Name: Streptomyces durhamensis 59123
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 15129

Type strain:

Species: Streptomyces durhamensis

Strain Designation: 59123

Culture col. no.: DSM 40539, ATCC 23194, CBS 742.72, IFO 13441, ISP 5539, JCM 4291, NBRC 13441, RIA 1402, BCRC 16203, CGMCC 4.1699, HAMBI 1064, IMET 43359, JCM 4747, KCTC 9723, NRRL B-3309, NRRL ISP-5539, VKM Ac-763

Strain history: KCC S-0291 <-- M. A. Gordon 59123.

NCBI tax ID(s): 68194 (species)

SI-ID 125798

ATCC 23194, IFO 13441, DSM 40539, JCM 4291, IMET 43359, NRRL B-3309, VKM Ac-763, JCM 4747, CBS 742.72, KCTC 9723, AS 4.1699, NBRC 13441, HAMBI 1064, BCRC 16203, CCRC 16203, CGMCC 4.1699

Special Collections

Other strains from Streptomyces durhamensis

Section

Streptomyces durhamensis 59123 is a spore-forming, Gram-positive bacterium that produces antibiotic compounds and was isolated from soil from potted tomato plants.

antibiotic compound production
Gram-positive
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 durhamensis**
	Full Scientific Name (LPSN)	Streptomyces durhamensis Gordon and Lapa 1966 (Approved Lists 1980)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9627]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #9627]

Culture medium growth

[Ref.: #9627]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9627]

Culture medium composition

expand / minimize

[Ref.: #9627]

Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

[Ref.: #9627]

Culture medium growth

[Ref.: #9627]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #9627]	growth	28 °C
[Ref.: #18605]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

yes Confidence in %100

[Ref.: #9627]	Name of produced compound	durhamycin
[Ref.: #20216]	Name of produced compound	Durhamycin

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #18605]	arabinose ChEBI	+
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18605]	cellulose ChEBI	+
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #18605]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18605]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #18605]	mannitol ChEBI	+
[Ref.: #18605]	myo-inositol ChEBI	+
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #18605]	raffinose ChEBI	+
[Ref.: #18605]	rhamnose ChEBI	+/-
[Ref.: #18605]	sucrose ChEBI	+
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18605]	xylose ChEBI	+/-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #67770]	durhamycin	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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E, API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68368]	gelatinase	+		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	+	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68368]	ornithine decarboxylase	+	4.1.1.17	* from API 20E
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	+	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #18605]	160	+	+	+	+	+	-	+	-	-	-	+	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.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #18605]	245	not determinedn.d.	+	+	+	-	+	+	+	-	-	+	+	+	+	-	+	+	+	+	-

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

[Ref.: #9627]	Sample type/isolated from	soil from potted tomato plants

[Ref.: #67770]	Sample type/isolated from	Soil of potted tomato plant in Durham, N. C., after spraying of the plants with 2,4-dichlorophenoxyacetic acid
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB184405 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	19
Soil Samples	547
Animal Samples	29
Plant Samples	192
Total Samples	787

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

[Ref.: #18605]	Biosafety level	1	German classification
[Ref.: #9627]	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 durhamensis gene for 16S rRNA, partial sequence	AB122732	564	GenBank ENA	68194 tax ID	*
[Ref.: #20218]	Streptomyces durhamensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4747	D44331	120	GenBank ENA	68194 tax ID	*
[Ref.: #20218]	Streptomyces durhamensis gene for 16S rRNA, partial sequence, strain: NBRC 13441	AB184405	1432	GenBank ENA	68194 tax ID	*
[Ref.: #20218]	Streptomyces durhamensis strain NRRL B-3309 16S ribosomal RNA gene, partial sequence	AY999785	1494	GenBank ENA	68194 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Streptomyces durhamensis NRRL B-3309	GCA_000725475	scaffold	GenBank ENA	68194 tax ID
[Ref.: #67770]	Streptomyces durhamensis NRRL ISP-5539	GCA_000722375	scaffold	GenBank ENA	68194 tax ID

[Ref.: #67770]

GC-content

71.7 mol%

genome sequence analysis

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 durhamensis NRRL B-3309 NCBI: GCA_000725475.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces durhamensis NRRL B-3309 NCBI: GCA_000725475.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.953	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.398	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	89.992	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	89.349	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	87	no

Availability in culture collections External links

[Ref.: #9627]

Culture collection no.

DSM 40539, ATCC 23194, CBS 742.72, IFO 13441, ISP 5539, JCM 4291, NBRC 13441, RIA 1402, BCRC 16203, CGMCC 4.1699, HAMBI 1064, IMET 43359, JCM 4747, KCTC 9723, NRRL B-3309, NRRL ISP-5539, VKM Ac-763

[Ref.: #84234]

SI-ID 125798

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	*
Phylogeny	Streptomyces fodineus sp. nov., an actinobacterium with antifungal activity isolated from mine area soil.	Kim MK, Kang HJ, Roh SG, Park JS, Kim SB	Int J Syst Evol Microbiol	10.1099/ijsem.0.003353	2019	*
Phylogeny	Streptomyces yaanensis sp. nov., isolated from soil.	Zheng J, Zhang X, Xin Y, Han X, Ni S, Zhang J	Int J Syst Evol Microbiol	10.1099/ijs.0.054734-0	2013	*

References

#9627

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40539

#18605

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68368

Automatically annotated from API 20E .

#68382

Automatically annotated from API zym .

#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 )

#84234

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-ID125798.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces durhamensis NRRL B-3309

Streptomyces durhamensis NRRL B-3309

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