Name: Nocardioides marmoribigeumensis MSL-05
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11087

Type strain:

Species: Nocardioides marmoribigeumensis

Strain Designation: MSL-05

Culture col. no.: DSM 19426, KCTC 19287, NBRC 105376, MSL 05, JCM 15624

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 433649 (species)

SI-ID 402737

DSM 19426

Special Collections

Section

Nocardioides marmoribigeumensis MSL-05 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil sample, farming field.

coccus-shaped
Gram-positive
motile
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides marmoribigeumensis**
	Full Scientific Name (LPSN)	Nocardioides marmoribigeumensis Wang et al. 2023

Synonym

Marmoricola bigeumensis

Information on morphological and physiological properties Morphology

[Ref.: #32493]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #32493]	Cell width	0.4 µm

[Ref.: #32493]	Cell shape	coccus-shaped

[Ref.: #32493]	Motility	yes

[Ref.: #18337]	Colony color	Pale yellow
[Ref.: #18337]	Incubation period	10-14 days
[Ref.: #18337]	Cultivation medium used	ISP 2

[Ref.: #18337]	Colony color	Beige (1001)
[Ref.: #18337]	Incubation period	10-14 days
[Ref.: #18337]	Cultivation medium used	ISP 3

[Ref.: #18337]	Colony color	Beige (1001)
[Ref.: #18337]	Incubation period	10-14 days
[Ref.: #18337]	Cultivation medium used	ISP 4

[Ref.: #18337]	Colony color	Beige (1001)
[Ref.: #18337]	Incubation period	10-14 days
[Ref.: #18337]	Cultivation medium used	ISP 5

[Ref.: #18337]	Colony color	Zinc yellow (1018)
[Ref.: #18337]	Incubation period	10-14 days
[Ref.: #18337]	Cultivation medium used	ISP 6

[Ref.: #18337]	Colony color	Beige (1001)
[Ref.: #18337]	Incubation period	10-14 days
[Ref.: #18337]	Cultivation medium used	ISP 7

[Ref.: #32493]

Pigment production

yes

[Ref.: #18337]	Multicellular complex forming ability	no
[Ref.: #18337]	Medium Name (multicellularity)	ISP 2

[Ref.: #18337]	Multicellular complex forming ability	no
[Ref.: #18337]	Medium Name (multicellularity)	ISP 3

[Ref.: #18337]	Multicellular complex forming ability	no
[Ref.: #18337]	Medium Name (multicellularity)	ISP 4

[Ref.: #18337]	Multicellular complex forming ability	no
[Ref.: #18337]	Medium Name (multicellularity)	ISP 5

[Ref.: #18337]	Multicellular complex forming ability	no
[Ref.: #18337]	Medium Name (multicellularity)	ISP 6

[Ref.: #18337]	Multicellular complex forming ability	no
[Ref.: #18337]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8008]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8008]

Culture medium growth

[Ref.: #8008]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8008]

Culture medium composition

expand / minimize

[Ref.: #18337]

Culture medium

ISP 2

[Ref.: #18337]

Culture medium growth

[Ref.: #18337]

Culture medium composition

expand / minimize

[Ref.: #18337]

Culture medium

ISP 3

[Ref.: #18337]

Culture medium growth

[Ref.: #18337]

Culture medium composition

expand / minimize

[Ref.: #18337]

Culture medium

ISP 4

[Ref.: #18337]

Culture medium growth

[Ref.: #18337]

Culture medium composition

expand / minimize

[Ref.: #18337]

Culture medium

ISP 5

[Ref.: #18337]

Culture medium growth

[Ref.: #18337]

Culture medium composition

expand / minimize

[Ref.: #18337]

Culture medium

ISP 6

[Ref.: #18337]

Culture medium growth

[Ref.: #18337]

Culture medium composition

expand / minimize

[Ref.: #18337]

Culture medium

ISP 7

[Ref.: #18337]

Culture medium growth

[Ref.: #18337]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8008]	growth	28 °C
[Ref.: #18337]	optimum	28 °C
[Ref.: #32493]	growth	20-37 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32493]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32493]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32493]		NaCl		growth	7	%

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32493]	arabinose ChEBI	+	carbon source
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32493]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	+	fermentation	* from API Coryne
[Ref.: #32493]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #32493]	rhamnose ChEBI	+	carbon source
[Ref.: #32493]	ribose ChEBI	+	carbon source
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #32493]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32493]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym, API Coryne
[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, 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.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[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, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[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.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #18337]	29	+	-	-	+	-	-	+	-	-	+	-	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.: #18337]	47	not determinedn.d.	+	+	+	-	+	+	+	-	-	+	-	-	-	-	+	+	-	-	-

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

[Ref.: #8008]	Sample type/isolated from	soil sample, farming field
[Ref.: #8008]	Geographic location (country and/or sea, region)	Bigeum Island
[Ref.: #8008]	Country	Republic of Korea
[Ref.: #8008]	Country ISO 3 Code	KOR
[Ref.: #8008]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil from an agricultural area in Bigeum Island
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From farming field
[Ref.: #67771]	Geographic location (country and/or sea, region)	Bikeum island
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #18337]	Biosafety level	1	German classification
[Ref.: #8008]	Biosafety level	1	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.: #8008]	Marmoricola bigeumensis strain MSL-05 16S ribosomal RNA gene, partial sequence	EF466120	1484	GenBank ENA	433649 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Marmoricola bigeumensis DSM 19426	2923456805	draft	JGI IMG/M	433649 tax ID	*

[Ref.: #8008]	GC-content	72.9 mol%
[Ref.: #67770]	GC-content	72.9 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #8008]

Culture collection no.

DSM 19426, KCTC 19287, NBRC 105376, MSL 05, JCM 15624

[Ref.: #80336]

SI-ID 402737

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Marmoricola caldifontis sp. nov., a novel actinobacterium isolated from a hot spring.	Habib N, Khan IU, Xiao M, Li S, Saqib M, Xian WD, Butt S, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004016	2020	*
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	Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil.	Yamamura H, Ohkubo SY, Nakagawa Y, Ishida Y, Hamada M, Otoguro M, Tamura T, Hayakawa M	Int J Syst Evol Microbiol	10.1099/ijs.0.025080-0	2010	*
Phylogeny	Marmoricola korecus sp. nov.	Lee SD, Lee DW, Ko YH	Int J Syst Evol Microbiol	10.1099/ijs.0.025460-0	2010	*
Phylogeny	Marmoricola bigeumensis sp. nov., a member of the family Nocardioidaceae.	Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65576-0	2008	*

References

#8008

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19426

#18337

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 )

#32493

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 #28713 (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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#80336

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-ID402737.1 )

#28713

IJSEM 1060 2008 ( DOI 10.1099/ijs.0.65576-0 , PubMed 18450688 )

* These data were automatically processed and therefore are not curated

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