	Genus	*Microbacterium*
	Species	**Microbacterium marinilacus**
	Full Scientific Name (LPSN)	Microbacterium marinilacus Kageyama et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32148]	Gram stain	positive
[Ref.: #120805]	Gram stain	positive

[Ref.: #32148]	Cell length	0.75 µm

[Ref.: #32148]	Cell width	0.5 µm

[Ref.: #32148]	Cell shape	rod-shaped
[Ref.: #120805]	Cell shape	rod-shaped

[Ref.: #120805]	Motility	no

[Ref.: #19772]	Colony color	Beige (1001)
[Ref.: #19772]	Incubation period	10-14 days
[Ref.: #19772]	Cultivation medium used	ISP 2

[Ref.: #19772]	Colony color	Beige
[Ref.: #19772]	Incubation period	10-14 days
[Ref.: #19772]	Cultivation medium used	ISP 4

[Ref.: #19772]	Colony color	Pale yellow
[Ref.: #19772]	Incubation period	10-14 days
[Ref.: #19772]	Cultivation medium used	ISP 5

[Ref.: #19772]	Colony color	Pale yellow
[Ref.: #19772]	Incubation period	10-14 days
[Ref.: #19772]	Cultivation medium used	ISP 6

[Ref.: #19772]	Colony color	Beige
[Ref.: #19772]	Incubation period	10-14 days
[Ref.: #19772]	Cultivation medium used	ISP 7

[Ref.: #19772]	Incubation period	10-14 days
[Ref.: #19772]	Cultivation medium used	ISP 3

[Ref.: #32148]

Pigment production

yes

[Ref.: #19772]	Multicellular complex forming ability	no
[Ref.: #19772]	Medium Name (multicellularity)	ISP 2

[Ref.: #19772]	Multicellular complex forming ability	no
[Ref.: #19772]	Medium Name (multicellularity)	ISP 3

[Ref.: #19772]	Multicellular complex forming ability	no
[Ref.: #19772]	Medium Name (multicellularity)	ISP 4

[Ref.: #19772]	Multicellular complex forming ability	no
[Ref.: #19772]	Medium Name (multicellularity)	ISP 5

[Ref.: #19772]	Multicellular complex forming ability	no
[Ref.: #19772]	Medium Name (multicellularity)	ISP 6

[Ref.: #19772]	Multicellular complex forming ability	no
[Ref.: #19772]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7613]

Culture medium

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

[Ref.: #7613]

Culture medium growth

[Ref.: #7613]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7613]

Culture medium composition

expand / minimize

[Ref.: #19772]

Culture medium

ISP 2

[Ref.: #19772]

Culture medium growth

[Ref.: #19772]

Culture medium composition

expand / minimize

[Ref.: #19772]

Culture medium

ISP 3

[Ref.: #19772]

Culture medium growth

[Ref.: #19772]

Culture medium composition

expand / minimize

[Ref.: #19772]

Culture medium

ISP 4

[Ref.: #19772]

Culture medium growth

[Ref.: #19772]

Culture medium composition

expand / minimize

[Ref.: #19772]

Culture medium

ISP 5

[Ref.: #19772]

Culture medium growth

[Ref.: #19772]

Culture medium composition

expand / minimize

[Ref.: #19772]

Culture medium

ISP 6

[Ref.: #19772]

Culture medium growth

[Ref.: #19772]

Culture medium composition

expand / minimize

[Ref.: #19772]

Culture medium

ISP 7

[Ref.: #19772]

Culture medium growth

[Ref.: #19772]

Culture medium composition

expand / minimize

[Ref.: #37849]

Culture medium

Marine agar (MA)

[Ref.: #37849]

Culture medium growth

[Ref.: #37849]

Culture medium composition

expand / minimize

[Ref.: #120805]

Culture medium

CIP Medium 13

[Ref.: #120805]

Culture medium growth

[Ref.: #120805]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7613]	growth	28 °C
[Ref.: #19772]	optimum	28 °C
[Ref.: #32148]	growth	12-38 °C
[Ref.: #32148]	optimum	25 °C
[Ref.: #37849]	growth	20 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #32148]			optimum	9
[Ref.: #32148]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32148]	Oxygen tolerance	aerobe
[Ref.: #120805]	Oxygen tolerance	obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32148]		NaCl		growth	<8	%
[Ref.: #32148]		NaCl		optimum	4	%

[Ref.: #67770]

Observation

quinones: MK-11, MK-12

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #32148]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #32148]	glucose ChEBI	+	carbon source
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	maltose ChEBI	+	carbon source
[Ref.: #32148]	mannitol ChEBI	+	carbon source
[Ref.: #32148]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #120805]	nitrate ChEBI	-	reduction
[Ref.: #120805]	nitrite ChEBI	-	reduction
[Ref.: #32148]	ornithine ChEBI	+	carbon source
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	rhamnose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32148]	trehalose ChEBI	+	carbon source
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32148]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120805]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	-	3.1.3.1	* from API Coryne
[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
[Ref.: #68379]	beta-glucosidase	-	3.2.1.21	* from API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #32148]	catalase	+	1.11.1.6
[Ref.: #120805]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym, API Coryne
[Ref.: #120805]	oxidase	+
[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.: #120805]	urease	-	3.5.1.5
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #7613]	14383	-	-	-	-	+	-	-	-	-	-	+	+	+	+	-	+	-	-	+	-	-	-	+	-	-	+	-	+	+	-	-	+	+	+	+	+	+	+	-	+	+	-	-	-	-	-	-	+	-	+
[Ref.: #120805]	11659	not determinedn.d.	+/-	-	-	+/-	-	+/-	-	-	-	+/-	+/-	+/-	+/-	-	+/-	-	-	+/-	-	-	-	-	-	-	+/-	-	+/-	+/-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	+/-	-	-

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.: #19772]	311	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:

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.: #19772]	596	not determinedn.d.	-	+	-	-	-	+	-	+	-	+	-	-	-	-	+	+	+	-	+
[Ref.: #120805]	12125	-	+	-	-	-	+	-	-	+	+	+	+	-	-	-	+	+	+	-	-

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

[Ref.: #7613]	Sample type/isolated from	hydra
[Ref.: #7613]	Geographic location (country and/or sea, region)	Sano Marine Lake
[Ref.: #7613]	Country	Palau
[Ref.: #7613]	Country ISO 3 Code	PLW
[Ref.: #7613]	Continent	Australia and Oceania

[Ref.: #67770]	Sample type/isolated from	Unidentified hydroid collected from the Sano Marine Lake
[Ref.: #67770]	Country	Palau
[Ref.: #67770]	Country ISO 3 Code	PLW
[Ref.: #67770]	Continent	Australia and Oceania

[Ref.: #120805]	Sample type/isolated from	Environment, Hydra, marine lake
[Ref.: #120805]	Country	Palau
[Ref.: #120805]	Country ISO 3 Code	PLW
[Ref.: #120805]	Continent	Australia and Oceania
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Cnidaria (Corals)

What are isolation sources categories?

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

[Ref.: #7613]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19772]	Biosafety level	1	Risk group (German classification)
[Ref.: #120805]	Biosafety level	1	Risk group (French classification)

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.: #7613]	Microbacterium marinilacus gene for 16S rRNA, partial sequence	AB286020	1465	GenBank ENA	415209 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microbacterium marinilacus YM11-607	GCA_019753765	scaffold	GenBank ENA	415209 tax ID	*

[Ref.: #7613]	GC-content	71.6 mol%
[Ref.: #67770]	GC-content	71.6 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Microbacterium marinilacus YM11-607 NCBI: GCA_019753765.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	80	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microbacterium marinilacus YM11-607 NCBI: GCA_019753765.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	84.335	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.253	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	83.707	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	73.965	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.467	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	76	no

Availability in culture collections External links

[Ref.: #7613]

Culture collection no.

DSM 18904, CIP 109810, JCM 16546, MBIC 07778, NBRC 104188

[Ref.: #76884]

SI-ID 310974

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 )

#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 (see below)

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76884

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-ID310974.1 )

#120805 Collection of Institut Pasteur ; Curators of the CIP; CIP 109810

#28391

IJSEM 2355 2007 ( DOI 10.1099/ijs.0.65038-0 , PubMed 17911310 )

* These data were automatically processed and therefore are not curated

Change proposal

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