Name: Nocardioides marmorisolisilvae KIS18-7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130489

Type strain:

Species: Nocardioides marmorisolisilvae

Strain Designation: KIS18-7

Culture col. no.: DSM 27140, KACC 17307, NBRC 109601

Strain history: <- S. W. Kwon, KACC; KIS18-7 <- H.-Y. Weon

NCBI tax ID(s): 1542737 (species)

SI-ID 397797

DSM 27140

Section

Nocardioides marmorisolisilvae KIS18-7 is a mesophilic, Gram-positive bacterium that was isolated from forest soil.

Gram-positive
mesophilic
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	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides marmorisolisilvae**
	Full Scientific Name (LPSN)	Nocardioides marmorisolisilvae Wang et al. 2023

Synonym

Marmoricola solisilvae

Information on morphological and physiological properties Morphology

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

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21648]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)

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Culture medium growth

[Ref.: #21648]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21648]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21648]			growth	28 °C

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Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.907

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	vitamin B12 metabolism	70.59	24 of 34
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
		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.: #21648]	Sample type/isolated from	forest soil
[Ref.: #21648]	Geographic location (country and/or sea, region)	Yellow Sea, Baengnyeong Island (Ongjin region)
[Ref.: #21648]	Country	Republic of Korea
[Ref.: #21648]	Country ISO 3 Code	KOR
[Ref.: #21648]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KM199638 (>99% sequence identity) for Marmoricola from Microbeatlas

Aquatic Samples	67
Soil Samples	562
Animal Samples	120
Plant Samples	11
Total Samples	760

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

[Ref.: #21648]

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.: #21648]	Marmoricola solisilvae strain KIS18-7 16S ribosomal RNA gene, partial sequence	KM199638	1455	ENA	1542737 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Marmoricola solisilvae KIS18-7	GCA_003725775	scaffold	GenBank	1542737 tax ID	*
[Ref.: #66792]	Marmoricola solisilvae KIS18-7	2866484330	draft	JGI IMG/M	1542737 tax ID	*

[Ref.: #21648]

GC-content

68.0 mol%

fluorimetric

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: Marmoricola solisilvae KIS18-7 NCBI: GCA_003725775.1
[Ref.: #69481]	spore-forming	yes	51	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Marmoricola solisilvae KIS18-7 NCBI: GCA_003725775.1
[Ref.: #69480]	motile	no	80.751	no
[Ref.: #69480]	flagellated	no	95.938	no
[Ref.: #69480]	gram-positive	yes	84.423	no
[Ref.: #69480]	anaerobic	no	98.252	no
[Ref.: #69480]	aerobic	yes	92.766	no
[Ref.: #69480]	halophile	no	97.18	no
[Ref.: #69480]	spore-forming	no	89.318	no
[Ref.: #69480]	glucose-util	yes	85.221	no
[Ref.: #69480]	thermophile	no	97	yes
[Ref.: #69480]	glucose-ferment	no	90.456	no

Availability in culture collections External links

[Ref.: #21648]

Culture collection no.

DSM 27140, KACC 17307, NBRC 109601

[Ref.: #89014]

SI-ID 397797

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola.	Kim SJ, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.000184	2015	*
Phylogeny	Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel.	Li FN, Jiang ZK, Liu SW, Tuo L, Lee SM, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003326	2019	*
Phylogeny	Marmoricola silvestris sp. nov., a novel actinobacterium isolated from alpine forest soil.	Schumann P, Zhang DC, Franca L, Margesin R	Int J Syst Evol Microbiol	10.1099/ijsem.0.002674	2018	*
Phylogeny	Marmoricola endophyticus sp. nov., an endophytic actinobacterium isolated from Thespesia populnea.	Jiang ZK, Pan Z, Li FN, Li XJ, Liu SW, Tuo L, Jiang MG, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002297	2017	*

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 )

#21648

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27140

#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 )

#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 )

#89014

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-ID397797.1 )

* These data were automatically processed and therefore are not curated

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Marmoricola solisilvae KIS18-7

Marmoricola solisilvae KIS18-7

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