Name: Nocardia miyunensis 117
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 10803

Type strain:

Species: Nocardia miyunensis

Strain Designation: 117

Culture col. no.: DSM 17685, AS 4.1904, CGMCC 4.1904, IFM 10632, JCM 12860, CIP 109011, NBRC 108239

Strain history: Y. Huang 117.

NCBI tax ID(s): 1210084 (strain), 282684 (species)

SI-ID 265618

CGMCC 4.1904, JCM 12860, DSM 17685, AS 4.1904, CIP 109011

Special Collections

Section

Nocardia miyunensis 117 is an aerobe, spore-forming, Gram-positive bacterium that builds an aerial mycelium and was isolated from pine-forest soil sample.

Gram-positive
rod-shaped
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 miyunensis**
	Full Scientific Name (LPSN)	Nocardia miyunensis Cui et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31480]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %90.578

[Ref.: #31480]	Cell shape	rod-shaped

[Ref.: #31480]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.5

[Ref.: #69285]	Colony color	Colourless
[Ref.: #69285]	Cultivation medium used	ISP 2

[Ref.: #69285]	Colony color	Colourless
[Ref.: #69285]	Cultivation medium used	ISP 4

[Ref.: #69285]	Colony color	Colourless
[Ref.: #69285]	Cultivation medium used	ISP 5

[Ref.: #69285]	Colony color	Colourless
[Ref.: #69285]	Cultivation medium used	ISP 7

[Ref.: #69285]	Colony color	Ivory (1014)
[Ref.: #69285]	Cultivation medium used	suter with tyrosine

[Ref.: #69285]	Colony color	Ivory (1014)
[Ref.: #69285]	Cultivation medium used	suter without tyrosine

[Ref.: #69285]	Colony color	Light ivory (1014)
[Ref.: #69285]	Cultivation medium used	ISP 3

[Ref.: #69285]	Colony color	Light ivory (1015)
[Ref.: #69285]	Cultivation medium used	ISP 6

[Ref.: #31480]	Pigment production	yes
[Ref.: #69285]	Pigment production	no
[Ref.: #69285]	Pigment name	Melanin
[Ref.: #69285]	Pigment production	yes
[Ref.: #69285]	Pigmentation color	Beige (1001)
[Ref.: #69285]	Pigment name	soluble pigment

[Ref.: #69285]	Multicellular complex forming ability	yes
[Ref.: #69285]	Multicellular complex name	Aerial mycelium
[Ref.: #69285]	Multicellular complex color	Pure white (9010)
[Ref.: #69285]	Medium Name (multicellularity)	ISP 2

[Ref.: #69285]	Multicellular complex forming ability	yes
[Ref.: #69285]	Multicellular complex name	Aerial mycelium
[Ref.: #69285]	Multicellular complex color	Pure white (9010)
[Ref.: #69285]	Medium Name (multicellularity)	ISP 3

[Ref.: #69285]	Multicellular complex forming ability	yes
[Ref.: #69285]	Multicellular complex name	Aerial mycelium
[Ref.: #69285]	Multicellular complex color	Pure white (9010)
[Ref.: #69285]	Medium Name (multicellularity)	ISP 4

[Ref.: #69285]	Multicellular complex forming ability	yes
[Ref.: #69285]	Multicellular complex name	Aerial mycelium
[Ref.: #69285]	Multicellular complex color	Pure white (9010)
[Ref.: #69285]	Medium Name (multicellularity)	ISP 5

[Ref.: #69285]	Multicellular complex forming ability	yes
[Ref.: #69285]	Multicellular complex name	Aerial mycelium
[Ref.: #69285]	Multicellular complex color	Pure white (9010)
[Ref.: #69285]	Medium Name (multicellularity)	ISP 6

[Ref.: #69285]	Multicellular complex forming ability	yes
[Ref.: #69285]	Multicellular complex name	Aerial mycelium
[Ref.: #69285]	Multicellular complex color	Pure white (9010)
[Ref.: #69285]	Medium Name (multicellularity)	ISP 7

[Ref.: #69285]	Multicellular complex forming ability	yes
[Ref.: #69285]	Multicellular complex name	Aerial mycelium
[Ref.: #69285]	Multicellular complex color	Cream (9001)
[Ref.: #69285]	Medium Name (multicellularity)	suter with tyrosine

[Ref.: #69285]	Multicellular complex forming ability	no
[Ref.: #69285]	Multicellular complex name	Aerial mycelium
[Ref.: #69285]	Medium Name (multicellularity)	suter without tyrosine

Multimedia content

[Ref.: #69285]

Caption:

Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69285]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

[Ref.: #69285]

Caption:

Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69285]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7127]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #7127]

Culture medium growth

[Ref.: #7127]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7127]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7127]	growth	28 °C
[Ref.: #31480]	growth	17-37 °C
[Ref.: #31480]	optimum	27 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #31480]			optimum	7
[Ref.: #31480]			growth	4.5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7127]	Oxygen tolerance	aerobe
[Ref.: #31480]	Oxygen tolerance	aerobe

[Ref.: #69481]

Ability of spore formation

yes Confidence in %98

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69285]		NaCl		growth	0-10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31480]	arabinose ChEBI	+	carbon source
[Ref.: #69285]	arabinose ChEBI	+/-	growth
[Ref.: #31480]	cellobiose ChEBI	+	carbon source
[Ref.: #69285]	cellulose ChEBI	-	growth
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #31480]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #31480]	fructose ChEBI	+	carbon source
[Ref.: #69285]	fructose ChEBI	+/-	growth
[Ref.: #31480]	galactose ChEBI	+	carbon source
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #31480]	glucose ChEBI	+	carbon source
[Ref.: #69285]	glucose ChEBI	+	growth
[Ref.: #31480]	glycerol ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #69285]	inositol ChEBI	-	growth
[Ref.: #31480]	lactose ChEBI	+	carbon source
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #31480]	maltose ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #31480]	mannose ChEBI	+	carbon source
[Ref.: #69285]	mannose ChEBI	+	growth
[Ref.: #31480]	myo-inositol ChEBI	+	carbon source
[Ref.: #31480]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #31480]	raffinose ChEBI	+	carbon source
[Ref.: #69285]	raffinose ChEBI	-	growth
[Ref.: #31480]	rhamnose ChEBI	+	carbon source
[Ref.: #69285]	rhamnose ChEBI	-	growth
[Ref.: #31480]	sorbitol ChEBI	+	carbon source
[Ref.: #31480]	sucrose ChEBI	+	carbon source
[Ref.: #69285]	sucrose ChEBI	+/-	growth
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #31480]	trehalose ChEBI	+	carbon source
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #31480]	xylose ChEBI	+	carbon source
[Ref.: #69285]	xylose ChEBI	+/-	growth
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	-	3.1.3.1	* from API Coryne
[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.: #68379]	alpha-glucosidase	+	3.2.1.20	* from API Coryne, API zym
[Ref.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne, API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68379]	beta-glucosidase	-	3.2.1.21	* from API Coryne
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #31480]	catalase	+	1.11.1.6
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne, API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

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

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #69285]	3779	+	-	-	-	-	-	+	-	-	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

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.: #69285]	5963	not determinedn.d.	+/-	+	+	-	+	+/-	+/-	-	-	+	+/-	-	-	-	+	+	-	+/-	-

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

[Ref.: #7127]	Sample type/isolated from	pine-forest soil sample
[Ref.: #7127]	Geographic location (country and/or sea, region)	Miyun County, Beijing
[Ref.: #7127]	Country	China
[Ref.: #7127]	Country ISO 3 Code	CHN
[Ref.: #7127]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Pine-forest soil (about pH 5.5)
[Ref.: #67770]	Geographic location (country and/or sea, region)	Miyun County, Beijing
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ376179 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples
Soil Samples	8
Animal Samples	5
Plant Samples	1
Total Samples	14

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

[Ref.: #7127]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #7127]	Nocardia miyunensis strain 117 16S ribosomal RNA gene, partial sequence	AY639901	1405	GenBank ENA	282684 tax ID
[Ref.: #20218]	Nocardia miyunensis 16S ribosomal RNA gene, partial sequence	GQ376179	1439	GenBank ENA	282684 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardia miyunensis NBRC 108239	GCA_001613065	contig	GenBank ENA	1210084 tax ID
[Ref.: #66792]	Nocardia miyunensis NBRC 108239	1210084.4	wgs	PATRIC	1210084 tax ID	*
[Ref.: #66792]	Nocardia miyunensis NBRC 108239	2731957742	draft	JGI IMG/M	1210084 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 miyunensis NBRC 108239 PATRIC: 1210084.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	98	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardia miyunensis NBRC 108239 PATRIC: 1210084.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.578	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.824	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	61.731	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.179	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.478	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90.5	no

Availability in culture collections External links

[Ref.: #7127]

Culture collection no.

DSM 17685, AS 4.1904, CGMCC 4.1904, IFM 10632, JCM 12860, CIP 109011, NBRC 108239

[Ref.: #80068]

SI-ID 265618

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardia albiluteola sp. nov., a novel lignin-degrading actinobacterium isolated from rhizosphere soil of pumpkin.	Shan Q, Han C, Zhao J, Yu B, Jiang M, Liu T, Wang X, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.005305	2022	*
Phylogeny	Nocardia macrotermitis sp. nov. and Nocardia aurantia sp. nov., isolated from the gut of the fungus-growing termite Macrotermes natalensis.	Benndorf R, Schwitalla JW, Martin K, de Beer ZW, Vollmers J, Kaster AK, Poulsen M, Beemelmanns C	Int J Syst Evol Microbiol	10.1099/ijsem.0.004398	2020	*
Phylogeny	Nocardia zhihengii sp. nov., an actinobacterium isolated from rhizosphere soil of Psammosilene tunicoides.	Huang MJ, Xiao M, Rao MPN, Cheng T, Yang YY, Alkhalifah DHM, Hozzein WN, Huang HQ, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-018-1107-8	2018	*
Phylogeny	Nocardia jiangxiensis sp. nov. and Nocardia miyunensis sp. nov., isolated from acidic soils.	Cui Q, Wang L, Huang Y, Liu Z, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijs.0.63644-0	2005	*

References

#7127

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17685

#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 )

#31480

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 #27778 (see below)

#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;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69285

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 .

#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 )

#80068

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-ID265618.1 )

#27778

IJSEM 1921 2005 ( DOI 10.1099/ijs.0.63644-0 , PubMed 16166688 )

* These data were automatically processed and therefore are not curated

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Nocardia miyunensis NBRC 108239

Nocardia miyunensis NBRC 108239

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