Name: Streptomyces rishiriensis 404Y3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 15552

Type strain:

Species: Streptomyces rishiriensis

Strain Designation: 404Y3

Culture col. no.: DSM 40489, ATCC 14812, CBS 708.72, IFO 13407, ISP 5489, JCM 4821, NBRC 13407, RIA 1368, BCRC 12333, CGMCC 4.1793, NCIMB 11890, NRRL B-3239, VKM Ac-1188

Strain history: KCC S-0821 <-- IFO 13407 <-- SAJ <-- ISP 5489 <-- ATCC 14812 <-- Banyu Res. Labs.; 404Y3.

NCBI tax ID(s): 68264 (species)

SI-ID 389317

ATCC 14812, IFO 13407, NCIB 11890, DSM 40489, JCM 4821, CCRC 12333, NCIMB 11890, NRRL B-3239, VKM Ac-1188, CBS 708.72, IMET 43843, NBRC 13407, BCRC 12333, CGMCC 4.1793, LMG 20297

Special Collections

Other strains from Streptomyces rishiriensis

Section

Streptomyces rishiriensis 404Y3 is a spore-forming bacterium that builds an aerial mycelium and produces antibiotic compounds.

antibiotic compound production
spore-forming
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	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Streptomyces*
	Species	**Streptomyces rishiriensis**
	Full Scientific Name (LPSN)	Streptomyces rishiriensis Kawaguchi et al. 1965 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %90.939

[Ref.: #19464]	Colony color	Brown
[Ref.: #19464]	Incubation period	10-14 days
[Ref.: #19464]	Cultivation medium used	ISP 2

[Ref.: #19464]	Colony color	Yellow
[Ref.: #19464]	Incubation period	10-14 days
[Ref.: #19464]	Cultivation medium used	ISP 3

[Ref.: #19464]	Colony color	Beige
[Ref.: #19464]	Incubation period	10-14 days
[Ref.: #19464]	Cultivation medium used	ISP 4

[Ref.: #19464]	Colony color	Yellow
[Ref.: #19464]	Incubation period	10-14 days
[Ref.: #19464]	Cultivation medium used	ISP 5

[Ref.: #19464]	Multicellular complex forming ability	yes
[Ref.: #19464]	Multicellular complex name	Aerial Mycelium
[Ref.: #19464]	Multicellular complex color	Grey
[Ref.: #19464]	Medium Name (multicellularity)	ISP 2

[Ref.: #19464]	Multicellular complex forming ability	yes
[Ref.: #19464]	Multicellular complex name	Aerial Mycelium
[Ref.: #19464]	Multicellular complex color	Yellow/ grey
[Ref.: #19464]	Medium Name (multicellularity)	ISP 3

[Ref.: #19464]	Multicellular complex forming ability	yes
[Ref.: #19464]	Multicellular complex name	Aerial Mycelium
[Ref.: #19464]	Multicellular complex color	Grey
[Ref.: #19464]	Medium Name (multicellularity)	ISP 4

[Ref.: #19464]	Multicellular complex forming ability	yes
[Ref.: #19464]	Multicellular complex name	Aerial Mycelium
[Ref.: #19464]	Multicellular complex color	White
[Ref.: #19464]	Medium Name (multicellularity)	ISP 5

[Ref.: #19464]	Multicellular complex forming ability	no
[Ref.: #19464]	Medium Name (multicellularity)	ISP 6

[Ref.: #19464]	Multicellular complex forming ability	no
[Ref.: #19464]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

ISP 2

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 3

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 4

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 5

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

SPORULATION-AGAR (SA) (DSMZ Medium 555)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #9594]	growth	28 °C
[Ref.: #19464]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Oxygen tolerance

aerobe Confidence in %92.469

[Ref.: #19464]	Spore description	Formation of spore chains (rectiflixibilis), spore surface smooth
[Ref.: #19464]	Type of spore	spore
[Ref.: #19464]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %90.85
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

[Ref.: #9594]	Name of produced compound	coumermycin complex
[Ref.: #9594]	Name of produced compound	notomycin
[Ref.: #20216]	Name of produced compound	Coumermycin complex
[Ref.: #20216]	Name of produced compound	Notomycin
[Ref.: #19464]	Name of produced compound	Ansatrienin
[Ref.: #19464]	Name of produced compound	Chloradenosin
[Ref.: #19464]	Name of produced compound	Phosphophenylalanylarginine
[Ref.: #19464]	Name of produced compound	Coumermycin (Notomycin)
[Ref.: #19464]	Name of produced compound	Rishirilide
[Ref.: #67770]	Name of produced compound	Coumermycins

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #19464]		NaCl		maximum	2.5	%

[Ref.: #19464]	Name of tolerated compound	Lysozyme
[Ref.: #19464]	Tolerance percentage	0.1

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #19464]	arabinose ChEBI	+
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #19464]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #19464]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #19464]	mannitol ChEBI	+
[Ref.: #19464]	myo-inositol ChEBI	+
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #19464]	raffinose ChEBI	-
[Ref.: #19464]	rhamnose ChEBI	+
[Ref.: #19464]	sucrose ChEBI	+
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #19464]	xylose ChEBI	+
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	+	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #19464]	325	+	-	-	-	-	-	-	+	-	-	-	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.

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

[Ref.: #9594]	Sample type/isolated from	soil
[Ref.: #9594]	Country	Japan
[Ref.: #9594]	Country ISO 3 Code	JPN
[Ref.: #9594]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Rishiri Island, Hokkaido
[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?

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Global distribution of 16S sequence AB184383 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	336
Soil Samples	6184
Animal Samples	393
Plant Samples	2931
Total Samples	9844

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

[Ref.: #9594]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19464]	Biosafety level	1	Risk group (German classification)

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.: #20218]	Streptomyces rishiriensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4821	D44388	120	GenBank ENA	68264 tax ID	*
[Ref.: #20218]	Streptomyces rishiriensis gene for 16S rRNA, partial sequence, strain: NBRC 13407	AB184383	1473	GenBank ENA	68264 tax ID	*
[Ref.: #20218]	Streptomyces rishiriensis strain NRRL B-3239 16S ribosomal RNA gene, partial sequence	EF178682	1474	GenBank ENA	68264 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Streptomyces rishiriensis NBRC 13407	GCA_003112535	scaffold	GenBank ENA	68264 tax ID
[Ref.: #66792]	Streptomyces rishiriensis strain NBRC 13407	68264.3	wgs	PATRIC	68264 tax ID	*
[Ref.: #66792]	Streptomyces rishiriensis DSM 40489	2563366710	draft	JGI IMG/M	68264 tax ID	*
[Ref.: #66792]	Streptomyces rishiriensis NBRC 13407	2862413135	draft	JGI IMG/M	68264 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Streptomyces rishiriensis NBRC 13407 NCBI: GCA_003112535.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces rishiriensis strain NBRC 13407 PATRIC: 68264.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.939	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.407	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	90.85	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	92.469	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.994	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	87.5	no

Availability in culture collections External links

[Ref.: #9594]

Culture collection no.

DSM 40489, ATCC 14812, CBS 708.72, IFO 13407, ISP 5489, JCM 4821, NBRC 13407, RIA 1368, BCRC 12333, CGMCC 4.1793, NCIMB 11890, NRRL B-3239, VKM Ac-1188

[Ref.: #84638]

SI-ID 389317

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Streptomyces phaeolivaceus sp. nov. and Streptomyces broussonetiae sp. nov., isolated from the leaves and rhizosphere soil of Broussonetia papyrifera.	Mo P, Liu J, Zhao Y, Xu Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004556	2020	*
Enzymology	Identification of a topoisomerase IV in actinobacteria: purification and characterization of ParYR and GyrBR from the coumermycin A1 producer Streptomyces rishiriensis DSM 40489.	Schmutz E, Hennig S, Li SM, Heide L	Microbiology (Reading)	10.1099/mic.0.26867-0	2004	*
Enzymology	An unusual amide synthetase (CouL) from the coumermycin A1 biosynthetic gene cluster from Streptomyces rishiriensis DSM 40489.	Schmutz E, Steffensky M, Schmidt J, Porzel A, Li SM, Heide L	Eur J Biochem	10.1046/j.1432-1033.2003.03830.x	2003	*
Enzymology	Identification of the coumermycin A(1) biosynthetic gene cluster of Streptomyces rishiriensis DSM 40489.	Wang ZX, Li SM, Heide L	Antimicrob Agents Chemother	10.1128/AAC.44.11.3040-3048.2000	2000	*

References

#9594

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40489

#19464

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

Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) .

#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 .

#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 .

#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 )

#84638

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-ID389317.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces rishiriensis NBRC 13407

Streptomyces rishiriensis strain NBRC 13407

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