Nocardia jejuensis (DSM 44959, JCM 13281, NRRL B-24430)

Name: Nocardia jejuensis (DSM 44959, JCM 13281, NRRL B-24430)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10808

Type strain

Strain Designation N 3-2, N3-2

Culture col. no. DSM 44959 JCM 13281 NRRL B-24430 N 3-2 NCIMB 14343 4 more

NCBI tax ID(s) 1210088 328049

Special Collections DSMZ JCM CIP Wink compendium Literature strains

History <- NRRL 2006, JCM S. D. Lee N3-2. CIP <- 2006, JCM <- S. D. Lee: strain N3-2

Links

Nocardia jejuensis N 3-2 is an aerobe, spore-forming, Gram-positive bacterium that builds an aerial mycelium and was isolated from natural cave.

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

Name and taxonomic classification

SI-ID 290998

JCM 13281,NRRL B-24430,DSM 44959,CIP 109185,NBRC 103114

@ref 20215

Last LPSN update 2026-02-09 11:20:21

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Nocardia

Species Nocardia jejuensis

Full scientific name Nocardia jejuensis Lee 2006

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31595	positive	rod-shaped
120327	positive	rod-shaped
125438	positive		91.998
125439	positive		98.9
125439			90

Colony morphology

@ref	Colony color	Medium used
69369	Beige red (3012)	ISP 5
69369	Beige red (3012)	ISP 7
69369	Ochre brown (8001)	suter with tyrosine
69369	Pastel yellow (1034)	ISP 3
69369	Pastel yellow (1034)	ISP 4
69369	Saffron yellow (1017)	suter without tyrosine
69369	Sand yellow (1002)	ISP 6
69369	Yellow orange (2000)	ISP 2

Multicellular morphology

@ref	Complex name	Complex color	Medium name
69369	Aerial mycelium	Cream (9001)	ISP 2
69369	Aerial mycelium	Oyster white (1013)	ISP 3
69369	Aerial mycelium		ISP 4
69369	Aerial mycelium	Cream (9001)	ISP 5
69369	Aerial mycelium	Light ivory (1015)	ISP 6
69369	Aerial mycelium	Cream (9001)	ISP 7
69369	Aerial mycelium	Beige (1001)	suter with tyrosine
69369	Aerial mycelium	Beige (1001)	suter without tyrosine

Pigmentation

@ref	Color	Name
31595
69369		melanin pigment
69369	Beige (1001), sand yellow (1002)	soluble pigment

Multimedia

@ref:	69369
multimedia content:	DSM_44959_image3.jpeg
multimedia.multimedia content:	DSM_44959_image3.jpeg
caption:	(ISP6, ISP7, SSM+T, SSM-T)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69369
multimedia content:	DSM_44959_image4.jpeg
multimedia.multimedia content:	DSM_44959_image4.jpeg
caption:	(ISP6, ISP7, SSM+T, SSM-T)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12212	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
12212	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
37473	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120327	CIP Medium 72	Medium recipe at CIP
120327	CIP Medium 115	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
12212	positive	growth	28
19894	positive	optimum	28
31595	positive	growth	10-37
31595	positive	optimum	30-37
37473	positive	growth	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31595	positive	optimum	7.1-8.1
31595	positive	growth	4.1-10.1	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
12212	aerobe
31595	aerobe
120327	obligate aerobe
125438	aerobe	90.414
125439	obligate aerobe	98.7

Spore formation

31595

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31595	NaCl	positive	growth	0-4 %
31595	NaCl	positive	optimum	0-4 %
69369	NaCl	positive	growth	0-2.5 %

Observation

@ref	Observation
31595	aggregates in chains
67770	quinones: MK-8(H₄, ω-cycl)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
69369	22599 ChEBI	arabinose	-	growth
31595	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
69369	62968 ChEBI	cellulose	-	growth
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	15824 ChEBI	D-fructose	+	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	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
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
31595	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
31595	28757 ChEBI	fructose	+	carbon source
69369	28757 ChEBI	fructose	-	growth
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
31595	17234 ChEBI	glucose	+	carbon source
69369	17234 ChEBI	glucose	+	growth
31595	17754 ChEBI	glycerol	+	carbon source
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
69369	17268 ChEBI	inositol	+	growth
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	62345 ChEBI	L-rhamnose	-	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
31595	17716 ChEBI	lactose	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
69369	37684 ChEBI	mannose	-	growth
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
31595	28053 ChEBI	melibiose	+	carbon source
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	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
31595	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
120327	17632 ChEBI	nitrate	+	reduction
120327	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
69369	16634 ChEBI	raffinose	-	growth
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
69369	26546 ChEBI	rhamnose	-	growth
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
31595	33942 ChEBI	ribose	+	carbon source
31595	17814 ChEBI	salicin	+	carbon source
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
31595	30911 ChEBI	sorbitol	+	carbon source
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
31595	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69369	17992 ChEBI	sucrose	-	growth
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
69369	18222 ChEBI	xylose	-	growth

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120327	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
31595	catalase	+	1.11.1.6
120327	catalase	+	1.11.1.6
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
120327	oxidase	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
31595	urease	+	3.5.1.5
120327	urease	+	3.5.1.5

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
69369	+	-	-	+	-	-	+	-	+/-	+/-	-	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
69369	not determinedn.d.	+	+/-	+/-	+/-	+	+/-	+/-	-	-	+	+	-	+/-	-	+	+	-	+/-	-
120327	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	+	-	-	-

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
120327	not determinedn.d.	+	-	-	+	+	+	-	-	-	+	+	+	+	-	-	-	-	+	-	+/-	+	+	+	+	+	+	+	+	+	+	+	+	-	-	-	-	-	-	+	+	-	+	-	-	-	-	+/-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12212	natural cave	Jeju Island	Republic of Korea	KOR	Asia
67770	Soil inside a natural cave	Jeju Island	Republic of Korea	KOR	Asia
120327	Environment, Soil sample	Jeju Island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence GQ376174 (>99% sequence identity) for Nocardia jejuensis subclade from Microbeatlas

Aquatic Samples	281
Soil Samples	520
Animal Samples	576
Plant Samples	54
Total Samples	1431

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12212	1	Risk group (German classification) According to TRBA 466
19894	1	Risk group (German classification) According to TRBA 466
120327	2	Risk group (French 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	ASM161314v1 assembly for Nocardia jejuensis NBRC 103114	contig	GCA_001613145	1210088.4	2681812981	1210088	60.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Nocardia jejuensis 16S ribosomal RNA gene, partial sequence	GQ376174	1437		328049
12212	Nocardia jejuensis strain N3-2 16S ribosomal RNA gene, partial sequence	AY964666	1395		328049

GC content

@ref	GC-content (mol%)	Method
12212	69.6
67770	69.6	high performance liquid chromatography (HPLC)
67770	67.6	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia jejuensis NBRC 103114
NCBI: GCA_001613145

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	83.40	no
125439	motility	BacteriaNetⓘ	no	90.00	no
125439	gram_stain	BacteriaNetⓘ	positive	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia jejuensis NBRC 103114
PATRIC: 1210088.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.00	yes
125438	anaerobic	anaerobicⓘ	no	98.60	no
125438	spore-forming	spore-formingⓘ	yes	65.08	yes
125438	aerobic	aerobicⓘ	yes	90.41	yes
125438	thermophilic	thermophileⓘ	no	95.50	no
125438	flagellated	motile2+ⓘ	no	86.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics and Metabolomics in the Genus Nocardia.	Mannle D, McKinnie SMK, Mantri SS, Steinke K, Lu Z, Moore BS, Ziemert N, Kaysser L.	mSystems	10.1128/msystems.00125-20	2020
Phylogeny	Nocardia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample.	Li QQ, Han MX, Fang BZ, Jiao JY, Liu L, Yang ZW, Zhang WQ, Wei DQ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002072	2017
Phylogeny	Nocardia ninae sp. nov., isolated from a bronchial aspirate.	Laurent F, Rodriguez-Nava V, Noussair L, Couble A, Nicolas-Chanoine MH, Boiron P	Int J Syst Evol Microbiol	10.1099/ijs.0.64476-0	2007
Phylogeny	Nocardia jejuensis sp. nov., a novel actinomycete isolated from a natural cave on Jeju Island, Republic of Korea.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.63866-0	2006

References

#12212	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44959
#19894	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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#27884	IJSEM 559 2006 ( DOI 10.1099/ijs.0.63866-0 , PubMed 16514027 )
#31595	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 #27884
#37473	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69369	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 .
#120327	Collection of Institut Pasteur ; Curators of the CIP; CIP 109185
#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 )

Rate our new design

Content

About us

Nocardia jejuensis (DSM 44959, JCM 13281, NRRL B-24430)

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

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001613145

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media