Streptomyces tubercidicus (DSM 40261, ATCC 25502, CBS 644.69)

Name: Streptomyces tubercidicus (DSM 40261, ATCC 25502, CBS 644.69)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16058

Type strain

Strain Designation IPCR 585

Culture col. no. DSM 40261 ATCC 25502 CBS 644.69 IFO 13090 ISP 5261 16 more

NCBI tax ID(s) 47759

Special Collections DSMZ JCM KCTC Wink compendium JMRC

History DSMZ <- E.B. Shirling, ISP <- S. Suzuki, IPCR, 585 JCM <-- KCC S-0054 <-- S. Suzuki 585.

Links

Streptomyces tubercidicus IPCR 585 is a bacterium that produces antibiotic compounds and was isolated from soil.

antibiotic compound production genome sequence 16S sequence Bacteria

Name and taxonomic classification

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,MTCC 1820,CBS 644.69,AS 4.1414,CECT 3272,KCTC 9109,NBRC 13090,BCRC 11886,CGMCC 4.1414

@ref 20215

Last LPSN update 2026-05-29 08:28:41

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces tubercidicus

Full scientific name Streptomyces tubercidicus Nakamura 1961 (Approved Lists 1980)

BacDive ID	Other strains from **Streptomyces tubercidicus** (2)	Type strain
16059	S. tubercidicus 1UA1, DSM 41958
16060	S. tubercidicus 5US2, DSM 41959

Morphology

Cell morphology

@ref	Confidence	Gram stain
125439	96.236
125439	99.398	positive
125438	90.161	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9415	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
9415	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)		Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
9415	positive	growth	28
18573	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	91.602
125439	facultative anaerobe	96.755

Spore formation

@ref	Spore formation	Confidence
125438		92.785
125439		92.112

Compound production

@ref	Compound
9415	tubercidin
20216	Tubercidin
20216	Endonuclease Stu I
67770	Endonuclease

Halophily

@ref	Salt	Growth	Tested relation	Concentration
18573	NaCl	positive	maximum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
18573	22599 ChEBI	arabinose	-
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
18573	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
18573	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
18573	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	+	degradation	from API 20E
18573	29864 ChEBI	mannitol	+
18573	17268 ChEBI	myo-inositol	+
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
18573	16634 ChEBI	raffinose	+
18573	26546 ChEBI	rhamnose	-
18573	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
18573	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E
67770	48267 ChEBI	tubercidin

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
18573	+	-	+	-	+	-	+	-	-	+	+	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	Geographic location	Country	Country ISO 3 Code	Continent
9415	soil		Japan	JPN	Asia
67770	Soil	Mobara, Chiba Pref.	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9415	1	Risk group (German classification) According to TRBA 466
18573	1	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
66792	ASM2749749v1 assembly for Streptomyces tubercidicus DSM 40261	complete	GCA_027497495	47759.4	8118122515	47759	98.79
67770	ASM981163v1 assembly for Streptomyces tubercidicus NBRC 13090	contig	GCA_009811635	47759.3	8112131506	47759	77.92
124043	ASM3953264v1 assembly for Streptomyces tubercidicus JCM 4054	contig	GCA_039532645			47759	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces tubercidicus strain AS 4.1414 16S ribosomal RNA gene, partial sequence	FJ406112	1362	47759
20218	Streptomyces tubercidicus 16S rRNA gene, type strain DSM 40261T	AJ621612	1498	47759
20218	Streptomyces tubercidicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4558	D44230	121	47759
20218	Streptomyces tubercidicus gene for 16S rRNA, partial sequence, strain: NBRC 13090	AB184304	1452	47759
124043	Streptomyces tubercidicus strain JCM 4054 16S ribosomal RNA gene, partial sequence.	MT760474	1328	47759

GC content

@ref	GC-content (mol%)	Method
67770	70.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM981163v1 assembly for Streptomyces tubercidicus NBRC 13090
BV-BRC: 47759.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.76	no
125439	motility	BacteriaNetⓘ	no	96.24	no
125439	gram_stain	BacteriaNetⓘ	positive	99.40	no
125439	spore_formation	BacteriaNetⓘ	yes	92.11	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces tubercidicus DSM 40261
NCBI: GCA_027497495.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.16	no
125438	anaerobic	anaerobicⓘ	no	97.52	no
125438	aerobic	aerobicⓘ	yes	91.60	no
125438	spore-forming	spore-formingⓘ	yes	92.79	no
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Biocatalytic conversion of avermectin to 4"-oxo-avermectin: characterization of biocatalytically active bacterial strains and of cytochrome p450 monooxygenase enzymes and their genes.	Jungmann V, Molnar I, Hammer PE, Hill DS, Zirkle R, Buckel TG, Buckel D, Ligon JM, Pachlatko JP.	Appl Environ Microbiol	10.1128/aem.71.11.6968-6976.2005	2005
	Discovery of PD-L1 Peptide Inhibitors from Ascidian Enzymatic Hydrolysates by Affinity Ultrafiltration Coupled to NanoLC-MS/MS.	Huang Q, Zang X, Jin X, Liu Q, Zhang X, Li X, Zhao L, Lv Z.	Mar Drugs	10.3390/md23040137	2025
	Drug repurposing screens identify Tubercidin as a potent antiviral agent against porcine nidovirus infections.	Wang T, Zheng G, Chen Z, Wang Y, Zhao C, Li Y, Yuan Y, Duan H, Zhu H, Yang X, Li W, Du W, Li Y, Li D.	Virus Res	10.1016/j.virusres.2023.199275	2024
	Tubercidin enhances apoptosis in serum-starved and hypoxic mouse cardiomyocytes by inducing nuclear speckle condensation.	Shen G, Cheng Q, Liang L, Qin Y, Cao Y, Li Q, Xiao S.	BMC Cardiovasc Disord	10.1186/s12872-025-04661-4	2025
	Isolation and Characterization of Lactic Acid Bacteria From "Trites" Having the Ability to Produce alpha-Glucosidase Inhibitors.	Fachrial E, Ismawati, Jati AP, Nugroho TT, Saryono.	Int J Microbiol	10.1155/ijm/8864668	2025
	Concentrative Nucleoside Transporter, CNT, Results in Selective Toxicity of Toyocamycin against Candida albicans.	Ojima Y, Yokota N, Tanibata Y, Nerome S, Azuma M.	Microbiol Spectr	10.1128/spectrum.01138-22	2022
Metabolism	Production of FK520 by Streptomyces tubercidicus.	Konya A, Szabo Z, Lang I, Barta I, Salat J.	Microbiol Res	10.1016/j.micres.2006.10.002	2008
Metabolism	Identification of a Biosynthetic Gene Cluster Responsible for the Production of a New Pyrrolopyrimidine Natural Product-Huimycin.	Shuai H, Myronovskyi M, Nadmid S, Luzhetskyy A.	Biomolecules	10.3390/biom10071074	2020
	Probing the DNA Reactivity and the Anticancer Properties of a Novel Tubercidin-Pt(II) Complex.	D'Errico S, Falanga AP, Capasso D, Di Gaetano S, Marzano M, Terracciano M, Roviello GN, Roviello GN, Piccialli G, Oliviero G, Borbone N.	Pharmaceutics	10.3390/pharmaceutics12070627	2020
	4E Interacting Protein as a Potential Novel Drug Target for Nucleoside Analogues in Trypanosoma brucei.	Mabille D, Cardoso Santos C, Hendrickx R, Claes M, Takac P, Clayton C, Hendrickx S, Hulpia F, Maes L, Van Calenbergh S, Caljon G.	Microorganisms	10.3390/microorganisms9040826	2021
Metabolism	Biotransformation of isoflavone using enzymatic reactions.	Roh C.	Molecules	10.3390/molecules18033028	2013
	5-Hydroxymethyltubercidin exhibits potent antiviral activity against flaviviruses and coronaviruses, including SARS-CoV-2.	Uemura K, Nobori H, Sato A, Sanaki T, Toba S, Sasaki M, Murai A, Saito-Tarashima N, Minakawa N, Orba Y, Kariwa H, Hall WW, Sawa H, Matsuda A, Maenaka K.	iScience	10.1016/j.isci.2021.103120	2021
Enzymology	Purification and characterization of GTP cyclohydrolase I from Streptomyces tubercidicus, a producer of tubercidin.	Yoo JC, Han JM, Ko OH, Bang HJ.	Arch Pharm Res	10.1007/bf02976759	1998
	Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes.	Richardson KE, Znosko BM.	RNA	10.1261/rna.055277.115	2016
Phylogeny	A taxonomic study of the genus Streptomyces by analysis of ribosomal protein AT-L30.	Ochi K.	Int J Syst Bacteriol	10.1099/00207713-45-3-507	1995
	Uncoupling of nucleo-cytoplasmic RNA export and localization during stress.	Hochberg-Laufer H, Schwed-Gross A, Neugebauer KM, Shav-Tal Y.	Nucleic Acids Res	10.1093/nar/gkz168	2019
Enzymology	A new site-specific endonuclease StuI from Streptomyces tubercidicus.	Shimotsu H, Takahashi H, Saito H.	Gene	10.1016/0378-1119(80)90062-1	1980
Enzymology	Actinopolysporins A-C and tubercidin as a Pdcd4 stabilizer from the halophilic actinomycete Actinopolyspora erythraea YIM 90600.	Zhao LX, Huang SX, Tang SK, Jiang CL, Duan Y, Beutler JA, Henrich CJ, McMahon JB, Schmid T, Blees JS, Colburn NH, Rajski SR, Shen B.	J Nat Prod	10.1021/np200603g	2011
Enzymology	Biocatalytic conversion of avermectin to 4"-oxo-avermectin: heterologous expression of the ema1 cytochrome P450 monooxygenase.	Molnar I, Hill DS, Zirkle R, Hammer PE, Gross F, Buckel TG, Jungmann V, Pachlatko JP, Ligon JM.	Appl Environ Microbiol	10.1128/aem.71.11.6977-6985.2005	2005
Metabolism	Comparative characterization of the lactimidomycin and iso-migrastatin biosynthetic machineries revealing unusual features for acyltransferase-less type I polyketide synthases and providing an opportunity to engineer new analogues.	Seo JW, Ma M, Kwong T, Ju J, Lim SK, Jiang H, Lohman JR, Yang C, Cleveland J, Zazopoulos E, Farnet CM, Shen B.	Biochemistry	10.1021/bi501396v	2014
Metabolism	Biocatalytic conversion of avermectin to 4''-oxo-avermectin: improvement of cytochrome p450 monooxygenase specificity by directed evolution.	Trefzer A, Jungmann V, Molnar I, Botejue A, Buckel D, Frey G, Hill DS, Jorg M, Ligon JM, Mason D, Moore D, Pachlatko JP, Richardson TH, Spangenberg P, Wall MA, Zirkle R, Stege JT.	Appl Environ Microbiol	10.1128/aem.02676-06	2007
Metabolism	The biosynthetic gene cluster of zorbamycin, a member of the bleomycin family of antitumor antibiotics, from Streptomyces flavoviridis ATCC 21892.	Galm U, Wendt-Pienkowski E, Wang L, George NP, Oh TJ, Yi F, Tao M, Coughlin JM, Shen B.	Mol Biosyst	10.1039/b814075h	2009
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
Phylogeny	Description of Streptomyces explomaris sp. nov., isolated from the coastal soil rhizosphere of Juniperus excelsa and reclassification of Streptomyces libani as a later heterotypic synonym of Streptomyces nigrescens.	Shu W, Ruckert-Reed C, Gromyko O, Tistechok S, Kalinowski J, Luzhetskyy A, Wittmann C.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006711	2025
	Genomic and Phenotypic Characterization of Streptomyces sirii sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil.	Zakalyukina YV, Alferova VA, Nikandrova AA, Kiriy AR, Chernyshova AP, Kabilov MR, Baturina OA, Biryukov MV, Sergiev PV, Lukianov DA.	Microorganisms	10.3390/microorganisms12122628	2024
	Streptomyces lydicamycinicus sp. nov. and Its Secondary Metabolite Biosynthetic Gene Clusters for Polyketide and Nonribosomal Peptide Compounds.	Komaki H, Hosoyama A, Igarashi Y, Tamura T.	Microorganisms	10.3390/microorganisms8030370	2020

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	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#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 .
#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 tubercidicus (DSM 40261, ATCC 25502, CBS 644.69)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

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_027497495

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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