Streptomyces ruber (DSM 40304, ATCC 17754, CBS 228.65)

Name: Streptomyces ruber (DSM 40304, ATCC 17754, CBS 228.65)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16298

Type strain

Culture col. no. DSM 40304 ATCC 17754 CBS 228.65 IFO 14600 ISP 5304 14 more

NCBI tax ID(s) 83378

Special Collections DSMZ JCM KCTC Wink compendium JMRC

History DSMZ <- E. B. Shirling, ISP (Chainia rubra) <- M. J. Thirumlachar, HACC-143 JCM <-- KCC A-0131 <-- Y. Okami <-- ATCC 17754 <-- HACC 143.

Links

Streptomyces ruber DSM 40304 is a spore-forming bacterium that builds an aerial mycelium.

spore-forming genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 36719

ATCC 17754,IFO 14600,NCIB 10983,DSM 40304,JCM 3131,CCRC 12358,NCIMB 10983,NRRL B-5315,CBS 228.65,NBRC 14600,BCRC 12358,BCRC 15138,CCRC 15138,KCTC 19969,CGMCC 4.1925

@ref 20215

Last LPSN update 2026-05-29 08:28:45

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces ruber

Full scientific name Streptomyces ruber (Thirumalachar 1955) Goodfellow et al. 1986

Synonyms (1)

Chainia rubra

BacDive ID	Other strains from **Streptomyces ruber** (1)	Type strain
16299	S. ruber DSM 41025, IMRU 3348

Morphology

Cell morphology

@ref	Gram stain	Confidence	Motility
125439	positive	99.092
125439		92.543

Colony morphology

@ref	Colony color	Incubation period	Medium used
19435	Red brown	10-14 days	ISP 2
19435	Red	10-14 days	ISP 3
19435	Orange	10-14 days	ISP 4
19435	Red brown	10-14 days	ISP 5
19435	Orange	10-14 days	ISP 6
19435	Red brown	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19435	Aerial Mycelium	Red brown	ISP 2
19435	Aerial Mycelium	Red	ISP 3
19435	Aerial Mycelium	Red	ISP 4
19435	Aerial Mycelium	Red	ISP 5
19435			ISP 6
19435	Aerial Mycelium	Red	ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
9446	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
19435	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
19435	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:
19435	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
19435	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
19435	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
19435	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
9446	STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)	Medium recipe at MediaDive	Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
9446	positive	growth	28
19435	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.11

Spore formation

@ref	Spore description	Confidence
19435	Formation of spore chains: spira, spore surface: smooth
125439		91.173
125438		94.683

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19435	NaCl	positive	maximum	2.5 %

Observation

67770

Observationquinones: MK-9(H₈), MK-9(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19435	22599 ChEBI	arabinose	-
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
19435	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
19435	28757 ChEBI	fructose	+/-
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
19435	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
19435	29864 ChEBI	mannitol	+
19435	17268 ChEBI	myo-inositol	-
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
19435	16634 ChEBI	raffinose	-
19435	26546 ChEBI	rhamnose	+/-
19435	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
19435	18222 ChEBI	xylose	+

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
19435	-	-	-	-	-	-	-	+	-	+	+	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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9446	1	Risk group (German classification) According to TRBA 466
19435	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
66792	ASM1464807v1 assembly for Streptomyces ruber JCM 3131	scaffold	GCA_014648075	83378.9	2997563707	83378	58.58

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces ruber gene for 16S rRNA, partial sequence	AB018203	121	83378
20218	Streptomyces ruber gene for 16S rRNA, partial sequence, strain: NBRC 14600	AB184604	1417	83378
124043	Streptomyces ruber strain JCM 3131 16S ribosomal RNA gene, partial sequence.	MT760411	1354	83378

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1464807v1 assembly for Streptomyces ruber JCM 3131
NCBI: GCA_014648075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.11	no
125439	motility	BacteriaNetⓘ	no	92.54	no
125439	gram_stain	BacteriaNetⓘ	positive	99.09	no
125439	spore_formation	BacteriaNetⓘ	yes	91.17	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces ruber JCM 3131
NCBI: GCA_014648075.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.98	no
125438	anaerobic	anaerobicⓘ	no	97.01	no
125438	aerobic	aerobicⓘ	yes	86.54	no
125438	spore-forming	spore-formingⓘ	yes	94.68	yes
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	85.57	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Streptomyces phytophilus sp. nov., an endophytic actinobacterium with biosynthesis potential as an antibiotic producer.	Kaewkla O, Suriyachadkun C, Franco CMM.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005834	2023

References

#9446	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40304
#19435	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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#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 )
#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;
#68368	Automatically annotated from API 20E .
#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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Streptomyces ruber (DSM 40304, ATCC 17754, CBS 228.65)

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

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014648075

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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