Name: Marinimicrobium agarilyticum M18
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 456

Type strain:

Species: Marinimicrobium agarilyticum

Strain Designation: M18, 27.101

Culture col. no.: DSM 16975, KCTC 12357, CIP 109192

Strain history: CIP <- 2006, KCTC <- C.J. Kim, KRIBB <- J.M. Lim, KRIBB

NCBI tax ID(s): 1122194 (strain), 306546 (species)

SI-ID 232847

KCTC 12357, DSM 16975, CIP 109192

Special Collections

Section

When using BacDive for research please cite our paper

Marinimicrobium agarilyticum M18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Cellvibrionales*
	Family	*Cellvibrionaceae*
	Genus	*Marinimicrobium*
	Species	**Marinimicrobium agarilyticum**
	Full Scientific Name (LPSN)	Marinimicrobium agarilyticum Lim et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31698]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #116151]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %96.7
[Ref.: #125438]	Gram stain	negative Confidence in %98.75

[Ref.: #31698]	Cell length	0.9-1.5 µm

[Ref.: #31698]	Cell width	0.5-0.8 µm

[Ref.: #31698]	Cell shape	rod-shaped
[Ref.: #116151]	Cell shape	rod-shaped

[Ref.: #31698]	Motility	yes
[Ref.: #116151]	Motility	yes

[Ref.: #31698]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6597]

Culture medium

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

[Ref.: #6597]

Culture medium growth

[Ref.: #6597]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6597]

Culture medium composition

expand / minimize

[Ref.: #116151]

Culture medium

CIP Medium 13

[Ref.: #116151]

Culture medium growth

[Ref.: #116151]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6597]	growth	28 °C
[Ref.: #31698]	growth	12-40 °C
[Ref.: #31698]	optimum	35 °C
[Ref.: #67771]	growth	35 °C

	pH	Kind of pH		pH
[Ref.: #31698]			optimum	07-08
[Ref.: #31698]			growth	6-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31698]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #116151]	Oxygen tolerance	obligate aerobe

[Ref.: #31698]	Ability of spore formation	no
[Ref.: #116151]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.6
[Ref.: #125438]	Ability of spore formation	no Confidence in %92.965

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31698]		NaCl		growth	0-13	%
[Ref.: #31698]		NaCl		optimum	0-1	%

[Ref.: #31698]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31698]	arabinose ChEBI	+	carbon source
[Ref.: #31698]	esculin ChEBI	+	hydrolysis
[Ref.: #31698]	fructose ChEBI	+	carbon source
[Ref.: #31698]	glucose ChEBI	+	carbon source
[Ref.: #31698]	lactose ChEBI	+	carbon source
[Ref.: #31698]	maltose ChEBI	+	carbon source
[Ref.: #31698]	mannose ChEBI	+	carbon source
[Ref.: #31698]	melibiose ChEBI	+	carbon source
[Ref.: #116151]	nitrate ChEBI	+	reduction
[Ref.: #116151]	nitrite ChEBI	+	reduction
[Ref.: #31698]	ribose ChEBI	+	carbon source
[Ref.: #31698]	sucrose ChEBI	+	carbon source
[Ref.: #31698]	trehalose ChEBI	+	carbon source
[Ref.: #31698]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #116151]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #31698]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[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
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116151]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31698]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[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
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #116151]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116151]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #116151]	11709	-	+	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #6597]	Sample type/isolated from	tidal flat sediment
[Ref.: #6597]	Geographic location (country and/or sea, region)	Jeonnam province in the South Sea of Korea (the Korea Strait)
[Ref.: #6597]	Country	Republic of Korea
[Ref.: #6597]	Country ISO 3 Code	KOR
[Ref.: #6597]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #116151]	Sample type/isolated from	Environment, Tidal flat sediment
[Ref.: #116151]	Geographic location (country and/or sea, region)	Jeonnam province in the South Sea of Korea (the Korea Strait)
[Ref.: #116151]	Country	Republic of Korea
[Ref.: #116151]	Country ISO 3 Code	KOR
[Ref.: #116151]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY839870 (>99% sequence identity) for Marinimicrobium agarilyticum from Microbeatlas

Aquatic Samples	85
Soil Samples	13
Animal Samples	15
Plant Samples	5
Total Samples	118

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

[Ref.: #6597]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116151]	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.: #6597]	Marinimicrobium agarilyticum strain M18 16S ribosomal RNA gene, partial sequence	AY839870	1455	GenBank ENA	306546 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Marinimicrobium agarilyticum DSM 16975	GCA_000423345	scaffold	GenBank ENA	1122194 tax ID	*
[Ref.: #66792]	Marinimicrobium agarilyticum DSM 16975	1122194.5	wgs	PATRIC	1122194 tax ID	*
[Ref.: #66792]	Marinimicrobium agarilyticum DSM 16975	2524023067	draft	JGI IMG/M	1122194 tax ID	*

[Ref.: #6597]	GC-content	58.0 mol%
[Ref.: #31698]	GC-content	58 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marinimicrobium agarilyticum DSM 16975 DSM 16975 NCBI: GCA_000423345.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.75	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	92.778	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	77.19	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	92.965	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.337	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	75.977	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Marinimicrobium agarilyticum DSM 16975 NCBI: GCA_000423345
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	72
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	96.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	66.9
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.6

Availability in culture collections External links

[Ref.: #6597]

Culture collection no.

DSM 16975, KCTC 12357, CIP 109192

[Ref.: #70135]

SI-ID 232847

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Marinimicrobium locisalis sp. nov., isolated from a marine solar saltern, and emended description of the genus Marinimicrobium.	Yoon JH, Kang SJ, Jung YT, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.008458-0	2009	*
Phylogeny	Marinimicrobium koreense gen. nov., sp. nov. and Marinimicrobium agarilyticum sp. nov., novel moderately halotolerant bacteria isolated from tidal flat sediment in Korea.	Lim JM, Jeon CO, Lee JC, Song SM, Kim KY, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64075-0	2006	*

References

#6597

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16975

#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 )

#31698

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 #27975 (see below)

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68382

Automatically annotated from API zym .

#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 .

#70135

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-ID232847.1 )

#116151 Collection of Institut Pasteur ; Curators of the CIP; CIP 109192

#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 .

#27975

IJSEM 653 2006 ( DOI 10.1099/ijs.0.64075-0 , PubMed 16514044 )

* These data were automatically processed and therefore are not curated

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Marinimicrobium agarilyticum DSM 16975 DSM 16975

Marinimicrobium agarilyticum DSM 16975

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