Nocardioides daedukensis (DSM 23819, CCUG 57505, KCTC 19601)

Name: Nocardioides daedukensis (DSM 23819, CCUG 57505, KCTC 19601)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11148

Type strain

Strain Designation MDN22

Culture col. no. DSM 23819 CCUG 57505 KCTC 19601 MDN22

NCBI tax ID(s) 634462

Special Collections DSMZ CCUG KCTC Wink compendium Literature strains

History <- CCUG <- <- J. H. Yoon, KRIBB, Taejon, South Korea

Links

Nocardioides daedukensis MDN22 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Soil around wastewater treatment plant.

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

Name and taxonomic classification

SI-ID 397275

KCTC 19601,DSM 23819,CCUG 57505

@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 daedukensis

Full scientific name Nocardioides daedukensis Yoon et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
29539	positive	1.9 µm	0.6 µm	rod-shaped
125439	positive					99.2

Colony morphology

@ref	Colony color	Incubation period	Medium used
21372	Pearl gold (1036)	10-14 days	ISP 2
21372		10-14 days	ISP 3
21372		10-14 days	ISP 4
21372		10-14 days	ISP 5
21372	Ocher brown (8001)	10-14 days	ISP 7
21372	Brown beige (1011)	10-14 days	suter with tyrosine
21372	Sand yellow (1002)	10-14 days	suter without tyrosine
61351		7 days

Multicellular morphology

@ref	Forms multicellular complex	Medium name
21372		ISP 2
21372		ISP 3
21372		ISP 4
21372		ISP 5
21372		ISP 7
21372		Suter with tyrosine
21372		Suter without tyrosine

Pigmentation

29539

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17387	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
21372	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21372	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21372	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21372	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21372	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21372	suter with tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21372	suter without tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
17387	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

Culture temp

@ref	Growth	Type	Temperature (°C)
17387	positive	growth	28
29539	positive	growth	04-37
29539	positive	optimum	30
61351	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
29539	positive	optimum	7.5
29539	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29539	aerobe
61351	aerobe
125439	obligate aerobe	90.9

Spore formation

29539

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
21372	NaCl	positive	maximum	5 %
29539	NaCl	positive	growth	0-9 %
29539	NaCl	positive	optimum	0.25 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
21372	22599 ChEBI	arabinose	-
68375	22599 ChEBI	arabinose	-	fermentation	from API ID32STA
68375	29016 ChEBI	arginine	+	hydrolysis	from API ID32STA
68375	17057 ChEBI	cellobiose	-	fermentation	from API ID32STA
21372	62968 ChEBI	cellulose	+
68375	15824 ChEBI	D-fructose	+	fermentation	from API ID32STA
68375	17634 ChEBI	D-glucose	+	fermentation	from API ID32STA
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68375	16899 ChEBI	D-mannitol	-	fermentation	from API ID32STA
68375	16024 ChEBI	D-mannose	+	fermentation	from API ID32STA
68375	16988 ChEBI	D-ribose	-	fermentation	from API ID32STA
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
29539	4853 ChEBI	esculin	+	hydrolysis
68375	4853 ChEBI	esculin	-	hydrolysis	from API ID32STA
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
21372	28757 ChEBI	fructose	-
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
21372	17234 ChEBI	glucose	+
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68375	17716 ChEBI	lactose	+	fermentation	from API ID32STA
29539	25115 ChEBI	malate	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68375	17306 ChEBI	maltose	+	fermentation	from API ID32STA
21372	37684 ChEBI	mannose	-
21372	17268 ChEBI	myo-inositol	-
68375	59640 ChEBI	N-acetylglucosamine	+	fermentation	from API ID32STA
29539	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68375	17632 ChEBI	nitrate	+	reduction	from API ID32STA
68375	18257 ChEBI	ornithine	-	degradation	from API ID32STA
21372	16634 ChEBI	raffinose	-
68375	16634 ChEBI	raffinose	-	fermentation	from API ID32STA
21372	26546 ChEBI	rhamnose	+
21372	17992 ChEBI	sucrose	-
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68375	17992 ChEBI	sucrose	+	fermentation	from API ID32STA
29539	27082 ChEBI	trehalose	+	carbon source
68375	27082 ChEBI	trehalose	-	fermentation	from API ID32STA
68375	32528 ChEBI	turanose	+	fermentation	from API ID32STA
68375	16199 ChEBI	urea	+	hydrolysis	from API ID32STA
21372	18222 ChEBI	xylose	+

Antibiotic resistance

@ref	ChEBI	Metabolite	Is resistant	Resistance conc.
68375	28368	novobiocin		1.8 µg	from API ID32STA

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68375	15688 ChEBI	acetoin		from API ID32STA

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
68375	15688 ChEBI	acetoin	+	from API ID32STA

Enzymes

@ref	Value	Activity	Ec
68375	alkaline phosphatase	+	3.1.3.1	from API ID32STA
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	alpha-mannosidase	-	3.2.1.24	from API zym
68375	arginine dihydrolase	+	3.5.3.6	from API ID32STA
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68375	beta-galactosidase	-	3.2.1.23	from API ID32STA
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68375	beta-glucosidase	-	3.2.1.21	from API ID32STA
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68375	beta-glucuronidase	-	3.2.1.31	from API ID32STA
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	cystine arylamidase	-	3.4.11.3	from API zym
29539	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68379	gelatinase	+		from API Coryne
68375	L-arginine arylamidase	-		from API ID32STA
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
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68375	ornithine decarboxylase	-	4.1.1.17	from API ID32STA
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
68375	pyrrolidonyl arylamidase	-	3.4.19.3	from API ID32STA
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68375	urease	+	3.5.1.5	from API ID32STA
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
21372	-	+	-	-	-	-	-	-	+	+/-	+	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
21372	not determinedn.d.	+/-	-	-	-	-	-	-	-	-	+/-	+	-	-	-	-	-	-	-	-

API ID32STA

@ref	URE	ADH (Arg)	ODC	ESC	GLU	FRU	MNE	MAL	LAC	TRE	MAN	RAF	RIB	CEL	Reduction of nitrateNIT	Acetoin production (Voges Proskauer test)VP	beta GAL	L-arginine arylamidaseArgA	PAL	Pyrrolidonyl arylamidasePyrA	NOVO	SAC	NAG	TUR	ARA	beta GUR
17387	+	+	-	-	+	+	+	+	+	-	-	-	-	-	+	+	-	-	+	-	+	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Water treatment plant
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
17387	Soil around wastewater treatment plant		Taejon	Republic of Korea	KOR	Asia
61351	Soil around wastewater treatment plant	2006-01-01	Taejon	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17387	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1340841v1 assembly for Nocardioides daedukensis DSM 23819	contig	GCA_013408415	634462.3	2844615251	634462	78.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17387	Nocardioides daedukensis strain MDN22 16S ribosomal RNA gene, partial sequence	FJ842646	1475		634462

GC content

@ref	GC-content (mol%)	Method
17387	68.7	high performance liquid chromatography (HPLC)
29539	68.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardioides daedukensis DSM 23819
NCBI: GCA_013408415

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	78.40	no
125439	motility	BacteriaNetⓘ	no	79.20	no
125439	gram_stain	BacteriaNetⓘ	positive	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides daedukensis strain DSM 23819
PATRIC: 634462.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.33	no
125438	anaerobic	anaerobicⓘ	no	94.86	yes
125438	spore-forming	spore-formingⓘ	no	66.48	yes
125438	aerobic	aerobicⓘ	yes	87.88	no
125438	thermophilic	thermophileⓘ	no	96.29	yes
125438	flagellated	motile2+ⓘ	no	62.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan.	Amin A, Ahmed I, Habib N, Abbas S, Xiao M, Hozzein WN, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0711-8	2016
Phylogeny	Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment.	Fan X, Qiao Y, Gao X, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijs.0.059873-0	2014
Phylogeny	Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.	Woo SG, Srinivasan S, Yang J, Jung YA, Kim MK, Lee M	Int J Syst Evol Microbiol	10.1099/ijs.0.033308-0	2011
Phylogeny	Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil.	Yoon JH, Park S, Kang SJ, Lee JS, Lee KC, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.015354-0	2009

References

#17387	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23819
#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 )
#21372	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#25936	IJSEM 1334 2010 ( DOI 10.1099/ijs.0.015354-0 , PubMed 19667373 )
#29539	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 #25936
#61351	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57505
#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) .
#68375	Automatically annotated from API ID32STA .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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 daedukensis (DSM 23819, CCUG 57505, KCTC 19601)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API coryne

API zym

API ID32STA

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013408415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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