Name: Miniimonas arenae YM18-15
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133608

Type strain:

Species: Miniimonas arenae

Strain Designation: YM18-15

Culture col. no.: NBRC 106267, KCTC 19750, MBIC 08348, DSM 109839

Strain history: <- A Katsuta, MBIC <- Y Matsuo

NCBI tax ID(s): 676201 (species)

SI-ID 401353

DSM 109839

Section

Miniimonas arenae YM18-15 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from marine sediment.

Gram-positive
rod-shaped
mesophilic
microaerophile
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	*Beutenbergiaceae*
	Genus	*Miniimonas*
	Species	**Miniimonas arenae**
	Full Scientific Name (LPSN)	Miniimonas arenae Ue et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29727]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29727]	Cell length	2.15 µm

[Ref.: #29727]	Cell width	1.35 µm

[Ref.: #29727]	Cell shape	rod-shaped

[Ref.: #29727]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.784

[Ref.: #29727]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #64733]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #64733]

Culture medium growth

[Ref.: #64733]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64733]

Culture medium composition

expand / minimize

[Ref.: #64733]

Culture medium

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

[Ref.: #64733]

Culture medium growth

[Ref.: #64733]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64733]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #29727]	growth	25-30 °C
[Ref.: #29727]	optimum	30 °C
[Ref.: #64733]	growth	28 °C
[Ref.: #67771]	growth	25-30 °C

[Ref.: #29727]	Temperature range	mesophilic
[Ref.: #64733]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29727]			optimum	7.25
[Ref.: #29727]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29727]	Oxygen tolerance	microaerophile
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29727]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29727]		NaCl		growth	0-5	%

[Ref.: #29727]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29727]	arabinose ChEBI	+	carbon source
[Ref.: #29727]	esculin ChEBI	+	hydrolysis
[Ref.: #29727]	fructose ChEBI	+	carbon source
[Ref.: #29727]	glucose ChEBI	+	carbon source
[Ref.: #29727]	maltose ChEBI	+	carbon source
[Ref.: #29727]	mannose ChEBI	+	carbon source
[Ref.: #29727]	nitrate ChEBI	+	reduction
[Ref.: #29727]	rhamnose ChEBI	+	carbon source
[Ref.: #29727]	xylose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #29727]	acid phosphatase	+	3.1.3.2
[Ref.: #29727]	alpha-galactosidase	+	3.2.1.22
[Ref.: #29727]	catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	myo-inositol biosynthesis	100	10 of 10
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	mevalonate metabolism	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	flavin biosynthesis	33.33	5 of 15
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	ubiquinone biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #29727]	Sample type/isolated from	marine sediment

[Ref.: #64733]	Sample type/isolated from	sea sand
[Ref.: #64733]	Geographic location (country and/or sea, region)	Teguma fishing harbour, Nagasaki prefecture
[Ref.: #64733]	Country	Japan
[Ref.: #64733]	Country ISO 3 Code	JPN
[Ref.: #64733]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sea sand
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* 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 AB522642 (>99% sequence identity) for Miniimonas arenae subclade from Microbeatlas

Aquatic Samples	183
Soil Samples	41
Animal Samples	339
Plant Samples	15
Total Samples	578

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

[Ref.: #64733]

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.: #64733]	Miniimonas arenae gene for 16S rRNA, partial sequence	AB522642	1447	ENA	676201 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Miniimonas arenae KCTC 19750	GCA_006351005	contig	GenBank	676201 tax ID	*
[Ref.: #66792]	Miniimonas arenae strain KCTC 19750	676201.3	wgs	PATRIC	676201 tax ID	*
[Ref.: #66792]	Miniimonas arenae KCTC 19750	2889606800	draft	JGI IMG/M	676201 tax ID	*

[Ref.: #29727]

GC-content

74.2 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Miniimonas arenae strain KCTC 19750 PATRIC: 676201.3
[Ref.: #69481]	spore-forming	no	84	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Miniimonas arenae strain KCTC 19750 PATRIC: 676201.3
[Ref.: #69480]	gram-positive	yes	88.891	no
[Ref.: #69480]	anaerobic	no	99.031	no
[Ref.: #69480]	halophile	no	89.014	no
[Ref.: #69480]	spore-forming	no	97.168	no
[Ref.: #69480]	glucose-util	yes	87.452	no
[Ref.: #69480]	thermophile	no	97.512	yes
[Ref.: #69480]	flagellated	no	97.895	no
[Ref.: #69480]	motile	no	90.697	yes
[Ref.: #69480]	aerobic	yes	83.48	no
[Ref.: #69480]	glucose-ferment	no	76.652	no

Availability in culture collections External links

[Ref.: #64733]

Culture collection no.

NBRC 106267, KCTC 19750, MBIC 08348, DSM 109839

[Ref.: #91522]

SI-ID 401353

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Miniimonas arenae gen. nov., sp. nov., an actinobacterium isolated from sea sand.	Ue H, Matsuo Y, Kasai H, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.019596-0	2010	*

References

#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 )

#29727

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 #26110 (see below)

#64733

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 109839

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

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

#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) .

#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 )

#91522

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-ID401353.1 )

#26110

IJSEM 123 2011 ( DOI 10.1099/ijs.0.019596-0 , PubMed 20173007 )

* These data were automatically processed and therefore are not curated

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Miniimonas arenae strain KCTC 19750

Miniimonas arenae strain KCTC 19750

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