Streptomyces violaceoruber (DSM 40421, ATCC 19830, CBS 679.72)

Name: Streptomyces violaceoruber (DSM 40421, ATCC 19830, CBS 679.72)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 15103

Type strain

Culture col. no. DSM 40421 ATCC 19830 CBS 679.72 IFO 13378 INMI 20-41 11 more

NCBI tax ID(s) 1935

Special Collections DSMZ JCM KCTC Wink compendium

History DSMZ <- E.B. Shirling, ISP <- N.A. Krassilnikov, INMI JCM <-- KCC S-0739 <-- IFO 13378 <-- SAJ <-- ISP 5421 <-- INMI 20-41.

Links

Streptomyces violaceoruber DSM 40421 is a spore-forming bacterium that builds an aerial mycelium.

spore-forming genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 76171

ATCC 19830,DSM 40421,IFO 13378,JCM 4739,NCIMB 10042,NRRL B-12348,VKM Ac-98,NCIB 10042,AS 4.1594,NBRC 13378,BCRC 16237,CCRC 16237,KCTC 19065,CGMCC 4.1594,VTT E-073027,CBS 679.72

@ref 20215

Last LPSN update 2026-05-29 08:28:27

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces violaceoruber

Full scientific name Streptomyces violaceoruber (Waksman and Curtis 1916) Pridham 1970 (Approved Lists 1980)

Synonyms (13)

"Actinomyces coelescens"
"Actinomyces violaceolatus"
"Actinomyces anthocyanicus"
Streptomyces humiferus
Streptomyces coelescens
Streptomyces anthocyanicus
Streptomyces tricolor
Streptomyces violaceolatus
Actinopycnidium caeruleum
"Actinomyces tricolor"
"Actinomyces violaceusruber"
"Actinomyces roseodiastaticus"
Streptomyces roseodiastaticus

BacDive ID	Other strains from **Streptomyces violaceoruber** (17)	Type strain
16080	S. violaceoruber DSM 40049, ATCC 14980, ATCC 19816, ATCC 3355, ... (type strain)
16081	S. violaceoruber A3(2), DSM 40783, JCM 4979, KCC S-0979, LBG ...
16082	S. violaceoruber B 241, DSM 40687
16084	S. violaceoruber DSM 41006, IMRU 3033
16085	S. violaceoruber DSM 41242, IMRU 3941, NRRL B-1257
16086	S. violaceoruber DSM 41244, IMRU 3943, NRRL B-1689
16087	S. violaceoruber DSM 41245, IMRU 3944, NRRL B-2787
16088	S. violaceoruber DSM 41246, IMRU 3945, NRRL B-3034
16089	S. violaceoruber 33C, ID 3844, DSM 41733
16090	S. violaceoruber Actino 7, DSM 41822
126467	S. violaceoruber ST033551(HKI), GT20051132, HKI 0475
126516	S. violaceoruber ST026834(HKI), Lorenz Actino7, GT20024038,
126517	S. violaceoruber ST004038,
126518	S. violaceoruber ST002898,
164994	S. violaceoruber JCM 4691, IFO 15731, NBRC 15731
176653	S. violaceoruber DSM 41013, IMRU 3047
176654	S. violaceoruber DSM 41017, IMRU 3071

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125439		91.578
125439		98.225	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
19452	Red	10-14 days	ISP 2
19452	Red	10-14 days	ISP 3
19452	Red	10-14 days	ISP 4
19452	Brown	10-14 days	ISP 5
19452	Beige	10-14 days	ISP 6
19452	Red	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19452	Aerial Mycelium	Grey	ISP 2
19452	Aerial Mycelium	White	ISP 3
19452			ISP 4
19452	Aerial Mycelium	White	ISP 5
19452			ISP 6
19452	Aerial Mycelium	White	ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
9530	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
19452	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
19452	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:
19452	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
19452	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
19452	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
19452	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
9530	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

Culture temp

@ref	Growth	Type	Temperature (°C)
9530	positive	growth	28
19452	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.248
125439	obligate aerobe	98.429

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
19452	Formation of spore chains: rectiflixibilis, spore surface: smooth	spore
125438				92.452

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19452	NaCl	positive	maximum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	gelatinase	+		from API 20E
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	+	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
19452	+	+	+	+	+	-	+	-	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence AY999786 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	991
Soil Samples	2201
Animal Samples	1970
Plant Samples	240
Total Samples	5402

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9530	1	Risk group (German classification) According to TRBA 466
19452	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	ASM1465079v1 assembly for Streptomyces anthocyanicus JCM 4739	scaffold	GCA_014650795	68189.4	8109647708	68174	63.3

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces coelescens 16S ribosomal RNA, partial sequence	AF503496	1515	68189
20218	Streptomyces coelescens strain DSM 40421 16S ribosomal RNA gene, partial sequence	GU383132	780	68189
20218	Streptomyces coelescens strain JCM 4739 16S ribosomal RNA gene, partial sequence	AY999761	1429	68189
20218	Streptomyces anthocyanicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4739	D44323	121	68189
20218	Streptomyces anthocyanicus gene for 16S rRNA, partial sequence, strain: NBRC 13378	AB184365	1478	68189
20218	Streptomyces coelescens strain NRRL B-12348 16S ribosomal RNA gene, partial sequence	AY999786	1495	68189
124043	Streptomyces coelescens strain JCM 4739 16S ribosomal RNA gene, partial sequence.	MT760605	1360	68174

GC content

@ref	GC-content (mol%)	Method
67770	72.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1465079v1 assembly for Streptomyces anthocyanicus JCM 4739
NCBI: GCA_014650795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	98.23	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.43	no
125439	motility	BacteriaNetⓘ	no	91.58	no
125439	spore_formation	BacteriaNetⓘ	yes	81.03	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces coelescens strain JCM 4739
PATRIC: 68189.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.27	no
125438	anaerobic	anaerobicⓘ	no	97.89	no
125438	spore-forming	spore-formingⓘ	yes	92.45	no
125438	aerobic	aerobicⓘ	yes	90.25	no
125438	thermophilic	thermophileⓘ	no	95.00	no
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Resolution of housekeeping gene sequences used in MLSA for the genus Streptomyces and reclassification of Streptomyces anthocyanicus and Streptomyces tricolor as heterotypic synonyms of Streptomyces violaceoruber.	Komaki H.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005370	2022
Phylogeny	Reclassification of 15 Streptomyces species as synonyms of Streptomyces albogriseolus, Streptomyces althioticus, Streptomyces anthocyanicus, Streptomyces calvus, Streptomyces griseoincarnatus, Streptomyces mutabilis, Streptomyces pilosus or Streptomyces rochei.	Komaki H.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004718	2019
Phylogeny	Genetic homologies among Streptomyces violaceoruber strains.	Monson AM, Bradley SG, Enquist LW, Cruces G.	J Bacteriol	10.1128/jb.99.3.702-706.1969	1969

References

#9530	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40421
#19452	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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#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 .
#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 )

Content

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Streptomyces violaceoruber (DSM 40421, ATCC 19830, CBS 679.72)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014650795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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