Name: Streptomyces fragilis DSM 40044
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 15205

Type strain:

Species: Streptomyces fragilis

Culture col. no.: DSM 40044, ATCC 23908, CBS 804.68, IFO 12862, ISP 5044, NBRC 12862, NRRL 2424, RIA 1111, PD 04926, JCM 4187, BCRC 13654, CGMCC 4.1955, HAMBI 1083, HAMBI 1090, IMET 43575, JCM 4638, NCIMB 9795, VKM Ac-1773

Strain history: KCC S-0187 <-- M. Hamada <-- Y. Okami (NIHJ 415) <-- Parke, Davis & Co.; PD 04926.

NCBI tax ID(s): 67301 (species)

SI-ID 38285

ATCC 23908, IFO 12862, NRRL 2424, DSM 40044, JCM 4187, CCRC 13654, IMET 43575, NCIMB 9795, VKM Ac-1773, JCM 4638, NRRL B-2424, CBS 804.68, NBRC 12862, BCRC 13654, HAMBI 1083, HAMBI 1090, CGMCC 4.1955

Other strains from Streptomyces fragilis

S. fragilis ST028775(HKI),

Section

Streptomyces fragilis DSM 40044 is a spore-forming, mesophilic bacterium that was isolated from soil.

spore-forming
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	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Streptomyces*
	Species	**Streptomyces fragilis**
	Full Scientific Name (LPSN)	Streptomyces fragilis Anderson et al. 1956 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %94.926

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

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

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #9123]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #9123]	growth	37 °C
[Ref.: #18471]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #9123]	Temperature range	mesophilic
[Ref.: #18471]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.646

[Ref.: #9123]	Name of produced compound	azaserine
[Ref.: #20216]	Name of produced compound	Azaserine

[Ref.: #67770]

Observation

quinones: MK-9(H₆), MK-9(H₈)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #18471]	arabinose ChEBI	+
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #18471]	cellulose ChEBI	-
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #18471]	fructose ChEBI	-
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18471]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #18471]	mannitol ChEBI	-
[Ref.: #18471]	myo-inositol ChEBI	-
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #18471]	raffinose ChEBI	-
[Ref.: #18471]	rhamnose ChEBI	-
[Ref.: #18471]	sucrose ChEBI	+
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #18471]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #67770]	azaserine ChEBI	yes
[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.: #18471]	56	+	-	-	-	-	-	-	+	-	-	+	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.: #9123]	Sample type/isolated from	soil
[Ref.: #9123]	Country	Argentina
[Ref.: #9123]	Country ISO 3 Code	ARG
[Ref.: #9123]	Continent	Middle and South America

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Country	Argentina
[Ref.: #67770]	Country ISO 3 Code	ARG
[Ref.: #67770]	Continent	Middle and South America
* 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.: #18471]	Biosafety level	1	German classification
[Ref.: #9123]	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 fragilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4638	D44280	120	ENA	67301 tax ID	*
[Ref.: #20218]	Streptomyces fragilis gene for 16S rRNA, partial sequence, strain: NBRC 12862	AB184200	1474	ENA	67301 tax ID	*
[Ref.: #20218]	Streptomyces fragilis strain NRRL 2424 16S ribosomal RNA gene, partial sequence	AY999917	1500	ENA	67301 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Streptomyces fragilis NBRC 12862	GCA_003112515	contig	GenBank	67301 tax ID
[Ref.: #66792]	Streptomyces fragilis strain NBRC 12862	67301.3	wgs	PATRIC	67301 tax ID	*
[Ref.: #66792]	Streptomyces fragilis NBRC 12862	2862407089	draft	JGI IMG/M	67301 tax ID	*

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: Streptomyces fragilis strain NBRC 12862 PATRIC: 67301.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces fragilis strain NBRC 12862 PATRIC: 67301.3
[Ref.: #69480]	gram-positive	yes	90.63	no
[Ref.: #69480]	anaerobic	no	98.949	no
[Ref.: #69480]	halophile	no	89.405	no
[Ref.: #69480]	spore-forming	yes	96.793	no
[Ref.: #69480]	glucose-util	yes	90.447	yes
[Ref.: #69480]	thermophile	no	98.96	yes
[Ref.: #69480]	flagellated	no	98.055	no
[Ref.: #69480]	aerobic	yes	90.833	no
[Ref.: #69480]	glucose-ferment	no	87.887	no
[Ref.: #69480]	motile	no	96.22	no

Availability in culture collections External links

[Ref.: #9123]

Culture collection no.

DSM 40044, ATCC 23908, CBS 804.68, IFO 12862, ISP 5044, NBRC 12862, NRRL 2424, RIA 1111, PD 04926, JCM 4187, BCRC 13654, CGMCC 4.1955, HAMBI 1083, HAMBI 1090, IMET 43575, JCM 4638, NCIMB 9795, VKM Ac-1773

[Ref.: #84303]

SI-ID 38285

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Diversity of PKS and NRPS gene clusters between Streptomyces abyssomicinicus sp. nov. and its taxonomic neighbor.	Komaki H, Sakurai K, Hosoyama A, Kimura A, Trujilo ME, Igarashi Y, Tamura T	J Antibiot (Tokyo)	10.1038/s41429-019-0261-1	2019	*
Phylogeny	Streptomyces chilikensis sp. nov., a halophilic streptomycete isolated from brackish water sediment.	Ray L, Suar M, Pattnaik AK, Raina V	Int J Syst Evol Microbiol	10.1099/ijs.0.046284-0	2013	*
Phylogeny	Streptomyces bullii sp. nov., isolated from a hyper-arid Atacama Desert soil.	Santhanam R, Rong X, Huang Y, Andrews BA, Asenjo JA, Goodfellow M	Antonie Van Leeuwenhoek	10.1007/s10482-012-9816-x	2012	*

References

#9123

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40044

#18471

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 .

#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 )

#84303

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-ID38285.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces fragilis strain NBRC 12862

Streptomyces fragilis strain NBRC 12862

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