Streptomyces echinoruber (DSM 41696, IFO 14238, JCM 5016)

Name: Streptomyces echinoruber (DSM 41696, IFO 14238, JCM 5016)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16335

Type strain

Culture col. no. DSM 41696 IFO 14238 JCM 5016 KCC S-0516 NBRC 14238 6 more

NCBI tax ID(s) 68898

Special Collections DSMZ JCM KCTC Wink compendium

History DSMZ <- NRRL <- Hoffmann-La-Roche Inc., X14077 JCM <-- KCC S-1016 <-- NRRL 8144 <-- Hoffmann-La Roche Inc.; X14077.

Links

Streptomyces echinoruber DSM 41696 is a spore-forming bacterium that builds an aerial mycelium and was isolated from soil.

spore-forming genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 307492

DSM 41696,IFO 14238,JCM 5016,NCIMB 12831,NRRL 8144,KCTC 9725,KCTC 9776,AS 4.1707,NBRC 14238,BCRC 16859,CCRC 16859,CGMCC 4.1707

@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 echinoruber

Full scientific name Streptomyces echinoruber Palleroni et al. 1981

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125439		95.267
125439		99.74	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
18713	Red	10-14 days	ISP 2
18713	Red	10-14 days	ISP 3
18713	Red	10-14 days	ISP 4
18713	Red	10-14 days	ISP 5
18713	Brown	10-14 days	ISP 6

Multicellular morphology

@ref	Complex name	Complex color	Medium name
18713	Aerial Mycelium	Grey	ISP 2
18713	Aerial Mycelium	Grey	ISP 3
18713	Aerial Mycelium	Grey	ISP 4
18713	Aerial Mycelium	White	ISP 5
18713			ISP 6
18713	Aerial Mycelium	Grey	ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
10478	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
18713	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
18713	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:
18713	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
18713	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
18713	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
10478	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)
10478	positive	growth	28
18713	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.45

Spore formation

@ref	Spore description	Confidence
18713	Formation of spore chains (retinaculiapetri), spore surface spiny
125439		97.391
125438		90.425

Compound production

@ref	Compound
10478	rubrolone
18713	Rubrolone

Halophily

@ref	Salt	Growth	Tested relation	Concentration
18713	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
67770	140148 ChEBI	rubrolone

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
18713	+	+	-	-	-	-	-	+	-	+	+	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

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
10478	soil	Argentina	ARG	Middle and South America
67770	Soil	Argentina	ARG	Middle and South America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18713	1	German classification According to TRBA 466
10478	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	ASM1465113v1 assembly for Streptomyces echinoruber JCM 5016	scaffold	GCA_014651135	68898.3	2997539458	68898	53.33
124043	ASM4264698v1 assembly for Streptomyces echinoruber JCM 5016	scaffold	GCA_042646985			68898	49.21

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces echinoruber gene for 16S ribosomal RNA, partial sequence, strain: JCM 5016	D44426	120	68898
20218	Streptomyces echinoruber strain NBRC 14238 16S ribosomal RNA gene, partial sequence	KC139252	1466	68898
124043	Streptomyces echinoruber strain JCM 5016 16S ribosomal RNA gene, partial sequence.	MT760643	706	68898

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1465113v1 assembly for Streptomyces echinoruber JCM 5016
NCBI: GCA_014651135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.45	no
125439	gram_stain	BacteriaNetⓘ	positive	99.74	no
125439	motility	BacteriaNetⓘ	no	95.27	no
125439	spore_formation	BacteriaNetⓘ	yes	97.39	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces echinoruber JCM 5016
NCBI: GCA_014651135.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.97	no
125438	anaerobic	anaerobicⓘ	no	96.15	no
125438	aerobic	aerobicⓘ	yes	87.30	no
125438	spore-forming	spore-formingⓘ	yes	90.43	yes
125438	thermophilic	thermophileⓘ	no	92.50	no
125438	flagellated	motile2+ⓘ	no	87.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Production of a novel red pigment, rubrolone, by Streptomyces echinoruber sp. nov. I. Taxonomy, fermentation and partial purification.	Palleroni NJ, Reichelt KE, Mueller D, Epps R, Tabenkin B, Bull DN, Schuep W, Berger J	J Antibiot (Tokyo)	10.7164/antibiotics.31.1218	1978

References

#10478	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 41696
#18713	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 )
#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 echinoruber (DSM 41696, IFO 14238, JCM 5016)

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

Compound production

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014651135

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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