Saccharothrix violaceirubra (DSM 45084, KCTC 19326, NBRC 102064)

Name: Saccharothrix violaceirubra (DSM 45084, KCTC 19326, NBRC 102064)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13490

Type strain

Strain Designation YU 692-1

Culture col. no. DSM 45084 KCTC 19326 NBRC 102064 YU 692-1 JCM 16955

NCBI tax ID(s) 413306

Special Collections DSMZ JCM KCTC Wink compendium Literature strains

Links

Saccharothrix violaceirubra YU 692-1 is an aerobe, spore-forming, mesophilic prokaryote that builds an aerial mycelium and was isolated from soil.

spore-forming Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 407888

KCTC 19326,NBRC 102064,JCM 16955,DSM 45084

@ref 20215

Last LPSN update 2025-12-16 09:50:06

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Saccharothrix

Species Saccharothrix violaceirubra

Full scientific name Saccharothrix violaceirubra Otoguro et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell shape
29009	positive	rod-shaped
125439	positive
125439

Colony morphology

@ref	Colony color	Incubation period	Medium used
20164	Saffron yellow (1017)	10-14 days	ISP 2
20164	Green beige (1000)	10-14 days	ISP 3
20164	Ivory (1014)	10-14 days	ISP 4
20164	Ivory (1014)	10-14 days	ISP 5
20164	Sand yellow (1002)	10-14 days	ISP 6
20164	Beige (1001)	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
20164	Aerial Mycelium	Sand yellow	ISP 2
20164	Aerial Mycelium	Oyster white	ISP 3
20164			ISP 4
20164			ISP 5
20164	Aerial Mycelium	Ivory	ISP 6
20164	Aerial Mycelium	Beige	ISP 7

Pigmentation

29009

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12326	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
12326	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
20164	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
20164	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:
20164	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
20164	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
20164	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
20164	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12326	positive	growth	28	mesophilic
20164	positive	optimum	28	mesophilic
29009	positive	growth	15-30
29009	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29009	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
29009
125439

Observation

67770

Observationquinones: MK-9(H₄), MK-9(H₈), MK-9(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity
20164	22599 ChEBI	arabinose	+/-
20164	62968 ChEBI	cellulose	-
20164	28757 ChEBI	fructose	-
20164	17234 ChEBI	glucose	+
29009	17234 ChEBI	glucose	+
29009	17306 ChEBI	maltose	+
20164	29864 ChEBI	mannitol	-
29009	37684 ChEBI	mannose	+
20164	17268 ChEBI	myo-inositol	+/-
20164	16634 ChEBI	raffinose	-
20164	26546 ChEBI	rhamnose	-
20164	17992 ChEBI	sucrose	+/-
29009	17992 ChEBI	sucrose	+
29009	27082 ChEBI	trehalose	+
20164	18222 ChEBI	xylose	-

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
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	-	3.4.21.4	from API zym
68382	valine arylamidase	+		from API zym

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
20164	not determinedn.d.	+	+	+	+	+	+	-	-	+	+	+	-	-	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12326	soil	Yamanashi prefecture	Japan	JPN	Asia
67770	Soil	Yamanashi Pref.	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12326	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	ASM1420375v1 assembly for Saccharothrix violaceirubra DSM 45084	contig	GCA_014203755	413306.3	2863357390	413306	77.94
124043	ASM3953734v1 assembly for Saccharothrix violaceirubra JCM 16955	scaffold	GCA_039537345			413306	59.87

Genome browser: GCA_014203755

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12326	Saccharothrix violaceirubra gene for 16S rRNA, partial sequence	AB284261	1470		413306

GC content

@ref	GC-content (mol%)	Method
12326	70.8	high performance liquid chromatography (HPLC)
29009	70.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Saccharothrix violaceirubra DSM 45084
NCBI: GCA_014203755

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.70	no
125439	motility	BacteriaNetⓘ	no	95.70	no
125439	gram_stain	BacteriaNetⓘ	positive	100.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Saccharothrix violaceirubra strain DSM 45084
PATRIC: 413306.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	85.34	yes
125438	anaerobic	anaerobicⓘ	no	95.23	yes
125438	spore-forming	spore-formingⓘ	yes	83.16	yes
125438	aerobic	aerobicⓘ	yes	88.26	yes
125438	thermophilic	thermophileⓘ	no	93.40	yes
125438	flagellated	motile2+ⓘ	no	63.43	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Saccharothrix violaceirubra sp. nov., isolated from soil and plant litter.	Otoguro M, Tamura T, Suzuki K, Hayakawa M	Int J Syst Evol Microbiol	10.1099/ijs.0.003723-0	2009

References

#12326	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45084
#20164	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 )
#29009	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 #25441 (see below)
#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;
#68382	Automatically annotated from API zym .
#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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Saccharothrix violaceirubra (DSM 45084, KCTC 19326, NBRC 102064)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014203755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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