Nocardioides panacihumi (DSM 18660, KCTC 19187, Gsoil 616)

Name: Nocardioides panacihumi (DSM 18660, KCTC 19187, Gsoil 616)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11122

Type strain

Culture col. no. DSM 18660 KCTC 19187 Gsoil 616 CIP 109747 JCM 15309

NCBI tax ID(s) 400774

Special Collections DSMZ JCM KCTC CIP Wink compendium Literature strains

History <- S.-T. Lee <- W.-T. Im; Gsoil 616 KCTC 19187 <-- S.-T. Lee Gsoil 616. <- ST Lee, KAIST CIP <- 2007, KCTC <- S.T. Lee, KAIST, Daejon, Korea: strain Gsoil 616

Links

Nocardioides panacihumi DSM 18660 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil, ginseng field.

Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 292499

LMG 23811,DSM 18660,KCTC 19187,CIP 109747,JCM 15309

@ref 20215

Last LPSN update 2026-02-09 11:20:27

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides panacihumi

Full scientific name Nocardioides panacihumi An et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
32010	positive	0.7-1.2 µm	0.3-0.5 µm	rod-shaped
67771	positive
121524	positive			oval-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7643	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
37831	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
7643	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
121524	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7643	positive	growth	28
19769	positive	optimum	28
32010	positive	growth	15-30
32010	positive	optimum	30
37831	positive	growth	30
67770	positive	growth	28
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
32010	positive	optimum	7
32010	positive	growth	5.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32010	aerobe
67771	aerobe

Spore formation

32010

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32010	NaCl	positive	growth	0-1 %
32010	NaCl	positive	optimum	0.5 %

Murein

@ref	Murein short key	Type
7643	A41.01	A3gamma LL-Dpm-Gly

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32010	16193 ChEBI	3-hydroxybenzoate	+	carbon source
32010	37054 ChEBI	3-hydroxybutyrate	+	carbon source
32010	17879 ChEBI	4-hydroxybenzoate	+	carbon source
32010	30089 ChEBI	acetate	+	carbon source
32010	16449 ChEBI	alanine	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
32010	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
32010	24265 ChEBI	gluconate	+	carbon source
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
32010	28087 ChEBI	glycogen	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
32010	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
32010	17632 ChEBI	nitrate	+	reduction
121524	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
121524	16301 ChEBI	nitrite	-	reduction
32010	18401 ChEBI	phenylacetate	+	carbon source
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
32010	26271 ChEBI	proline	+	carbon source
32010	17272 ChEBI	propionate	+	carbon source
32010	26546 ChEBI	rhamnose	+	carbon source
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
32010	17814 ChEBI	salicin	+	carbon source
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
32010	31011 ChEBI	valerate	+	carbon source
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121524	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
32010	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
32010	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
121524	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
121524	oxidase	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
121524	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
19769	-	-	-	-	-	-	+	-	+	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
19769	not determinedn.d.	-	+	+	-	+	+	-	-	-	+	+	-	-	-	+	+	-	-	-
121524	-	-	+	+	-	+	+	-	+	-	+	-	-	-	-	+	+	+	+	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
121524	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	+/-	+/-	-	-	+/-	-	-	-	-	-	-	-	+/-	-	+/-	+/-	+/-	+/-	-	-	+/-	-	-	-	+/-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7643	soil, ginseng field	Pocheon province	Republic of Korea	KOR	Asia
67770	Soil of a ginseng field	Pocheon Province	Republic of Korea	KOR	Asia
67771	From soil, ginseng field		Republic of Korea	KOR	Asia
121524	Environment, Soil, ginseng field	Pocheon	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7643	1	Risk group (German classification) According to TRBA 466
19769	1	Risk group (German classification) According to TRBA 466
121524	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953092v1 assembly for Nocardioides panacihumi JCM 15309	scaffold	GCA_039530925	400774	61.97

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7643	Nocardioides panacihumi gene for 16S rRNA, partial sequence	AB271053	1457		400774

GC content

@ref	GC-content (mol%)	Method
7643	73
67770	73	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	In Vitro Assessment of Biocontrol Effects on Fusarium Head Blight and Deoxynivalenol (DON) Accumulation by DON-Degrading Bacteria.	Morimura H, Ito M, Yoshida S, Koitabashi M, Tsushima S, Camagna M, Chiba S, Takemoto D, Kawakita K, Sato I.	Toxins (Basel)	10.3390/toxins12060399	2020
Metabolism	Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China.	Bazhanov DP, Li C, Li H, Li J, Zhang X, Chen X, Yang H.	BMC Microbiol	10.1186/s12866-016-0868-3	2016
Phylogeny	Nocardioides lacus sp. nov., a novel member of the Actinomycetota isolated from a freshwater pond.	Nam YH, Jung JY, Kang HK, Ryu BG, Hwang YJ, Kim TJ, Lee MH, Jin HM, Han KI.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006929	2025
Phylogeny	Nocardioides cynanchi sp. nov., isolated from soil of rhizosphere of Cynanchum wilfordii.	Suh MK, Lee KC, Kim JS, Han KI, Kim HS, Eom MK, Shin YK, Lee JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004640	2021
Phylogeny	Nocardioides opuntiae sp. nov., isolated from soil of a cactus.	Lee SD, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.060400-0	2014
Phylogeny	Nocardioides terrae sp. nov., isolated from forest soil.	Zhang JY, Liu XY, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.010785-0	2009
Phylogeny	Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field.	An DS, Im WT, Lee ST, Yoon MH	Int J Syst Evol Microbiol	10.1099/ijs.0.64806-0	2007

References

#7643	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18660
#19769	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 )
#28264	IJSEM 2143 2007 ( DOI 10.1099/ijs.0.64806-0 , PubMed 17766888 )
#32010	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 #28264
#37831	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68371	Automatically annotated from API 50CH acid .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#121524	Collection of Institut Pasteur ; Curators of the CIP; CIP 109747
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Nocardioides panacihumi (DSM 18660, KCTC 19187, Gsoil 616)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039530925

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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