Name: Nocardioides panacisoli DSM 21348
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11147

Type strain:

Species: Nocardioides panacisoli

Culture col. no.: DSM 21348, KCTC 19470, Gsoil 346, JCM 16953

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 627624 (species)

SI-ID 397406

DSM 21348

Special Collections

Section

Nocardioides panacisoli DSM 21348 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil of a ginseng field.

Gram-positive
rod-shaped
aerobe
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 panacisoli**
	Full Scientific Name (LPSN)	Nocardioides panacisoli Cho et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29416]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #29416]	Cell length	1 µm

[Ref.: #29416]	Cell width	0.3 µm

[Ref.: #29416]	Cell shape	rod-shaped

[Ref.: #29416]	Motility	no

[Ref.: #21353]	Colony color	Sand yellow (1002)
[Ref.: #21353]	Incubation period	10-14 days
[Ref.: #21353]	Cultivation medium used	ISP 2

[Ref.: #21353]	Colony color	Pearl white (1013)
[Ref.: #21353]	Incubation period	10-14 days
[Ref.: #21353]	Cultivation medium used	ISP 3

[Ref.: #21353]	Colony color	Light ivory (1015) - ochre brown (8001)
[Ref.: #21353]	Incubation period	10-14 days
[Ref.: #21353]	Cultivation medium used	ISP 4

[Ref.: #21353]	Colony color	Light ivory (1015)
[Ref.: #21353]	Incubation period	10-14 days
[Ref.: #21353]	Cultivation medium used	ISP 5

[Ref.: #21353]	Colony color	Ivory (1014)
[Ref.: #21353]	Incubation period	10-14 days
[Ref.: #21353]	Cultivation medium used	ISP 7

[Ref.: #21353]	Colony color	Sand yellow (1002)
[Ref.: #21353]	Incubation period	10-14 days
[Ref.: #21353]	Cultivation medium used	suter with tyrosine

[Ref.: #21353]	Colony color	Ivory (1014)
[Ref.: #21353]	Incubation period	10-14 days
[Ref.: #21353]	Cultivation medium used	suter without tyrosine

[Ref.: #29416]

Pigment production

yes

[Ref.: #21353]	Multicellular complex forming ability	no
[Ref.: #21353]	Medium Name (multicellularity)	ISP 2

[Ref.: #21353]	Multicellular complex forming ability	no
[Ref.: #21353]	Medium Name (multicellularity)	ISP 3

[Ref.: #21353]	Multicellular complex forming ability	no
[Ref.: #21353]	Medium Name (multicellularity)	ISP 4

[Ref.: #21353]	Multicellular complex forming ability	no
[Ref.: #21353]	Medium Name (multicellularity)	ISP 5

[Ref.: #21353]	Multicellular complex forming ability	no
[Ref.: #21353]	Medium Name (multicellularity)	ISP 7

[Ref.: #21353]	Multicellular complex forming ability	no
[Ref.: #21353]	Medium Name (multicellularity)	Suter with tyrosine

[Ref.: #21353]	Multicellular complex forming ability	no
[Ref.: #21353]	Medium Name (multicellularity)	Suter without tyrosine

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15633]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15633]

Culture medium growth

[Ref.: #15633]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15633]

Culture medium composition

expand / minimize

[Ref.: #21353]

Culture medium

ISP 2

[Ref.: #21353]

Culture medium growth

[Ref.: #21353]

Culture medium composition

expand / minimize

[Ref.: #21353]

Culture medium

ISP 3

[Ref.: #21353]

Culture medium growth

[Ref.: #21353]

Culture medium composition

expand / minimize

[Ref.: #21353]

Culture medium

ISP 4

[Ref.: #21353]

Culture medium growth

[Ref.: #21353]

Culture medium composition

expand / minimize

[Ref.: #21353]

Culture medium

ISP 5

[Ref.: #21353]

Culture medium growth

[Ref.: #21353]

Culture medium composition

expand / minimize

[Ref.: #21353]

Culture medium

ISP 7

[Ref.: #21353]

Culture medium growth

[Ref.: #21353]

Culture medium composition

expand / minimize

[Ref.: #21353]

Culture medium

suter with tyrosine

[Ref.: #21353]

Culture medium growth

[Ref.: #21353]

Culture medium composition

expand / minimize

[Ref.: #21353]

Culture medium

suter without tyrosine

[Ref.: #21353]

Culture medium growth

[Ref.: #21353]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15633]	growth	28 °C
[Ref.: #29416]	growth	10-42 °C
[Ref.: #29416]	optimum	27.5 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #29416]			optimum	7
[Ref.: #29416]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29416]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29416]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #21353]		NaCl		maximum	5	%
[Ref.: #29416]		NaCl		growth	0-2	%

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29416]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #29416]	acetate ChEBI	+	carbon source
[Ref.: #29416]	adipate ChEBI	+	carbon source
[Ref.: #21353]	arabinose ChEBI	+
[Ref.: #21353]	cellulose ChEBI	-
[Ref.: #29416]	citrate ChEBI	+	carbon source
[Ref.: #68379]	D-glucose 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.: #21353]	fructose ChEBI	+
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #29416]	gluconate ChEBI	+	carbon source
[Ref.: #21353]	glucose ChEBI	+
[Ref.: #29416]	glucose ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29416]	malate ChEBI	+	carbon source
[Ref.: #29416]	maltose ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	+	fermentation	* from API Coryne
[Ref.: #21353]	mannose ChEBI	+
[Ref.: #21353]	myo-inositol ChEBI	-
[Ref.: #29416]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #29416]	proline ChEBI	+	carbon source
[Ref.: #29416]	propionate ChEBI	+	carbon source
[Ref.: #21353]	raffinose ChEBI	-
[Ref.: #21353]	rhamnose ChEBI	-
[Ref.: #21353]	sucrose ChEBI	+
[Ref.: #29416]	sucrose ChEBI	+	carbon source
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #29416]	valerate ChEBI	+	carbon source
[Ref.: #21353]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #29416]		hydrogen sulfide ChEBI	yes

	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-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68379]	alpha-glucosidase	+	3.2.1.20	* from API Coryne, API zym
[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.: #29416]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29416]	cytochrome oxidase	+	1.9.3.1
[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]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
	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.: #21353]	482	+	+/-	+	+	-	+	+	+	+	+/-	+	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.: #21353]	994	not determinedn.d.	+	+	+	-	+	+/-	-	+/-	+/-	+	+	+/-	+	-	+	+	+	-	-

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

[Ref.: #15633]	Sample type/isolated from	soil of a ginseng field
[Ref.: #15633]	Geographic location (country and/or sea, region)	Pocheon province (37° 58' N 127°15' E)
[Ref.: #15633]	Country	Republic of Korea
[Ref.: #15633]	Country ISO 3 Code	KOR
[Ref.: #15633]	Continent	Asia
[Ref.: #15633]	Geographic location	37.9667°/127.2500°

[Ref.: #67770]	Sample type/isolated from	Soil of a ginseng field
[Ref.: #67770]	Geographic location (country and/or sea, region)	Pocheon Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil of ginseng field
[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
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ666101 (>99% sequence identity) for Nocardioides panacisoli subclade from Microbeatlas

Aquatic Samples	7
Soil Samples	221
Animal Samples	10
Plant Samples	1
Total Samples	239

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

[Ref.: #15633]

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.: #15633]	Nocardioides panacisoli strain GSoil 346 16S ribosomal RNA gene, partial sequence	FJ666101	1449	GenBank ENA	627624 tax ID

[Ref.: #15633]	GC-content	73.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29416]	GC-content	73 mol%
[Ref.: #67770]	GC-content	73 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #15633]

Culture collection no.

DSM 21348, KCTC 19470, Gsoil 346, JCM 16953

[Ref.: #80396]

SI-ID 397406

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides pelophilus sp. nov., isolated from freshwater mud.	Yan ZF, Lin P, Li CT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002776	2018	*
Phylogeny	Nocardioides litorisoli sp. nov., isolated from lakeside soil.	Wang Y, Xu D, Luo A, Wang G, Zheng S	Int J Syst Evol Microbiol	10.1099/ijsem.0.002283	2017	*
Phylogeny	Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field.	Cho CH, Lee JS, An DS, Whon TW, Kim SG	Int J Syst Evol Microbiol	10.1099/ijs.0.012690-0	2009	*

References

#15633

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21348

#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 )

#21353

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#29416

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 #25823 (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 .

#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 .

#80396

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-ID397406.1 )

#25823

IJSEM 387 2010 ( DOI 10.1099/ijs.0.012690-0 , PubMed 19651712 )

* These data were automatically processed and therefore are not curated

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