Name: Nocardia coubleae DSM 44960
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 10809

Type strain:

Species: Nocardia coubleae

Culture col. no.: DSM 44960, CIP 108996, OFN N12, JCM 15318, IFM 10920, NBRC 108252

Strain history: CIP <- 2005, P. Boiron, C. Bernard Univ., Lyon, France: strain OFN N12

NCBI tax ID(s): 1210069 (strain), 356147 (species)

SI-ID 309472

CIP 108996, DSM 44960, JCM 15318

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Nocardiaceae*
	Genus	*Nocardia*
	Species	**Nocardia coubleae**
	Full Scientific Name (LPSN)	Nocardia coubleae Rodríguez-Nava et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32015]	Gram stain	positive
[Ref.: #118769]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %90.515

[Ref.: #118769]	Cell shape	rod-shaped

[Ref.: #118769]	Motility	no

[Ref.: #20145]	Colony color	Deep orange (2011)
[Ref.: #20145]	Incubation period	10-14 days
[Ref.: #20145]	Cultivation medium used	ISP 2

[Ref.: #20145]	Colony color	Cream (9001)
[Ref.: #20145]	Incubation period	10-14 days
[Ref.: #20145]	Cultivation medium used	ISP 3

[Ref.: #20145]	Colony color	Cream (9001)
[Ref.: #20145]	Incubation period	10-14 days
[Ref.: #20145]	Cultivation medium used	ISP 4

[Ref.: #20145]	Colony color	Cream (9001)
[Ref.: #20145]	Incubation period	10-14 days
[Ref.: #20145]	Cultivation medium used	ISP 5

[Ref.: #20145]	Colony color	Cream (9001)
[Ref.: #20145]	Incubation period	10-14 days
[Ref.: #20145]	Cultivation medium used	ISP 6

[Ref.: #20145]	Colony color	Cream (9001)
[Ref.: #20145]	Incubation period	10-14 days
[Ref.: #20145]	Cultivation medium used	ISP 7

[Ref.: #20145]	Multicellular complex forming ability	yes
[Ref.: #20145]	Multicellular complex name	Aerial Mycelium
[Ref.: #20145]	Multicellular complex color	Cream
[Ref.: #20145]	Medium Name (multicellularity)	ISP 2

[Ref.: #20145]	Multicellular complex forming ability	yes
[Ref.: #20145]	Multicellular complex name	Aerial Mycelium
[Ref.: #20145]	Multicellular complex color	Cream
[Ref.: #20145]	Medium Name (multicellularity)	ISP 3

[Ref.: #20145]	Multicellular complex forming ability	no
[Ref.: #20145]	Medium Name (multicellularity)	ISP 4

[Ref.: #20145]	Multicellular complex forming ability	no
[Ref.: #20145]	Medium Name (multicellularity)	ISP 5

[Ref.: #20145]	Multicellular complex forming ability	yes
[Ref.: #20145]	Multicellular complex name	Aerial Mycelium
[Ref.: #20145]	Multicellular complex color	Cream
[Ref.: #20145]	Medium Name (multicellularity)	ISP 6

[Ref.: #20145]	Multicellular complex forming ability	no
[Ref.: #20145]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #12213]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #12213]

Culture medium growth

[Ref.: #12213]

Culture medium link

Medium recipe at MediaDive

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Culture medium composition

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

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Culture medium

ISP 2

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 3

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 4

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Culture medium growth

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Culture medium

ISP 5

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 6

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 7

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Culture medium growth

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Culture medium composition

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[Ref.: #41981]

Culture medium

MEDIUM 129 - for Pseudonocardia, Nocardia, Skermania and Streptomyces seoulensis, Streptomyces stramineus

[Ref.: #41981]

Culture medium growth

[Ref.: #41981]

Culture medium composition

expand / minimize

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Culture medium

CIP Medium 129

[Ref.: #118769]

Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #12213]	growth	28 °C
[Ref.: #32015]	growth	25-37 °C
[Ref.: #32015]	optimum	37 °C
[Ref.: #41981]	growth	37 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #12213]	Oxygen tolerance	aerobe
[Ref.: #32015]	Oxygen tolerance	aerobe
[Ref.: #118769]	Oxygen tolerance	obligate aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %90.091

[Ref.: #69481]

Ability of spore formation

yes Confidence in %100

[Ref.: #67770]

Observation

quinones: MK-8(H₄, ω-cycl)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #20145]	arabinose ChEBI	+/-
[Ref.: #20145]	cellulose ChEBI	-
[Ref.: #20145]	fructose ChEBI	+
[Ref.: #32015]	fructose ChEBI	+	carbon source
[Ref.: #32015]	galactose ChEBI	+	carbon source
[Ref.: #20145]	glucose ChEBI	+
[Ref.: #32015]	glucose ChEBI	+	carbon source
[Ref.: #32015]	glycerol ChEBI	+	carbon source
[Ref.: #32015]	maltose ChEBI	+	carbon source
[Ref.: #20145]	mannitol ChEBI	-
[Ref.: #32015]	mannitol ChEBI	+	carbon source
[Ref.: #32015]	mannose ChEBI	+	carbon source
[Ref.: #20145]	myo-inositol ChEBI	-
[Ref.: #118769]	nitrate ChEBI	+	reduction
[Ref.: #118769]	nitrite ChEBI	-	reduction
[Ref.: #20145]	raffinose ChEBI	-
[Ref.: #32015]	raffinose ChEBI	+	carbon source
[Ref.: #20145]	rhamnose ChEBI	-
[Ref.: #32015]	ribose ChEBI	+	carbon source
[Ref.: #20145]	sucrose ChEBI	-
[Ref.: #32015]	sucrose ChEBI	+	carbon source
[Ref.: #20145]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118769]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118769]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118769]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118769]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #20145]	926	not determinedn.d.	+	+	+	+	+	+	-	-	-	+	+	-	-	-	+	+	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #12213]	Sample type/isolated from	soil in the Ahmadi oil field
[Ref.: #12213]	Country	Kuwait
[Ref.: #12213]	Country ISO 3 Code	KWT
[Ref.: #12213]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Oil-contaminated soil from the Ahmadi oilfield
[Ref.: #67770]	Country	Kuwait
[Ref.: #67770]	Country ISO 3 Code	KWT
[Ref.: #67770]	Continent	Asia

[Ref.: #118769]	Sample type/isolated from	Environment, Oil, contaminated soil
[Ref.: #118769]	Country	Kuwait
[Ref.: #118769]	Country ISO 3 Code	KWT
[Ref.: #118769]	Continent	Asia
[Ref.: #118769]	Isolation date	1997
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Oil reservoir
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #20145]	Biosafety level	1	German classification
[Ref.: #12213]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118769]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #32015]	Nocardia coublieae strain OFN N11 16S ribosomal RNA gene, partial sequence	DQ235688	1322	GenBank ENA	356147 tax ID
[Ref.: #20218]	Nocardia coubleae strain DSM 44960 16S ribosomal RNA gene, partial sequence	JN041456	462	GenBank ENA	356147 tax ID	*
[Ref.: #20218]	Nocardia coubleae strain OFN N12 16S ribosomal RNA gene, partial sequence	DQ235689	1322	GenBank ENA	356147 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardia coubleae NBRC 108252	GCA_001612805	contig	GenBank ENA	1210069 tax ID
[Ref.: #67770]	Nocardia coubleae DSM 44960	GCA_012395945	contig	GenBank ENA	356147 tax ID
[Ref.: #66792]	Nocardia coubleae NBRC 108252	1210069.4	wgs	PATRIC	1210069 tax ID	*
[Ref.: #66792]	Nocardia coubleae strain DSM 44960	356147.3	wgs	PATRIC	356147 tax ID	*
[Ref.: #66792]	Nocardia coubleae DSM 44960	2902498892	draft	JGI IMG/M	356147 tax ID	*
[Ref.: #66792]	Nocardia coubleae NBRC 108252	2731957729	draft	JGI IMG/M	1210069 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nocardia coubleae strain DSM 44960 PATRIC: 356147.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardia coubleae NBRC 108252 PATRIC: 1210069.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.515	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.589	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	59.332	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	90.091	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.9	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	88.9	no

Availability in culture collections External links

[Ref.: #12213]

Culture collection no.

DSM 44960, CIP 108996, OFN N12, JCM 15318, IFM 10920, NBRC 108252

[Ref.: #80073]

SI-ID 309472

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#41981 ; Curators of the CIP;

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#80073

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID309472.1 )

#118769 Collection of Institut Pasteur ; Curators of the CIP; CIP 108996

#28268

IJSEM 1482 2007 ( DOI 10.1099/ijs.0.64815-0 , PubMed 17625180 )

* These data were automatically processed and therefore are not curated

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Nocardia coubleae strain DSM 44960

Nocardia coubleae NBRC 108252

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