Name: Streptomyces clavifer DSM 40843
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 15100

Type strain:

Species: Streptomyces clavifer

Culture col. no.: DSM 40843, CBS 101.27, NRRL B-2557, JCM 5059, CGMCC 4.1604, IFO 15398, NBRC 15398

Strain history: KCC S-1059 <-- MS 1479 <-- CBS 101.27 <-- W. A. Millard.

NCBI tax ID(s): 68188 (species)

SI-ID 49809

DSM 40843, NRRL B-2557, JCM 5059, IFO 15398, CBS 101.27, AS 4.1604, NBRC 15398, CGMCC 4.1604

Section

Streptomyces clavifer DSM 40843 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from limed plot and scab on Solanum tuberosum.

Gram-positive
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 clavifer**
	Full Scientific Name (LPSN)	Streptomyces clavifer (Millard and Burr 1926) Waksman 1953 (Approved Lists 1980)

Synonym

"Actinomyces clavifer"

Information on morphological and physiological properties Morphology

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

[Ref.: #19492]	Colony color	Sand yellow
[Ref.: #19492]	Incubation period	10-14 days
[Ref.: #19492]	Cultivation medium used	ISP 2

[Ref.: #19492]	Colony color	Grey yellow
[Ref.: #19492]	Incubation period	10-14 days
[Ref.: #19492]	Cultivation medium used	ISP 3

[Ref.: #19492]	Incubation period	10-14 days
[Ref.: #19492]	Cultivation medium used	ISP 4

[Ref.: #19492]	Incubation period	10-14 days
[Ref.: #19492]	Cultivation medium used	ISP 5

[Ref.: #19492]	Incubation period	10-14 days
[Ref.: #19492]	Cultivation medium used	ISP 6

[Ref.: #19492]	Incubation period	10-14 days
[Ref.: #19492]	Cultivation medium used	ISP 7

[Ref.: #19492]	Multicellular complex forming ability	no
[Ref.: #19492]	Medium Name (multicellularity)	ISP 2

[Ref.: #19492]	Multicellular complex forming ability	no
[Ref.: #19492]	Medium Name (multicellularity)	ISP 3

[Ref.: #19492]	Multicellular complex forming ability	no
[Ref.: #19492]	Medium Name (multicellularity)	ISP 4

[Ref.: #19492]	Multicellular complex forming ability	no
[Ref.: #19492]	Medium Name (multicellularity)	ISP 5

[Ref.: #19492]	Multicellular complex forming ability	no
[Ref.: #19492]	Medium Name (multicellularity)	ISP 6

[Ref.: #19492]	Multicellular complex forming ability	no
[Ref.: #19492]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9843]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #9843]

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

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Culture medium composition

expand / minimize

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Culture medium

ISP 2

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 3

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 4

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 5

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 6

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 7

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Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #9843]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #9843]	growth	28 °C
[Ref.: #19492]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #9843]	Temperature range	mesophilic
[Ref.: #19492]	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 %100

[Ref.: #19492]

Name of produced compound

Melanostatin

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #19492]		NaCl		maximum	2.5	%

	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.: #68368]	acetoin ChEBI	yes	* 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.: #19492]	350	+	+	+	+	+	-	+	-	-	+	+	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.: #19492]	376	not determinedn.d.	+	+	+	+	+	+	+	+	-	+	+	+	+	-	+	+	-	-	-

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

[Ref.: #9843]	Sample type/isolated from	limed plot and scab on Solanum tuberosum
[Ref.: #9843]	Host species	Solanum tuberosum
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	-
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Other	#Wound
#Host Body-Site	#Plant	#Fruit (Seed)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB184649 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	286
Soil Samples	2441
Animal Samples	1009
Plant Samples	294
Total Samples	4030

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

[Ref.: #9843]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19492]	Biosafety level	1	Risk group (German classification)

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 clavifer strain AS 4.1604 16S ribosomal RNA gene, partial sequence	FJ405904	1387	ENA	68188 tax ID	*
[Ref.: #20218]	Streptomyces clavifer gene for 16S ribosomal RNA, partial sequence, strain: JCM 5059	D44428	120	ENA	68188 tax ID	*
[Ref.: #20218]	Streptomyces clavifer gene for 16S rRNA, partial sequence, strain: NBRC 15398	AB184649	1477	ENA	68188 tax ID	*
[Ref.: #20218]	Streptomyces clavifer strain NRRL B-2557 16S ribosomal RNA gene, partial sequence	DQ026670	1499	ENA	68188 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Streptomyces clavifer DSM 40843	GCA_017876255	contig	GenBank	68188 tax ID	*
[Ref.: #66792]	Streptomyces clavifer JCM 5059	GCA_014651175	scaffold	GenBank	68188 tax ID	*
[Ref.: #66792]	Streptomyces clavifer strain DSM 40843	68188.4	wgs	PATRIC	68188 tax ID	*
[Ref.: #66792]	Streptomyces clavifer strain JCM 5059	68188.3	wgs	PATRIC	68188 tax ID	*
[Ref.: #66792]	Streptomyces clavifer DSM 40843	2918298223	draft	JGI IMG/M	68188 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 clavifer JCM 5059 NCBI: GCA_014651175.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces clavifer JCM 5059 NCBI: GCA_014651175.1
[Ref.: #69480]	flagellated	no	97.792	no
[Ref.: #69480]	gram-positive	yes	89.522	no
[Ref.: #69480]	anaerobic	no	99.182	no
[Ref.: #69480]	aerobic	yes	92.928	no
[Ref.: #69480]	halophile	no	90.996	no
[Ref.: #69480]	spore-forming	yes	93.565	no
[Ref.: #69480]	thermophile	no	99.113	yes
[Ref.: #69480]	glucose-util	yes	90.759	no
[Ref.: #69480]	motile	no	93.297	no
[Ref.: #69480]	glucose-ferment	no	90.019	no

Availability in culture collections External links

[Ref.: #9843]

Culture collection no.

DSM 40843, CBS 101.27, NRRL B-2557, JCM 5059, CGMCC 4.1604, IFO 15398, NBRC 15398

[Ref.: #84207]

SI-ID 49809

References

#9843

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40843

#19492

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 .

#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 )

#84207

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-ID49809.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces clavifer JCM 5059

Streptomyces clavifer JCM 5059

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