Nocardia miyunensis (DSM 17685, AS 4.1904, CGMCC 4.1904)

Name: Nocardia miyunensis (DSM 17685, AS 4.1904, CGMCC 4.1904)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10803

Type strain

Strain Designation 117

Culture col. no. DSM 17685 AS 4.1904 CGMCC 4.1904 IFM 10632 JCM 12860 3 more

NCBI tax ID(s) 1210084 282684

Special Collections DSMZ JCM CIP Wink compendium Literature strains

History DSMZ <- M. Goodfellow <- Y. Huang; 117 JCM <-- Y. Huang 117.

Links

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

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

Name and taxonomic classification

SI-ID 265618

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

@ref 20215

Last LPSN update 2026-05-29 08:27:25

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Nocardia

Species Nocardia miyunensis

Full scientific name Nocardia miyunensis Cui et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31480	positive	rod-shaped
125438			90.5
125438	positive		90.578
125439	positive		92.778

Colony morphology

@ref	Colony color	Medium used
69285	Colourless	ISP 2
69285	Colourless	ISP 4
69285	Colourless	ISP 5
69285	Colourless	ISP 7
69285	Ivory (1014)	suter with tyrosine
69285	Ivory (1014)	suter without tyrosine
69285	Light ivory (1014)	ISP 3
69285	Light ivory (1015)	ISP 6

Multicellular morphology

@ref	Complex name	Complex color	Medium name
69285	Aerial mycelium	Pure white (9010)	ISP 2
69285	Aerial mycelium	Pure white (9010)	ISP 3
69285	Aerial mycelium	Pure white (9010)	ISP 4
69285	Aerial mycelium	Pure white (9010)	ISP 5
69285	Aerial mycelium	Pure white (9010)	ISP 6
69285	Aerial mycelium	Pure white (9010)	ISP 7
69285	Aerial mycelium	Cream (9001)	suter with tyrosine
69285	Aerial mycelium		suter without tyrosine

Pigmentation

@ref	Color	Name
31480
69285		melanin pigment
69285	Beige (1001)	soluble pigment

Multimedia

@ref:	69285
multimedia content:	DSM_17685_image3.jpeg
multimedia.multimedia content:	DSM_17685_image3.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69285
multimedia content:	DSM_17685_image4.jpeg
multimedia.multimedia content:	DSM_17685_image4.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7127	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

Culture temp

@ref	Growth	Type	Temperature (°C)
7127	positive	growth	28
31480	positive	growth	17-37
31480	positive	optimum	27
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31480	positive	optimum	7
31480	positive	growth	4.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7127	aerobe
31480	aerobe
125439	obligate aerobe	96.062

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69285	NaCl	positive	growth	0-10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31480	22599 ChEBI	arabinose	+	carbon source
69285	22599 ChEBI	arabinose	+/-	growth
31480	17057 ChEBI	cellobiose	+	carbon source
69285	62968 ChEBI	cellulose	-	growth
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
31480	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
31480	28757 ChEBI	fructose	+	carbon source
69285	28757 ChEBI	fructose	+/-	growth
31480	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
31480	17234 ChEBI	glucose	+	carbon source
69285	17234 ChEBI	glucose	+	growth
31480	17754 ChEBI	glycerol	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
31480	17716 ChEBI	lactose	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
31480	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
31480	37684 ChEBI	mannose	+	carbon source
69285	37684 ChEBI	mannose	+	growth
31480	17268 ChEBI	myo-inositol	+	carbon source
69285	17268 ChEBI	myo-inositol	-	growth
31480	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
31480	16634 ChEBI	raffinose	+	carbon source
69285	16634 ChEBI	raffinose	-	growth
31480	26546 ChEBI	rhamnose	+	carbon source
69285	26546 ChEBI	rhamnose	-	growth
31480	30911 ChEBI	sorbitol	+	carbon source
31480	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69285	17992 ChEBI	sucrose	+/-	growth
31480	27082 ChEBI	trehalose	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
31480	18222 ChEBI	xylose	+	carbon source
69285	18222 ChEBI	xylose	+/-	growth

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	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	beta-galactosidase	-	3.2.1.23	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
31480	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	lipase (C 14)	-		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
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
68379	urease	-	3.5.1.5	from API Coryne

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
69285	+	-	-	-	-	-	+	-	-	-	-	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
69285	not determinedn.d.	+/-	+	+	-	+	+/-	+/-	-	-	+	+/-	-	-	-	+	+	-	+/-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7127	pine-forest soil sample	Miyun County, Beijing	China	CHN	Asia
67770	Pine-forest soil (about pH 5.5)	Miyun County, Beijing	China	CHN	Asia

Taxonmaps

69479

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

Aquatic Samples	0
Soil Samples	8
Animal Samples	5
Plant Samples	1
Total Samples	14

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7127	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	ASM161306v1 assembly for Nocardia miyunensis NBRC 108239	contig	GCA_001613065	1210084.4	2731957742	1210084	34.18

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Nocardia miyunensis 16S ribosomal RNA gene, partial sequence	GQ376179	1439		282684
7127	Nocardia miyunensis strain 117 16S ribosomal RNA gene, partial sequence	AY639901	1405		282684

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM161306v1 assembly for Nocardia miyunensis NBRC 108239
NCBI: GCA_001613065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.06	no
125439	gram_stain	BacteriaNetⓘ	positive	92.78	no
125439	spore_formation	BacteriaNetⓘ	yes	44.45	no
125439	motility	BacteriaNetⓘ	no	89.56	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia miyunensis NBRC 108239
PATRIC: 1210084.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.58	yes
125438	anaerobic	anaerobicⓘ	no	94.82	yes
125438	spore-forming	spore-formingⓘ	yes	61.73	no
125438	aerobic	aerobicⓘ	yes	85.18	yes
125438	thermophilic	thermophileⓘ	no	96.48	no
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov.	Nouioui I, Ha SM, Baek I, Chun J, Goodfellow M.	BMC Genomics	10.1186/s12864-021-08257-y	2022
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 )
#27778	IJSEM 1921 2005 ( DOI 10.1099/ijs.0.63644-0 , PubMed 16166688 )
#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
#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 .
#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 miyunensis (DSM 17685, AS 4.1904, CGMCC 4.1904)

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

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_001613065

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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