Nocardia coubleae (DSM 44960, CIP 108996, OFN N12)

Name: Nocardia coubleae (DSM 44960, CIP 108996, OFN N12)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10809

Type strain

Culture col. no. DSM 44960 CIP 108996 OFN N12 NBRC 108252 IFM 10920 1 more

NCBI tax ID(s) 1210069 356147

Special Collections DSMZ JCM CIP Wink compendium Literature strains

History <- P. Boiron; OFN N12 <- Z. U Khan 2005, P. Boiron, C. Bernard Univ., Lyon, France: strain OFN N12 IFM 10920 <-- DSM 44960 <-- P. Boiron OFN N12 <-- Z. U. Khan. CIP <- 2005, P. Boiron, C. Bernard Univ., Lyon, France: strain OFN N12

Links

Nocardia coubleae DSM 44960 is an aerobe, mesophilic, Gram-positive prokaryote that builds an aerial mycelium and was isolated from soil in the Ahmadi oil field.

Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 309472

NBRC 108252,CIP 108996,DSM 44960,JCM 15318

@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 coubleae

Full scientific name Nocardia coubleae Rodríguez-Nava et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32015	positive
118769	positive	rod-shaped
125438	positive		90.515
125439			91.3
125439	positive		99.2

Colony morphology

@ref	Colony color	Incubation period	Medium used
20145	Deep orange (2011)	10-14 days	ISP 2
20145	Cream (9001)	10-14 days	ISP 3
20145	Cream (9001)	10-14 days	ISP 4
20145	Cream (9001)	10-14 days	ISP 5
20145	Cream (9001)	10-14 days	ISP 6
20145	Cream (9001)	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
20145	Aerial Mycelium	Cream	ISP 2
20145	Aerial Mycelium	Cream	ISP 3
20145			ISP 4
20145			ISP 5
20145	Aerial Mycelium	Cream	ISP 6
20145			ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12213	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
12213	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
20145	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
20145	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:
20145	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
20145	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
20145	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20145	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
41981	MEDIUM 129 - for Pseudonocardia, Nocardia, Skermania and Streptomyces seoulensis, Streptomyces stramineus		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (10.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
118769	CIP Medium 129	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12213	positive	growth	28	mesophilic
32015	positive	growth	25-37	mesophilic
32015	positive	optimum	37	mesophilic
41981	positive	growth	37	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
12213	aerobe
32015	aerobe
118769	obligate aerobe
125438	aerobe	90.091
125439	obligate aerobe	95

Observation

67770

Observationquinones: MK-8(H₄, ω-cycl)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
20145	22599 ChEBI	arabinose	+/-
20145	62968 ChEBI	cellulose	-
20145	28757 ChEBI	fructose	+
32015	28757 ChEBI	fructose	+	carbon source
32015	28260 ChEBI	galactose	+	carbon source
20145	17234 ChEBI	glucose	+
32015	17234 ChEBI	glucose	+	carbon source
32015	17754 ChEBI	glycerol	+	carbon source
32015	17306 ChEBI	maltose	+	carbon source
20145	29864 ChEBI	mannitol	-
32015	29864 ChEBI	mannitol	+	carbon source
32015	37684 ChEBI	mannose	+	carbon source
20145	17268 ChEBI	myo-inositol	-
118769	17632 ChEBI	nitrate	+	reduction
118769	16301 ChEBI	nitrite	-	reduction
20145	16634 ChEBI	raffinose	-
32015	16634 ChEBI	raffinose	+	carbon source
20145	26546 ChEBI	rhamnose	-
32015	33942 ChEBI	ribose	+	carbon source
20145	17992 ChEBI	sucrose	-
32015	17992 ChEBI	sucrose	+	carbon source
20145	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118769	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118769	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
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	+		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118769	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
118769	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

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
20145	not determinedn.d.	+	+	+	+	+	+	-	-	-	+	+	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Oil reservoir
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Isolation date
12213	soil in the Ahmadi oil field	Kuwait	KWT	Asia
67770	Oil-contaminated soil from the Ahmadi oilfield	Kuwait	KWT	Asia
118769	Environment, Oil, contaminated soil	Kuwait	KWT	Asia	1997

Taxonmaps

69479

Global distribution of 16S sequence DQ235689 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples	2
Soil Samples	10
Animal Samples	12
Plant Samples	30
Total Samples	54

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12213	1	Risk group (German classification) According to TRBA 466
20145	1	German classification According to TRBA 466
118769	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	ASM1239594v1 assembly for Nocardia coubleae DSM 44960	contig	GCA_012395945	356147.3	2902498892	356147	73.13
67770	ASM161280v1 assembly for Nocardia coubleae NBRC 108252	contig	GCA_001612805	1210069.4	2731957729	1210069	70

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Nocardia coubleae strain DSM 44960 16S ribosomal RNA gene, partial sequence	JN041456	462	356147
20218	Nocardia coubleae strain OFN N12 16S ribosomal RNA gene, partial sequence	DQ235689	1322	356147
32015	Nocardia coublieae strain OFN N11 16S ribosomal RNA gene, partial sequence	DQ235688	1322	356147

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia coubleae NBRC 108252
NCBI: GCA_001612805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.20	no
125439	motility	BacteriaNetⓘ	no	91.30	no
125439	spore_formation	BacteriaNetⓘ	yes	79.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia coubleae NBRC 108252
PATRIC: 1210069.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.52	no
125438	anaerobic	anaerobicⓘ	no	98.59	yes
125438	spore-forming	spore-formingⓘ	yes	59.33	no
125438	aerobic	aerobicⓘ	yes	90.09	yes
125438	thermophilic	thermophileⓘ	no	97.90	no
125438	flagellated	motile2+ⓘ	no	88.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome-guided discovery of coublibactins from Nocardia coubleae and their gallium complexes with potent antileukemic activity.	Tao Q, Cai T, Xiao Y, Han T, Shen L, Cheng C, Xu S, Li A, Zhang P, Chen J, Zhang Y, Tong Q, Cai X.	Bioorg Chem	10.1016/j.bioorg.2025.108508	2025
Phylogeny	Reclassification of Nocardia species based on whole genome sequence and associated phenotypic data.	Tamura T, Ohji S, Ichikawa N, Hosoyama A, Yamazoe A, Hamada M, Komaki H, Shibata C, Matsuzawa T, Gonoi T, Suzuki KI, Fujita N.	J Antibiot (Tokyo)	10.1038/s41429-018-0043-1	2018
Metabolism	Biodegradation of polycyclic aromatic hydrocarbons, phenol and sodium sulfate by Nocardia species isolated and characterized from Iranian ecosystems.	Azadi D, Shojaei H.	Sci Rep	10.1038/s41598-020-78821-1	2020
Phylogeny	Nocardia lasii sp. nov., a novel actinomycete isolated from the cuticle of an ant (Lasius fuliginosus L).	Liu C, Bai L, Ye L, Zhao J, Yan K, Xiang W, Wang X	Antonie Van Leeuwenhoek	10.1007/s10482-016-0753-y	2016
Phylogeny	Nocardia coubleae sp. nov., isolated from oil-contaminated Kuwaiti soil.	Rodriguez-Nava V, Khan ZU, Potter G, Kroppenstedt RM, Boiron P, Laurent F	Int J Syst Evol Microbiol	10.1099/ijs.0.64815-0	2007

References

#12213	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44960
#20145	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 )
#28268	IJSEM 1482 2007 ( DOI 10.1099/ijs.0.64815-0 , PubMed 17625180 )
#32015	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 #28268
#41981	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#118769	Collection of Institut Pasteur ; Curators of the CIP; CIP 108996
#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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Nocardia coubleae (DSM 44960, CIP 108996, OFN N12)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_012395945

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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