Name: Nocardioides bigeumensis DSM 19320
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11141

Type strain:

Species: Nocardioides bigeumensis

Culture col. no.: DSM 19320, KCTC 19290, MSL 19, JCM 16021

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 433657 (species)

SI-ID 407824

DSM 19320

Section

Nocardioides bigeumensis DSM 19320 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, farming field.

Gram-positive
motile
ovoid-shaped
aerobe
mesophilic
16S sequence
Bacteria

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 bigeumensis**
	Full Scientific Name (LPSN)	Nocardioides bigeumensis Dastager et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32484]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #32484]	Cell length	0.8-4 µm

[Ref.: #32484]	Cell width	0.3-0.8 µm

[Ref.: #32484]	Cell shape	ovoid-shaped

[Ref.: #32484]	Motility	yes

[Ref.: #19780]	Colony color	Beige (1001)
[Ref.: #19780]	Incubation period	10-14 days
[Ref.: #19780]	Cultivation medium used	ISP 2

[Ref.: #19780]	Colony color	Beige (1001)
[Ref.: #19780]	Incubation period	10-14 days
[Ref.: #19780]	Cultivation medium used	ISP 3

[Ref.: #19780]	Colony color	Beige (1001)
[Ref.: #19780]	Incubation period	10-14 days
[Ref.: #19780]	Cultivation medium used	ISP 4

[Ref.: #19780]	Colony color	Beige (1001)
[Ref.: #19780]	Incubation period	10-14 days
[Ref.: #19780]	Cultivation medium used	ISP 5

[Ref.: #19780]	Colony color	Beige (1001)
[Ref.: #19780]	Incubation period	10-14 days
[Ref.: #19780]	Cultivation medium used	ISP 6

[Ref.: #19780]	Colony color	Beige (1001)
[Ref.: #19780]	Incubation period	10-14 days
[Ref.: #19780]	Cultivation medium used	ISP 7

[Ref.: #32484]

Pigment production

yes

[Ref.: #19780]	Multicellular complex forming ability	no
[Ref.: #19780]	Medium Name (multicellularity)	ISP 2

[Ref.: #19780]	Multicellular complex forming ability	no
[Ref.: #19780]	Medium Name (multicellularity)	ISP 3

[Ref.: #19780]	Multicellular complex forming ability	no
[Ref.: #19780]	Medium Name (multicellularity)	ISP 4

[Ref.: #19780]	Multicellular complex forming ability	no
[Ref.: #19780]	Medium Name (multicellularity)	ISP 5

[Ref.: #19780]	Multicellular complex forming ability	no
[Ref.: #19780]	Medium Name (multicellularity)	ISP 6

[Ref.: #19780]	Multicellular complex forming ability	no
[Ref.: #19780]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8035]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8035]

Culture medium growth

[Ref.: #8035]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8035]

Culture medium composition

expand / minimize

[Ref.: #19780]

Culture medium

ISP 2

[Ref.: #19780]

Culture medium growth

[Ref.: #19780]

Culture medium composition

expand / minimize

[Ref.: #19780]

Culture medium

ISP 3

[Ref.: #19780]

Culture medium growth

[Ref.: #19780]

Culture medium composition

expand / minimize

[Ref.: #19780]

Culture medium

ISP 4

[Ref.: #19780]

Culture medium growth

[Ref.: #19780]

Culture medium composition

expand / minimize

[Ref.: #19780]

Culture medium

ISP 5

[Ref.: #19780]

Culture medium growth

[Ref.: #19780]

Culture medium composition

expand / minimize

[Ref.: #19780]

Culture medium

ISP 6

[Ref.: #19780]

Culture medium growth

[Ref.: #19780]

Culture medium composition

expand / minimize

[Ref.: #19780]

Culture medium

ISP 7

[Ref.: #19780]

Culture medium growth

[Ref.: #19780]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8035]	growth	28 °C
[Ref.: #19780]	optimum	28 °C
[Ref.: #32484]	growth	20-35 °C
[Ref.: #32484]	optimum	28 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #8035]	Temperature range	mesophilic
[Ref.: #19780]	Temperature range	mesophilic
[Ref.: #32484]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32484]			optimum	7.5-9
[Ref.: #32484]			growth	7.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32484]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32484]

Ability of spore formation

[Ref.: #32484]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[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.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #32484]	lactose ChEBI	+	carbon source
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32484]	mannose ChEBI	+	carbon source
[Ref.: #32484]	melibiose ChEBI	+	carbon source
[Ref.: #68379]	nitrate ChEBI	+	reduction	* 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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne, 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.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68379]	beta-galactosidase	+	3.2.1.23	* from API Coryne, API zym
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne, API zym
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[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.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne, API zym
[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.: #19780]	318	+	+	-	+	-	+	-	-	+	-	+	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.: #19780]	604	not determinedn.d.	+	+	+	+	+	-	-	-	+	+	+	+	+	-	+	+	-	-	-

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

[Ref.: #8035]	Sample type/isolated from	soil, farming field
[Ref.: #8035]	Geographic location (country and/or sea, region)	Bigeum Island
[Ref.: #8035]	Country	Republic of Korea
[Ref.: #8035]	Country ISO 3 Code	KOR
[Ref.: #8035]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	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.: #8035]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19780]	Biosafety level	1	Risk group (German 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.: #8035]	Nocardioides sp. MSL 19 16S ribosomal RNA gene, partial sequence	EF466114	1398	ENA	433657 tax ID

[Ref.: #8035]	GC-content	69.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32484]	GC-content	69.3 mol%

Availability in culture collections External links

[Ref.: #8035]

Culture collection no.

DSM 19320, KCTC 19290, MSL 19, JCM 16021

[Ref.: #80390]

SI-ID 407824

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea.	Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65566-0	2008	*

References

#8035

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19320

#19780

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 )

#32484

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 #28704 (see below)

#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 .

#80390

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-ID407824.1 )

#28704

IJSEM 2292 2008 ( DOI 10.1099/ijs.0.65566-0 , PubMed 18842843 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Nocardioides bigeumensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF