Name: Saccharothrix violaceirubra YU 692-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13490

Type strain:

Species: Saccharothrix violaceirubra

Strain Designation: YU 692-1

Culture col. no.: DSM 45084, KCTC 19326, NBRC 102064, JCM 16955

Strain history: KCTC 19326 <-- M. Otoguro <-- M. Hayakawa YU 692-1.

NCBI tax ID(s): 413306 (species)

SI-ID 407888

DSM 45084

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Saccharothrix*
	Species	**Saccharothrix violaceirubra**
	Full Scientific Name (LPSN)	Saccharothrix violaceirubra Otoguro et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29009]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29009]	Cell shape	rod-shaped

[Ref.: #29009]	Motility	no

[Ref.: #20164]	Colony color	Saffron yellow (1017)
[Ref.: #20164]	Incubation period	10-14 days
[Ref.: #20164]	Cultivation medium used	ISP 2

[Ref.: #20164]	Colony color	Green beige (1000)
[Ref.: #20164]	Incubation period	10-14 days
[Ref.: #20164]	Cultivation medium used	ISP 3

[Ref.: #20164]	Colony color	Ivory (1014)
[Ref.: #20164]	Incubation period	10-14 days
[Ref.: #20164]	Cultivation medium used	ISP 4

[Ref.: #20164]	Colony color	Ivory (1014)
[Ref.: #20164]	Incubation period	10-14 days
[Ref.: #20164]	Cultivation medium used	ISP 5

[Ref.: #20164]	Colony color	Sand yellow (1002)
[Ref.: #20164]	Incubation period	10-14 days
[Ref.: #20164]	Cultivation medium used	ISP 6

[Ref.: #20164]	Colony color	Beige (1001)
[Ref.: #20164]	Incubation period	10-14 days
[Ref.: #20164]	Cultivation medium used	ISP 7

[Ref.: #29009]

Pigment production

yes

[Ref.: #20164]	Multicellular complex forming ability	yes
[Ref.: #20164]	Multicellular complex name	Aerial Mycelium
[Ref.: #20164]	Multicellular complex color	Sand yellow
[Ref.: #20164]	Medium Name (multicellularity)	ISP 2

[Ref.: #20164]	Multicellular complex forming ability	yes
[Ref.: #20164]	Multicellular complex name	Aerial Mycelium
[Ref.: #20164]	Multicellular complex color	Oyster white
[Ref.: #20164]	Medium Name (multicellularity)	ISP 3

[Ref.: #20164]	Multicellular complex forming ability	no
[Ref.: #20164]	Medium Name (multicellularity)	ISP 4

[Ref.: #20164]	Multicellular complex forming ability	no
[Ref.: #20164]	Medium Name (multicellularity)	ISP 5

[Ref.: #20164]	Multicellular complex forming ability	yes
[Ref.: #20164]	Multicellular complex name	Aerial Mycelium
[Ref.: #20164]	Multicellular complex color	Ivory
[Ref.: #20164]	Medium Name (multicellularity)	ISP 6

[Ref.: #20164]	Multicellular complex forming ability	yes
[Ref.: #20164]	Multicellular complex name	Aerial Mycelium
[Ref.: #20164]	Multicellular complex color	Beige
[Ref.: #20164]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #12326]

Culture medium

STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)

[Ref.: #12326]

Culture medium growth

[Ref.: #12326]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12326]

Culture medium composition

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[Ref.: #12326]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #12326]

Culture medium growth

[Ref.: #12326]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12326]

Culture medium composition

expand / minimize

[Ref.: #20164]

Culture medium

ISP 2

[Ref.: #20164]

Culture medium growth

[Ref.: #20164]

Culture medium composition

expand / minimize

[Ref.: #20164]

Culture medium

ISP 3

[Ref.: #20164]

Culture medium growth

[Ref.: #20164]

Culture medium composition

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[Ref.: #20164]

Culture medium

ISP 4

[Ref.: #20164]

Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #20164]

Culture medium

ISP 5

[Ref.: #20164]

Culture medium growth

[Ref.: #20164]

Culture medium composition

expand / minimize

[Ref.: #20164]

Culture medium

ISP 6

[Ref.: #20164]

Culture medium growth

[Ref.: #20164]

Culture medium composition

expand / minimize

[Ref.: #20164]

Culture medium

ISP 7

[Ref.: #20164]

Culture medium growth

[Ref.: #20164]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #12326]	growth	28 °C
[Ref.: #20164]	optimum	28 °C
[Ref.: #29009]	growth	15-30 °C
[Ref.: #29009]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #12326]	Temperature range	mesophilic
[Ref.: #20164]	Temperature range	mesophilic
[Ref.: #29009]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29009]

Oxygen tolerance

aerobe

[Ref.: #29009]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[Ref.: #67770]

Observation

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

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #20164]	arabinose ChEBI	+/-
[Ref.: #20164]	cellulose ChEBI	-
[Ref.: #20164]	fructose ChEBI	-
[Ref.: #20164]	glucose ChEBI	+
[Ref.: #29009]	glucose ChEBI	+	carbon source
[Ref.: #29009]	maltose ChEBI	+	carbon source
[Ref.: #20164]	mannitol ChEBI	-
[Ref.: #29009]	mannose ChEBI	+	carbon source
[Ref.: #20164]	myo-inositol ChEBI	+/-
[Ref.: #20164]	raffinose ChEBI	-
[Ref.: #20164]	rhamnose ChEBI	-
[Ref.: #20164]	sucrose ChEBI	+/-
[Ref.: #29009]	sucrose ChEBI	+	carbon source
[Ref.: #29009]	trehalose ChEBI	+	carbon source
[Ref.: #20164]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #20164]	945	not determinedn.d.	+	+	+	+	+	+	-	-	+	+	+	-	-	-	+	-	+	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #12326]	Sample type/isolated from	soil
[Ref.: #12326]	Geographic location (country and/or sea, region)	Yamanashi prefecture
[Ref.: #12326]	Country	Japan
[Ref.: #12326]	Country ISO 3 Code	JPN
[Ref.: #12326]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yamanashi Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #12326]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #12326]	Saccharothrix violaceirubra gene for 16S rRNA, partial sequence	AB284261	1470	ENA	413306 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Saccharothrix violaceirubra DSM 45084	GCA_014203755	contig	GenBank	413306 tax ID	*
[Ref.: #66792]	Saccharothrix violaceirubra strain DSM 45084	413306.3	wgs	PATRIC	413306 tax ID	*
[Ref.: #66792]	Saccharothrix violaceirubra DSM 45084	2863357390	draft	JGI IMG/M	413306 tax ID	*

[Ref.: #12326]	GC-content	70.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29009]	GC-content	70.8 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Saccharothrix violaceirubra strain DSM 45084 PATRIC: 413306.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Saccharothrix violaceirubra strain DSM 45084 PATRIC: 413306.3
[Ref.: #69480]	gram-positive	yes	88.632	no
[Ref.: #69480]	anaerobic	no	99.091	no
[Ref.: #69480]	halophile	no	94.14	no
[Ref.: #69480]	spore-forming	yes	91.893	yes
[Ref.: #69480]	glucose-util	yes	88.099	yes
[Ref.: #69480]	aerobic	yes	88.053	no
[Ref.: #69480]	flagellated	no	90.77	no
[Ref.: #69480]	thermophile	no	96.398	yes
[Ref.: #69480]	motile	no	57.86	yes
[Ref.: #69480]	glucose-ferment	no	90.843	no

Availability in culture collections External links

[Ref.: #12326]

Culture collection no.

DSM 45084, KCTC 19326, NBRC 102064, JCM 16955

[Ref.: #82682]

SI-ID 407888

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82682

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID407888.1 )

#25441

IJSEM 1504 2009 ( DOI 10.1099/ijs.0.003723-0 , PubMed 19502343 )

* These data were automatically processed and therefore are not curated

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Saccharothrix violaceirubra strain DSM 45084

Saccharothrix violaceirubra strain DSM 45084

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