Name: Streptomyces gardneri DSM 40064
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 15216

Type strain:

Species: Streptomyces gardneri

Culture col. no.: DSM 40064, ATCC 23911, ATCC 9604, CBS 832.68, DSM 43020, ETH 28347, IFO 12865, IFO 13974, IFO 3385, IMET 7182, IMRU 3834, ISP 5064, JCM 3004, JCM 4375, KCC A-0004, KCC S-0375, NBRC 12865, NBRC 13974, NBRC 3385, RIA 1117, RIA 634, BCRC 12346, BCRC 13687, BCRC 13731, CGMCC 4.1956, NCTC 6531, NRRL B-5615, VKM Ac-1829

Strain history: KCC A-0004 <-- T. Yamaguchi (IAM 0105) <-- ATCC 9604 <-- NCTC 6531.

NCBI tax ID(s): 66892 (species)

SI-ID 35082

ATCC 9604, NCTC 6531, ATCC 23911, IFO 13974, DSM 40064, DSM 43020, IFO 12865, IFO 3385, IMET 7182, JCM 3004, JCM 4375, CCRC 12346, CCRC 13687, CCRC 13731, NRRL B-5615, VKM Ac-1829, CBS 832.68, NBRC 12865, NBRC 13974, NBRC 3385, BCRC 12346, BCRC 13731, BCRC 13687, CGMCC 4.1956, CGMCC 4.1210

Section

Streptomyces gardneri DSM 40064 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from air contamination.

antibiotic compound production
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 gardneri**
	Full Scientific Name (LPSN)	Streptomyces gardneri (Waksman 1942) Waksman 1961 (Approved Lists 1980)

Synonym

"Proactinomyces gardneri"

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %94.038

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9265]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #9265]

Culture medium growth

[Ref.: #9265]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9265]

Culture medium composition

expand / minimize

[Ref.: #9265]

Culture medium

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

[Ref.: #9265]

Culture medium growth

[Ref.: #9265]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #9265]	growth	28 °C
[Ref.: #18476]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #9265]	Temperature range	mesophilic
[Ref.: #18476]	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 %98
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[Ref.: #9265]	Name of produced compound	proactinomycin A, B, C
[Ref.: #9265]	Name of produced compound	proactinomycin B
[Ref.: #9265]	Name of produced compound	proactinomycin C
[Ref.: #9265]	Name of produced compound	proactinomycin A
[Ref.: #67770]	Name of produced compound	Proactinomycins A, B and C

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #18476]	arabinose ChEBI	+
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18476]	cellulose ChEBI	+
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #18476]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18476]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #18476]	mannitol ChEBI	-
[Ref.: #18476]	myo-inositol ChEBI	-
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #18476]	raffinose ChEBI	+
[Ref.: #18476]	rhamnose ChEBI	+
[Ref.: #18476]	sucrose ChEBI	+
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18476]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	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.: #18476]	60	+	+	+	+	+	-	+	-	-	+	+	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.: #18476]	178	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	+	+	+	-

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

[Ref.: #9265]	Sample type/isolated from	air contamination

[Ref.: #67770]	Sample type/isolated from	Air contamination
* marker position based on {}

Isolation sources categories

#Engineered	#Laboratory	#Contaminant
#Environmental	#Air	-

What are isolation sources categories?

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

[Ref.: #18476]	Biosafety level	1	German classification
[Ref.: #9265]	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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Actinomyces israeli serotype 1 partial 16S rRNA	X53228	1386	ENA	1659 tax ID	*
[Ref.: #20218]	Streptomyces gardneri gene for 16S rRNA, partial sequence	AB122713	564	ENA	66892 tax ID	*
[Ref.: #20218]	Streptomyces gardneri gene for 16S ribosomal RNA, partial sequence, strain: JCM 4375	D44091	120	ENA	66892 tax ID	*
[Ref.: #20218]	Streptomyces gardneri gene for 16S rRNA, partial sequence, strain: NBRC 12865	AB249908	1451	ENA	66892 tax ID	*
[Ref.: #20218]	Streptomyces gardneri gene for 16S rRNA, partial sequence, strain: NBRC 3385	AB184754	1470	ENA	66892 tax ID	*
[Ref.: #20218]	Streptomyces gardneri strain NRRL B-5615T 16S ribosomal RNA gene, partial sequence	DQ442500	1442	ENA	66892 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Streptomyces gardneri NBRC 12865	GCA_006539185	contig	GenBank	66892 tax ID
[Ref.: #66792]	Streptomyces gardneri JCM 4375	GCA_014655085	contig	GenBank	66892 tax ID	*
[Ref.: #66792]	Streptomyces gardneri strain JCM 4375	66892.4	wgs	PATRIC	66892 tax ID	*
[Ref.: #66792]	Streptomyces gardneri strain NBRC 12865	66892.3	wgs	PATRIC	66892 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 gardneri strain NBRC 12865 PATRIC: 66892.3
[Ref.: #69481]	spore-forming	yes	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces gardneri strain JCM 4375 PATRIC: 66892.4
[Ref.: #69480]	gram-positive	yes	87.627	no
[Ref.: #69480]	anaerobic	no	99.418	no
[Ref.: #69480]	halophile	no	93.656	no
[Ref.: #69480]	spore-forming	yes	94.318	no
[Ref.: #69480]	glucose-util	yes	90.227	no
[Ref.: #69480]	thermophile	no	99.158	no
[Ref.: #69480]	flagellated	no	97.335	no
[Ref.: #69480]	motile	no	94.159	no
[Ref.: #69480]	aerobic	yes	92.249	no
[Ref.: #69480]	glucose-ferment	no	84.942	no

Availability in culture collections External links

[Ref.: #9265]

Culture collection no.

DSM 40064, ATCC 23911, ATCC 9604, CBS 832.68, DSM 43020, ETH 28347, IFO 12865, IFO 13974, IFO 3385, IMET 7182, IMRU 3834, ISP 5064, JCM 3004, JCM 4375, KCC A-0004, KCC S-0375, NBRC 12865, NBRC 13974, NBRC 3385, RIA 1117, RIA 634, BCRC 12346, BCRC 13687, BCRC 13731, CGMCC 4.1956, NCTC 6531, NRRL B-5615, VKM Ac-1829

[Ref.: #84314]

SI-ID 35082

Literature:

	Title	Authors	Journal	DOI	Year
	Polyclonal B cell activation by cell wall preparations of gram-positive bacteria. In vitro responses of spleen cells obtained from Balb/c, nu/nu, nu/+, C3H/He, C3H/HeJ and hybrid (DBA/N x Balb/c)F1 mice.	Saito-Taki T, Tanabe MJ, Mochizuki H, Matsumoto T, Nakano M, Takada H, Tsujimoto M, Kotani S, Kusumoto S, Shiba T, Yokogawa K, Kawata S	Microbiol Immunol	10.1111/j.1348-0421.1980.tb00580.x	1980	*

References

#9265

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40064

#18476

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 .

#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 )

#84314

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-ID35082.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces gardneri strain NBRC 12865

Streptomyces gardneri strain JCM 4375

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