Name: Streptomyces nojiriensis DSM 41655
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16313

Type strain:

Species: Streptomyces nojiriensis

Culture col. no.: DSM 41655, ATCC 29781, IFO 13794, JCM 3382, NBRC 13794, NRRL B-16930, CGMCC 4.1897, KCTC 9784

Strain history: Meiji Seika Kaisha, Ltd.; SF-426.

NCBI tax ID(s): 66374 (species)

SI-ID 39716

ATCC 29781, IFO 13794, DSM 41655, JCM 3382, NRRL B-16930, KCTC 9784, NBRC 13794, LMG 20094, CGMCC 4.1897, AS 4.1897

Special Collections

Section

Streptomyces nojiriensis DSM 41655 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

antibiotic compound production
spore-forming
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Streptomyces*
	Species	**Streptomyces nojiriensis**
	Full Scientific Name (LPSN)	Streptomyces nojiriensis Ishida et al. 1967 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #18700]	Colony color	Beige
[Ref.: #18700]	Incubation period	10-14 days
[Ref.: #18700]	Cultivation medium used	ISP 2

[Ref.: #18700]	Colony color	Beige
[Ref.: #18700]	Incubation period	10-14 days
[Ref.: #18700]	Cultivation medium used	ISP 3

[Ref.: #18700]	Colony color	Beige
[Ref.: #18700]	Incubation period	10-14 days
[Ref.: #18700]	Cultivation medium used	ISP 4

[Ref.: #18700]	Colony color	Beige
[Ref.: #18700]	Incubation period	10-14 days
[Ref.: #18700]	Cultivation medium used	ISP 5

[Ref.: #18700]	Colony color	Brown
[Ref.: #18700]	Incubation period	10-14 days
[Ref.: #18700]	Cultivation medium used	ISP 6

[Ref.: #18700]	Colony color	Brown
[Ref.: #18700]	Incubation period	10-14 days
[Ref.: #18700]	Cultivation medium used	ISP 7

[Ref.: #18700]	Multicellular complex forming ability	yes
[Ref.: #18700]	Multicellular complex name	Aerial Mycelium
[Ref.: #18700]	Multicellular complex color	Grey
[Ref.: #18700]	Medium Name (multicellularity)	ISP 2

[Ref.: #18700]	Multicellular complex forming ability	yes
[Ref.: #18700]	Multicellular complex name	Aerial Mycelium
[Ref.: #18700]	Multicellular complex color	Grey
[Ref.: #18700]	Medium Name (multicellularity)	ISP 3

[Ref.: #18700]	Multicellular complex forming ability	yes
[Ref.: #18700]	Multicellular complex name	Aerial Mycelium
[Ref.: #18700]	Multicellular complex color	Grey
[Ref.: #18700]	Medium Name (multicellularity)	ISP 4

[Ref.: #18700]	Multicellular complex forming ability	yes
[Ref.: #18700]	Multicellular complex name	Aerial Mycelium
[Ref.: #18700]	Multicellular complex color	Grey
[Ref.: #18700]	Medium Name (multicellularity)	ISP 5

[Ref.: #18700]	Multicellular complex forming ability	no
[Ref.: #18700]	Medium Name (multicellularity)	ISP 6

[Ref.: #18700]	Multicellular complex forming ability	yes
[Ref.: #18700]	Multicellular complex name	Aerial Mycelium
[Ref.: #18700]	Multicellular complex color	Grey
[Ref.: #18700]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

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Culture medium growth

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Medium recipe at MediaDive

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Culture medium composition

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Culture medium

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

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Medium recipe at MediaDive

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Culture medium

ISP 2

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Culture medium

ISP 3

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Culture medium

ISP 4

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Culture medium

ISP 5

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Culture medium

ISP 6

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Culture medium

ISP 7

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Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

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		Temperature
[Ref.: #10431]	growth	28 °C
[Ref.: #18700]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Oxygen tolerance

aerobe Confidence in %90.084

[Ref.: #18700]	Spore description	Formation of spore chains (spirales)(sp), spore surface smooth
[Ref.: #18700]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %91.857
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

[Ref.: #10431]	Name of produced compound	nojirimycin
[Ref.: #18700]	Name of produced compound	Streptothricines

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #18700]		NaCl		maximum	5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E

	Metabolite	Production
[Ref.: #67770]	nojirimycin ChEBI	yes
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	yes	* 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.: #18700]	208	-	+	-	-	+	+	+	+	-	-	-	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.: #10431]	Sample type/isolated from	soil
[Ref.: #10431]	Geographic location (country and/or sea, region)	Nagano Pref., Nojiri
[Ref.: #10431]	Country	Japan
[Ref.: #10431]	Country ISO 3 Code	JPN
[Ref.: #10431]	Continent	Asia

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

[Ref.: #69479]

Global distribution of 16S sequence AJ781355 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	1680
Soil Samples	19336
Animal Samples	1702
Plant Samples	3681
Total Samples	26399

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

[Ref.: #18700]	Biosafety level	1	German classification
[Ref.: #10431]	Biosafety level	1	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.: #20218]	Streptomyces nojiriensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 3382	D43984	120	GenBank ENA	66374 tax ID	*
[Ref.: #20218]	Streptomyces nojiriensis strain KCTC 9784 16S ribosomal RNA gene, partial sequence	AY999814	1419	GenBank ENA	66374 tax ID	*
[Ref.: #20218]	Streptomyces nojiriensis 16S rRNA gene, type strain LMG 20094	AJ781355	1477	GenBank ENA	66374 tax ID	*
[Ref.: #20218]	Streptomyces nojiriensis gene for 16S rRNA, partial sequence, strain: NBRC 13794	AB184485	1475	GenBank ENA	66374 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Streptomyces nojiriensis JCM 3382	GCA_017639205	complete	GenBank ENA	66374 tax ID	*
[Ref.: #66792]	Streptomyces nojiriensis NBRC 13794	GCA_016755855	contig	GenBank ENA	66374 tax ID	*
[Ref.: #66792]	Streptomyces nojiriensis JCM 3382	GCA_014648615	scaffold	GenBank ENA	66374 tax ID	*
[Ref.: #66792]	Streptomyces nojiriensis strain JCM 3382	66374.6	complete	PATRIC	66374 tax ID	*
[Ref.: #66792]	Streptomyces nojiriensis strain JCM 3382	66374.4	wgs	PATRIC	66374 tax ID	*
[Ref.: #66792]	Streptomyces nojiriensis strain NBRC 13794	66374.5	wgs	PATRIC	66374 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 nojiriensis JCM 3382 NCBI: GCA_017639205.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces nojiriensis JCM 3382 NCBI: GCA_017639205.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.534	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.861	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	90.084	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	91.857	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.5	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	86.1	no

Availability in culture collections External links

[Ref.: #10431]

Culture collection no.

DSM 41655, ATCC 29781, IFO 13794, JCM 3382, NBRC 13794, NRRL B-16930, CGMCC 4.1897, KCTC 9784

[Ref.: #85369]

SI-ID 39716

Literature:

	Title	Authors	Journal	DOI	Year
	Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces.	Park JS, Kim DE, Hong SC, Kim SY, Kwon HC, Hyun CG, Choi J	Microorganisms	10.3390/microorganisms9091802	2021	*

References

#10431

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 41655

#18700

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 .

#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 )

#85369

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-ID39716.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces nojiriensis JCM 3382

Streptomyces nojiriensis JCM 3382

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