Streptomyces fragilis (DSM 40044, ATCC 23908, CBS 804.68)

Name: Streptomyces fragilis (DSM 40044, ATCC 23908, CBS 804.68)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 15205

Type strain

Culture col. no. DSM 40044 ATCC 23908 CBS 804.68 IFO 12862 ISP 5044 13 more

NCBI tax ID(s) 67301

Special Collections DSMZ JCM Wink compendium

History <- E.B. Shirling, ISP <- L. Anderson, Res. Lab., Parke, Davis and Co., PD 04926 KCC S-0187 <-- M. Hamada <-- Y. Okami (NIHJ 415) <-- Parke, Davis & Co.; PD 04926.

Links

Streptomyces fragilis DSM 40044 is a mesophilic prokaryote that was isolated from soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2025-12-16 09:50:32

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces fragilis

Full scientific name Streptomyces fragilis Anderson et al. 1956 (Approved Lists 1980)

BacDive ID	Other strains from **Streptomyces fragilis** (1)	Type strain
128266	S. fragilis ST028775(HKI),

Morphology

Cell morphology

@ref	Gram stain	Confidence	Motility
125439	positive	96.3
125438		90.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9123	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
9123	STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)		Medium recipe at MediaDive	Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
9123	positive	growth	37	mesophilic
18471	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93

Compound production

@ref	Compound
9123	azaserine
20216	Azaserine

Observation

67770

Observationquinones: MK-9(H₆), MK-9(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
18471	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
18471	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
18471	28757 ChEBI	fructose	-
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
18471	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
18471	29864 ChEBI	mannitol	-
18471	17268 ChEBI	myo-inositol	-
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
18471	16634 ChEBI	raffinose	-
18471	26546 ChEBI	rhamnose	-
18471	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
18471	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
67770	74846 ChEBI	azaserine
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	gelatinase	+		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	+	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
18471	+	-	-	-	-	-	-	+	-	-	+	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.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
9123	soil	Argentina	ARG	Middle and South America
67770	Soil	Argentina	ARG	Middle and South America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18471	1	German classification According to TRBA 466
9123	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM311251v1 assembly for Streptomyces fragilis NBRC 12862	contig	GCA_003112515	67301.3	2862407089	67301	74.85
124043	ASM3013548v1 assembly for Streptomyces fragilis ISP 5044	scaffold	GCA_030135485	67301.6	8116917945	67301	47.3

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces fragilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4638	D44280	120	67301
20218	Streptomyces fragilis gene for 16S rRNA, partial sequence, strain: NBRC 12862	AB184200	1474	67301
20218	Streptomyces fragilis strain NRRL 2424 16S ribosomal RNA gene, partial sequence	AY999917	1500	67301

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Streptomyces fragilis NBRC 12862
NCBI: GCA_003112515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	75.20	no
125439	motility	BacteriaNetⓘ	no	79.30	no
125439	gram_stain	BacteriaNetⓘ	positive	96.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces fragilis strain NBRC 12862
PATRIC: 67301.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.46	no
125438	anaerobic	anaerobicⓘ	no	97.99	no
125438	spore-forming	spore-formingⓘ	yes	89.31	no
125438	aerobic	aerobicⓘ	yes	86.41	no
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete integration of carbene-transfer chemistry into biosynthesis.	Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD.	Nature	10.1038/s41586-023-06027-2	2023
	Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for alpha-Diazoester Production.	Van Cura D, Ng TL, Huang J, Hager H, Hartwig JF, Keasling JD, Balskus EP.	Angew Chem Int Ed Engl	10.1002/anie.202304646	2023
	In vitro characterization of nonribosomal peptide synthetase-dependent O-(2-hydrazineylideneacetyl)serine synthesis indicates a stepwise oxidation strategy to generate the alpha-diazo ester moiety of azaserine.	Shikai Y, Kawai S, Katsuyama Y, Ohnishi Y.	Chem Sci	10.1039/d3sc01906c	2023
	Post-transcriptional regulation of aromatic amino acid metabolism by GcvB small RNA in Escherichia coli.	Kanda T, Sekijima T, Miyakoshi M.	Microbiol Spectr	10.1128/spectrum.02035-24	2025
Genetics	Exploration of genomic and functional features of chitinolytic bacterium Streptomyces chilikensis RC1830, isolated from Chilika Lake, India.	Tanaya Behera H, Mojumdar A, Kumari K, Kumar Gouda S, Das S, Ray L.	3 Biotech	10.1007/s13205-022-03184-5	2022
	Purification, characterization, and statistical optimization of a thermostable alpha-amylase from desert actinobacterium Streptomyces fragilis DA7-7.	Nithya K, Muthukumar C, Kadaikunnan S, Alharbi NS, Khaled JM, Dhanasekaran D.	3 Biotech	10.1007/s13205-017-0981-5	2017
Enzymology	Characterization in the archaeological excavation site of heterotrophic bacteria and fungi of deteriorated wall painting of Herculaneum in Italy.	Pepe O, Palomba S, Sannino L, Blaiotta G, Ventorino V, Moschetti G, Villani F.	J Environ Biol		2011
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	Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) . 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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Streptomyces fragilis (DSM 40044, ATCC 23908, CBS 804.68)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003112515

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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