Virgisporangium aurantiacum (DSM 44794, CCUG 46559, CIP 107212)

Name: Virgisporangium aurantiacum (DSM 44794, CCUG 46559, CIP 107212)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8036

Type strain

Strain Designation Yu 438-5

Culture col. no. DSM 44794 CCUG 46559 CIP 107212 IFO 16421 JCM 11002 5 more

NCBI tax ID(s) 175570

Special Collections DSMZ CCUG JCM KCTC CIP Wink compendium

Links

Virgisporangium aurantiacum Yu 438-5 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil vegetable field.

Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 101058

IFO 16421,JCM 11002,KCTC 13916,CCUG 46559,CIP 107212,NBRC 16421,DSM 44794,BCRC 16331,CCRC 16331

@ref 20215

Last LPSN update 2025-12-16 09:48:44

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Virgisporangium

Species Virgisporangium aurantiacum

Full scientific name Virgisporangium aurantiacum corrig. Tamura et al. 2001

Synonyms (1)

Virgosporangium aurantiacum

Morphology

Cell morphology

@ref	Gram stain
67771	positive
116559	positive
125439	positive

Colony morphology

@ref	Colony color	Medium used
69363	Deep orange (2011)	ISP 6
69363	Clay brown (8003)	ISP 7
69363	Bright red orange (2008)	ISP 3
69363	Bright red orange (2008)	ISP 4
69363	Bright red orange (2008)	ISP 5
69363	Bright red orange (2008)	ISP 2
69363	Yellow orange (2000)	suter without tyrosine
69363	Yellow orange (2000), clay brown (8003)	suter with tyrosine
116559

Multicellular morphology

@ref	Complex name	Medium name
69363	Aerial mycelium	ISP 2
69363	Aerial mycelium	ISP 3
69363	Aerial mycelium	ISP 4
69363	Aerial mycelium	ISP 5
69363	Aerial mycelium	ISP 6
69363	Aerial mycelium	ISP 7
69363	Aerial mycelium	suter with tyrosine
69363	Aerial mycelium	suter without tyrosine

Pigmentation

@ref	Production	Name
69363		Melanin
69363		soluble pigment

Multimedia

@ref:	11981
multimedia content:	DSM_44794.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44794.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

@ref:	69363
multimedia content:	DSM_44794_image3.jpeg
multimedia.multimedia content:	DSM_44794_image3.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69363
multimedia content:	DSM_44794_image4.jpeg
multimedia.multimedia content:	DSM_44794_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	Medium link	Composition
11981	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
38193	MEDIUM 366 - for Actinoalloteichus cyanogriseus		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
11981	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
116559	CIP Medium 366	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11981	positive	growth	28	mesophilic
38193	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
67771	positive	growth	28	mesophilic
116559	positive	growth	10-30
116559	negative	growth	37
116559	negative	growth	41
116559	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
67771	aerobe
116559	obligate aerobe
125439	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69363	NaCl	positive	growth	0 %
116559	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: MK-10(H₈), MK-10(H₄), MK-10(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69363	22599 ChEBI	arabinose	+	growth
69363	62968 ChEBI	cellulose	+/-	growth
116559	16947 ChEBI	citrate	-	carbon source
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
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
116559	4853 ChEBI	esculin	+	hydrolysis
69363	28757 ChEBI	fructose	+	growth
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
69363	17234 ChEBI	glucose	+	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
116559	606565 ChEBI	hippurate	-	hydrolysis
69363	17268 ChEBI	inositol	+/-	growth
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69363	37684 ChEBI	mannose	+	growth
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
116559	17632 ChEBI	nitrate	-	reduction
116559	17632 ChEBI	nitrate	-	respiration
116559	16301 ChEBI	nitrite	-	reduction
69363	16634 ChEBI	raffinose	+	growth
69363	26546 ChEBI	rhamnose	+	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69363	17992 ChEBI	sucrose	+	growth
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
69363	18222 ChEBI	xylose	+	growth

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
116559	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116559	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
116559	15688 ChEBI	acetoin	-
116559	17234 ChEBI	glucose

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
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
116559	amylase	+
116559	beta-galactosidase	+	3.2.1.23
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
116559	caseinase	+	3.4.21.50
116559	catalase	+	1.11.1.6
116559	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116559	gamma-glutamyltransferase	+	2.3.2.2
116559	gelatinase	+
68379	gelatinase	+		from API Coryne
116559	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116559	lipase	-
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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116559	oxidase	-
116559	phenylalanine ammonia-lyase	-	4.3.1.24
116559	protease	+
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
116559	tryptophan deaminase	-
116559	tween esterase	+
116559	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

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
69363	+	-	+	+	-	+	+	-	+	-	+	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
69363	not determinedn.d.	+	+	+	-	+	+	+/-	+	+	+	+	+	+	-	+	+	+	+	-
116559	-	+	+	+	-	+	+	-	-	-	+	+	+	+	-	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
11981	soil vegetable field	Japan	JPN	Asia
67770	Soil of vegetable field	Japan	JPN	Asia
67771	From soil	Japan	JPN	Asia
116559	Environment, Soil, vegetable field	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11981	1	Risk group (German classification) According to TRBA 466
20120	1	German classification According to TRBA 466
116559	1	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
66792	ASM1686363v1 assembly for Virgisporangium aurantiacum NBRC 16421	contig	GCA_016863635	175570.3	2993804794	175570	25.57
124043	ASM3952554v1 assembly for Virgisporangium aurantiacum JCM 11002	scaffold	GCA_039525545			175570

Genome browser: GCA_016863635

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11981	Virgosporangium aurantiacum gene for 16S rRNA, partial sequence, strain:YU438-5	AB006169	1469		175570

GC content

@ref	GC-content (mol%)
11981	71
67770	71

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Virgisporangium aurantiacum NBRC 16421
NCBI: GCA_016863635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	75.50	no
125439	motility	BacteriaNetⓘ	no	83.30	no
125439	gram_stain	BacteriaNetⓘ	positive	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Virgisporangium aurantiacum strain NBRC 16421
PATRIC: 175570.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.45	yes
125438	anaerobic	anaerobicⓘ	no	93.61	no
125438	spore-forming	spore-formingⓘ	yes	83.92	no
125438	aerobic	aerobicⓘ	yes	85.85	no
125438	thermophilic	thermophileⓘ	no	95.00	no
125438	flagellated	motile2+ⓘ	no	66.50	no

Literature

References

#11981	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44794
#20120	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 )
#38193	; 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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69363	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#116559	Collection of Institut Pasteur ; Curators of the CIP; CIP 107212
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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