Nocardioides daejeonensis (DSM 25320, JCM 16922, KCTC 19772)

Name: Nocardioides daejeonensis (DSM 25320, JCM 16922, KCTC 19772)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11155

Type strain

Strain Designation MJ31

Culture col. no. DSM 25320 JCM 16922 KCTC 19772 MJ31

NCBI tax ID(s) 1046556

Special Collections DSMZ JCM KCTC Wink compendium Literature strains

Links

Nocardioides daejeonensis MJ31 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from sludge sample of a sewage disposal plant.

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

Name and taxonomic classification

SI-ID 398561

KCTC 19772,JCM 16922,DSM 25320

@ref 20215

Last LPSN update 2025-12-16 09:49:31

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides daejeonensis

Full scientific name Nocardioides daejeonensis Woo et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30315	positive	0.8-2 µm	0.5-0.8 µm	rod-shaped
125439	positive					97.4

Colony morphology

@ref	Colony color	Medium used
69321	Beige (1001)	ISP 2
69321	Beige (1001)	ISP 6
69321	Beige (1001)	suter with tyrosine
69321	Ivory (1014)	suter without tyrosine
69321	Light ivory (1015)	ISP 7
69321	Oyster white (1013)	ISP 3
69321	Oyster white (1013)	ISP 4
69321	Oyster white (1013), ivory (1014)	ISP 5

Multicellular morphology

@ref	Complex name	Medium name
69321	Aerial mycelium	ISP 2
69321	Aerial mycelium	ISP 3
69321	Aerial mycelium	ISP 4
69321	Aerial mycelium	ISP 5
69321	Aerial mycelium	ISP 6
69321	Aerial mycelium	ISP 7
69321	Aerial mycelium	suter with tyrosine
69321	Aerial mycelium	suter without tyrosine

Pigmentation

@ref	Production	Name
30315
69321		Melanin
69321		soluble pigment

Multimedia

@ref:	69321
multimedia content:	DSM_25320_image5.jpeg
multimedia.multimedia content:	DSM_25320_image5.jpeg
caption:	(ISP6, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69321
multimedia content:	DSM_25320_image6.jpeg
multimedia.multimedia content:	DSM_25320_image6.jpeg
caption:	(ISP6, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17996	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
17996	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
17996	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17996	positive	growth	28	mesophilic
30315	positive	growth	15-37
30315	positive	optimum	30	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30315	positive	optimum	7.5-8
30315	positive	growth	5.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30315	aerobe
125439	obligate aerobe	98.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30315	NaCl	positive	growth	0-10 %
30315	NaCl	positive	optimum	2 %
69321	NaCl	positive	growth	0-5 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30315	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
30315	16193 ChEBI	3-hydroxybenzoate	+	carbon source
30315	17879 ChEBI	4-hydroxybenzoate	+	carbon source
69321	22599 ChEBI	arabinose	+	growth
30315	22599 ChEBI	arabinose	+	carbon source
69321	62968 ChEBI	cellulose	-	growth
30315	16947 ChEBI	citrate	+	carbon source
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
30315	27689 ChEBI	decanoate	+	carbon source
30315	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
69321	28757 ChEBI	fructose	+	growth
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
69321	17234 ChEBI	glucose	+	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
69321	17268 ChEBI	inositol	+	growth
30315	24996 ChEBI	lactate	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
30315	15792 ChEBI	malonate	+	carbon source
30315	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69321	37684 ChEBI	mannose	+	growth
30315	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
69321	16634 ChEBI	raffinose	+	growth
30315	26546 ChEBI	rhamnose	+	carbon source
69321	26546 ChEBI	rhamnose	+	growth
30315	17822 ChEBI	serine	+	carbon source
69321	17992 ChEBI	sucrose	+	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
69321	18222 ChEBI	xylose	+	growth

Enzymes

@ref	Value	Activity	Ec
30315	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
30315	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	alpha-mannosidase	-	3.2.1.24	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
30315	catalase	+	1.11.1.6
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	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
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
69321	+	-	-	+	-	-	-	-	-	-	-	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
69321	not determinedn.d.	+	+	+	+/-	+	+	+/-	+/-	-	+	+	-	+/-	-	-	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Water treatment plant
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17996	sludge sample of a sewage disposal plant	Daejeon	Republic of Korea	KOR	Asia
67770	Sludge at the Daejeon sewage-disposal plant		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence JF937066 (>99% sequence identity) for Nocardioides daejeonensis from Microbeatlas

Aquatic Samples	37
Soil Samples	53
Animal Samples	170
Plant Samples	14
Total Samples	274

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17996	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
67770	ASM319458v1 assembly for Nocardioides daejeonensis MJ31	contig	GCA_003194585	1046556.3	2866264325	1046556	74.84

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17996	Nocardioides daejeonensis strain MJ31 16S ribosomal RNA gene, partial sequence	JF937066	1468		1046556

GC content

@ref	GC-content (mol%)	Method
17996	71.2	high performance liquid chromatography (HPLC)
30315	71.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardioides daejeonensis MJ31
NCBI: GCA_003194585

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	74.80	no
125439	motility	BacteriaNetⓘ	no	61.20	no
125439	gram_stain	BacteriaNetⓘ	positive	97.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces.	Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Zhang G, Huang Y, Zhu W, Wu X, Liang H, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003076	2018
Phylogeny	Nocardioides gilvus sp. nov., isolated from Namtso Lake.	Zhang HX, Wang K, Xu ZX, Chen GJ, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0735-0	2016
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 solisilvae sp. nov., isolated from a forest soil.	Sultanpuram VR, Mothe T, Mohammed F	Antonie Van Leeuwenhoek	10.1007/s10482-015-0455-x	2015
Phylogeny	Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla).	Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH, Shen FT, Lai WA, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.000206	2015
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

References

#17996	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25320
#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 )
#30315	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 #26656 (see below)
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69321	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 .
#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 daejeonensis (DSM 25320, JCM 16922, KCTC 19772)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003194585

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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