Name: Streptomyces tubercidicus IPCR 585
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 16058

Type strain:

Species: Streptomyces tubercidicus

Strain Designation: IPCR 585

Culture col. no.: DSM 40261, ATCC 25502, CBS 644.69, IFO 13090, ISP 5261, JCM 4054, NBRC 13090, RIA 1282, BCRC 11886, CECT 3272, CGMCC 4.1414, IFM 1064, IMET 43517, JCM 4558, KCTC 9109, LMG 19361, MTCC 1820, NRRL B-5440, VKM Ac-1073

Strain history: KCC S-0054 <-- S. Suzuki 585.

NCBI tax ID(s): 47759 (species)

SI-ID 14117

LMG 19361, ATCC 25502, CCRC 11886, DSM 40261, IFO 13090, IMET 43517, JCM 4054, JCM 4558, NRRL B-5440, VKM Ac-1073, CBS 644.69, AS 4.1414, CECT 3272, KCTC 9109, NBRC 13090, BCRC 11886, CGMCC 4.1414

Other strains from Streptomyces tubercidicus

S. tubercidicus 1UA1, DSM 41958
S. tubercidicus 5US2, DSM 41959
S. tubercidicus ST028272(HKI), FSU-3851,

Section

Streptomyces tubercidicus IPCR 585 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

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 tubercidicus**
	Full Scientific Name (LPSN)	Streptomyces tubercidicus Nakamura 1961 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %96.631

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9415]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #9415]

Culture medium growth

[Ref.: #9415]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9415]

Culture medium composition

expand / minimize

[Ref.: #9415]

Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

[Ref.: #9415]

Culture medium growth

[Ref.: #9415]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #9415]	growth	28 °C
[Ref.: #18573]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #9415]	Temperature range	mesophilic
[Ref.: #18573]	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.: #9415]	Name of produced compound	tubercidin
[Ref.: #20216]	Name of produced compound	Tubercidin
[Ref.: #20216]	Name of produced compound	Endonuclease Stu I
[Ref.: #67770]	Name of produced compound	Endonuclease

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #18573]		NaCl		maximum	2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #18573]	arabinose ChEBI	-
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #18573]	cellulose ChEBI	-
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #18573]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18573]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #18573]	mannitol ChEBI	+
[Ref.: #18573]	myo-inositol ChEBI	+
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #18573]	raffinose ChEBI	+
[Ref.: #18573]	rhamnose ChEBI	-
[Ref.: #18573]	sucrose ChEBI	+
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
[Ref.: #18573]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #67770]	tubercidin ChEBI	yes
[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.: #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.: #18573]	131	+	-	+	-	+	-	+	-	-	+	+	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.: #9415]	Sample type/isolated from	soil
[Ref.: #9415]	Country	Japan
[Ref.: #9415]	Country ISO 3 Code	JPN
[Ref.: #9415]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Mobara, Chiba Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* 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.: #18573]	Biosafety level	1	German classification
[Ref.: #9415]	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 tubercidicus strain AS 4.1414 16S ribosomal RNA gene, partial sequence	FJ406112	1362	ENA	47759 tax ID	*
[Ref.: #20218]	Streptomyces tubercidicus 16S rRNA gene, type strain DSM 40261T	AJ621612	1498	ENA	47759 tax ID	*
[Ref.: #20218]	Streptomyces tubercidicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4558	D44230	121	ENA	47759 tax ID	*
[Ref.: #20218]	Streptomyces tubercidicus gene for 16S rRNA, partial sequence, strain: NBRC 13090	AB184304	1452	ENA	47759 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Streptomyces tubercidicus NBRC 13090	GCA_009811635	contig	GenBank	47759 tax ID
[Ref.: #66792]	Streptomyces tubercidicus strain NBRC 13090	47759.3	wgs	PATRIC	47759 tax ID	*
[Ref.: #66792]	Streptomyces tubercidicus DSM 40261	GCA_027497495	complete	GenBank	47759 tax ID	*

[Ref.: #67770]

GC-content

70.7 mol%

genome sequence analysis

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 tubercidicus strain NBRC 13090 PATRIC: 47759.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces tubercidicus DSM 40261 NCBI: GCA_027497495.1
[Ref.: #69480]	motile	no	93.445	no
[Ref.: #69480]	flagellated	no	98.168	no
[Ref.: #69480]	gram-positive	yes	89.384	no
[Ref.: #69480]	anaerobic	no	99.303	no
[Ref.: #69480]	aerobic	yes	92.873	no
[Ref.: #69480]	halophile	no	88.658	no
[Ref.: #69480]	spore-forming	yes	96.303	no
[Ref.: #69480]	glucose-ferment	no	91.912	no
[Ref.: #69480]	thermophile	no	97.507	yes
[Ref.: #69480]	glucose-util	yes	91.715	yes

Availability in culture collections External links

[Ref.: #9415]

Culture collection no.

DSM 40261, ATCC 25502, CBS 644.69, IFO 13090, ISP 5261, JCM 4054, NBRC 13090, RIA 1282, BCRC 11886, CECT 3272, CGMCC 4.1414, IFM 1064, IMET 43517, JCM 4558, KCTC 9109, LMG 19361, MTCC 1820, NRRL B-5440, VKM Ac-1073

[Ref.: #85131]

SI-ID 14117

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Discovery and characterization of the tubercidin biosynthetic pathway from Streptomyces tubercidicus NBRC 13090.	Liu Y, Gong R, Liu X, Zhang P, Zhang Q, Cai YS, Deng Z, Winkler M, Wu J, Chen W	Microb Cell Fact	10.1186/s12934-018-0978-8	2018	*

References

#9415

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40261

#18573

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 )

#85131

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-ID14117.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Streptomyces tubercidicus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Streptomyces tubercidicus strain NBRC 13090

Streptomyces tubercidicus DSM 40261

Change proposal

Change proposal