Name: Streptomyces atratus DSM 41673
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16320

Type strain:

Species: Streptomyces atratus

Culture col. no.: DSM 41673, ATCC 14046, IFO 3897, JCM 3386, NBRC 3897, CBS 364.68, CGMCC 4.1632, NRRL B-16927

Strain history: IFO 3897 <-- K. Nakazawa 46408.

NCBI tax ID(s): 1893 (species)

SI-ID 35958

ATCC 14046, IFO 3897, DSM 41673, JCM 3386, NRRL B-16927, CBS 364.68, AS 4.1632, NBRC 3897, CGMCC 4.1632

Special Collections

Section

Streptomyces atratus DSM 41673 is a bacterium that builds an aerial mycelium and produces antibiotic compounds.

antibiotic compound production
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 atratus**
	Full Scientific Name (LPSN)	Streptomyces atratus Shibata et al. 1962 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %91.189

[Ref.: #18706]	Colony color	Yellow
[Ref.: #18706]	Incubation period	10-14 days
[Ref.: #18706]	Cultivation medium used	ISP 2

[Ref.: #18706]	Colony color	Yellow
[Ref.: #18706]	Incubation period	10-14 days
[Ref.: #18706]	Cultivation medium used	ISP 3

[Ref.: #18706]	Colony color	Yellow
[Ref.: #18706]	Incubation period	10-14 days
[Ref.: #18706]	Cultivation medium used	ISP 4

[Ref.: #18706]	Colony color	Yellow
[Ref.: #18706]	Incubation period	10-14 days
[Ref.: #18706]	Cultivation medium used	ISP 5

[Ref.: #18706]	Colony color	Yellow
[Ref.: #18706]	Incubation period	10-14 days
[Ref.: #18706]	Cultivation medium used	ISP 6

[Ref.: #18706]	Colony color	Yellow
[Ref.: #18706]	Incubation period	10-14 days
[Ref.: #18706]	Cultivation medium used	ISP 7

[Ref.: #18706]	Multicellular complex forming ability	yes
[Ref.: #18706]	Multicellular complex name	Aerial Mycelium
[Ref.: #18706]	Multicellular complex color	Beige (1001)
[Ref.: #18706]	Medium Name (multicellularity)	ISP 2

[Ref.: #18706]	Multicellular complex forming ability	yes
[Ref.: #18706]	Multicellular complex name	Aerial Mycelium
[Ref.: #18706]	Multicellular complex color	Beige (1001)
[Ref.: #18706]	Medium Name (multicellularity)	ISP 3

[Ref.: #18706]	Multicellular complex forming ability	yes
[Ref.: #18706]	Multicellular complex name	Aerial Mycelium
[Ref.: #18706]	Multicellular complex color	Beige (1001)
[Ref.: #18706]	Medium Name (multicellularity)	ISP 4

[Ref.: #18706]	Multicellular complex forming ability	yes
[Ref.: #18706]	Multicellular complex name	Aerial Mycelium
[Ref.: #18706]	Multicellular complex color	Beige (1001)
[Ref.: #18706]	Medium Name (multicellularity)	ISP 5

[Ref.: #18706]	Multicellular complex forming ability	yes
[Ref.: #18706]	Multicellular complex name	Aerial Mycelium
[Ref.: #18706]	Multicellular complex color	Beige (1001)
[Ref.: #18706]	Medium Name (multicellularity)	ISP 6

[Ref.: #18706]	Multicellular complex forming ability	yes
[Ref.: #18706]	Multicellular complex name	Aerial Mycelium
[Ref.: #18706]	Multicellular complex color	Beige (1001)
[Ref.: #18706]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

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Culture medium

YEAST-STARCH-AGAR(B) (DSMZ Medium 656)

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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

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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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

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

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Medium recipe at MediaDive

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Culture medium composition

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		Temperature
[Ref.: #10456]	growth	28 °C
[Ref.: #18706]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #18706]	Spore description	Formation of spore chains (rectiflixibilis), spore surface smooth
[Ref.: #18706]	Ability of spore formation	no

[Ref.: #10456]	Name of produced compound	rufomycins A and B
[Ref.: #18706]	Name of produced compound	Atramycin A
[Ref.: #18706]	Name of produced compound	Ilamycin
[Ref.: #67770]	Name of produced compound	Rufomycins A and B

	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.: #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.: #18706]	211	+	-	+	+	-	-	+	-	-	-	+	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.: #10456]	Sample type/isolated from	soil
[Ref.: #10456]	Geographic location (country and/or sea, region)	Wakayama Pref., Shimoneda
[Ref.: #10456]	Country	Japan
[Ref.: #10456]	Country ISO 3 Code	JPN
[Ref.: #10456]	Continent	Asia

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

[Ref.: #69479]

Global distribution of 16S sequence AB184811 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	125
Soil Samples	1589
Animal Samples	280
Plant Samples	537
Total Samples	2531

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

[Ref.: #18706]	Biosafety level	1	German classification
[Ref.: #10456]	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 atratus gene for 16S rRNA, partial sequence	AB122768	564	GenBank ENA	1893 tax ID	*
[Ref.: #20218]	Streptomyces atratus gene for 16S ribosomal RNA, partial sequence, strain: JCM 3386	D43986	120	GenBank ENA	1893 tax ID	*
[Ref.: #20218]	Streptomyces atratus gene for 16S rRNA, partial sequence, strain: NBRC 3897	AB184811	1477	GenBank ENA	1893 tax ID	*
[Ref.: #20218]	Streptomyces atratus strain NRRL B-16927 16S ribosomal RNA gene, partial sequence	DQ026638	1487	GenBank ENA	1893 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Streptomyces atratus JCM 3386	GCA_014648655	scaffold	GenBank ENA	1893 tax ID	*
[Ref.: #66792]	Streptomyces atratus strain JCM 3386	1893.11	wgs	PATRIC	1893 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces atratus JCM 3386 NCBI: GCA_014648655.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.189	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.992	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.375	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	80.944	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	87.5	no

Availability in culture collections External links

[Ref.: #10456]

Culture collection no.

DSM 41673, ATCC 14046, IFO 3897, JCM 3386, NBRC 3897, CBS 364.68, CGMCC 4.1632, NRRL B-16927

[Ref.: #85376]

SI-ID 35958

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Purification and N-terminal amino-acid sequences of bacterial malate dehydrogenases from six actinomycetales strains and from Phenylobacterium immobile, strain E.	Rommel TO, Hund HK, Speth AR, Lingens F	Biol Chem Hoppe Seyler	10.1515/bchm3.1989.370.2.763	1989	*
Metabolism	Identification and characterization of a bacterial cytochrome P450 monooxygenase catalyzing the 3-nitration of tyrosine in rufomycin biosynthesis.	Tomita H, Katsuyama Y, Minami H, Ohnishi Y	J Biol Chem	10.1074/jbc.M117.791269	2017	*
Pathogenicity	Glutathione S-transferase pi (GST-pi) inhibition and anti-inflammation activity of the ethyl acetate extract of Streptomyces sp. strain MJM 8637.	Lee SK, Lee DR, Choi BK, Palaniyandi SA, Yang SH, Suh JW	Saudi J Biol Sci	10.1016/j.sjbs.2015.04.003	2015	*

References

#10456

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 41673

#18706

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) .

#85376

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-ID35958.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces atratus JCM 3386

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