Saccharothrix syringae (DSM 43886, ATCC 51364, IFO 14523)

Name: Saccharothrix syringae (DSM 43886, ATCC 51364, IFO 14523)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13480

Type strain

Culture col. no. DSM 43886 ATCC 51364 IFO 14523 IMET 9675 INA 2240 7 more

NCBI tax ID(s) 103733

Special Collections DSMZ JCM KCTC Wink compendium

History <- N. Agre, INA A. Shimazu AIAM 5063 <-- IFO 14523 <-- INA 2240.

Links

Saccharothrix syringae DSM 43886 is a bacterium that builds an aerial mycelium and produces antibiotic compounds.

antibiotic compound production genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42951

ATCC 51364,DSM 43886,IFO 14523,IMET 9675,JCM 6844,NRRL B-16468,VKM Ac-1858,KCTC 9398,AS 4.1716,NBRC 14523,BCRC 16262,CCRC 16262,CGMCC 4.1716

@ref 20215

Last LPSN update 2026-02-09 11:21:09

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Saccharothrix

Species Saccharothrix syringae

Full scientific name Saccharothrix syringae (Gauze and Sveshnikova 1985) Grund and Kroppenstedt 1990

Synonyms (1)

Nocardiopsis syringae

BacDive ID	Other strains from **Saccharothrix syringae** (4)	Type strain
105442	S. syringae STH00369(ZIMET), GT20024029, HKI 0369, NCIMB ...
105443	S. syringae STH00372(ZIMET), ST 26558, GT20024021, HKI ...
105444	S. syringae STH00370(ZIMET), ST 27023, HKI 0370, VTT ...
105445	S. syringae STH00371(ZIMET), ST 26567, GT20024030, HKI ...

Morphology

Colony morphology

@ref	Colony color	Incubation period	Medium used
19974	Yellow beige	10-14 days	ISP 2
19974	Yellow beige	10-14 days	ISP 3
19974	Yellow beige	10-14 days	ISP 4
19974	Yellow beige	10-14 days	ISP 5
19974	Yellow beige	10-14 days	ISP 6
19974	Yellow beige	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19974	Aerial Mycelium	White	ISP 2
19974			ISP 3
19974			ISP 4
19974			ISP 5
19974			ISP 6
19974			ISP 7

Multimedia

@ref:	11365
multimedia content:	DSM_43886.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_43886.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11365	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
19974	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19974	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19974	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19974	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19974	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19974	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)
11365	positive	growth	28
19974	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Compound production

11365

Compoundnocamycin

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19974	NaCl	positive	maximum	2.5 %

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19974	22599 ChEBI	arabinose	+
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
19974	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
19974	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
19974	17234 ChEBI	glucose	+
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
19974	29864 ChEBI	mannitol	+
19974	17268 ChEBI	myo-inositol	-
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
19974	16634 ChEBI	raffinose	-
19974	26546 ChEBI	rhamnose	+
19974	17992 ChEBI	sucrose	+
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68368	27897 ChEBI	tryptophan	+	energy source	from API 20E
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
19974	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68369	35581 ChEBI	indole	from API 20NE
68368	35581 ChEBI	indole	from API 20E
67770		nocamycin

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68369	35581 ChEBI	indole		-	from API 20NE
68368	35581 ChEBI	indole		+	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase lipase (C 8)	-		from API zym
68368	gelatinase	+		from API 20E
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68369	urease	-	3.5.1.5	from API 20NE
68368	urease	+	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

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
19974	+	+	+	+	+	-	+	-	+	+	+	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

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
11365	-	-	+/-	-	-	+/-	-	-	-	-	-	-	-	-	-	+	+/-	+	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
11365	+	-	-	-	-	+	+/-	+	+	+	+	+	+	+	+	-	+/-	+	+/-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
11365	soil
67770	Soil

Taxonmaps

69479

Global distribution of 16S sequence AF114812 (>99% sequence identity) for Saccharothrix from Microbeatlas

Aquatic Samples	7
Soil Samples	59
Animal Samples	4
Plant Samples	2
Total Samples	72

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11365	1	Risk group (German classification) According to TRBA 466
19974	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
67770	ASM949803v1 assembly for Saccharothrix syringae NRRL B-16468	complete	GCA_009498035	103733.7	8066685052	103733	96.56
67770	ASM71675v1 assembly for Saccharothrix syringae NRRL B-16468	contig	GCA_000716755	103733.3	2751185736	103733	39.25

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Saccharothrix syringae strain NRRL B-16468T 16S ribosomal RNA gene, partial sequence	AF114812	1510		103733

GC content

@ref	GC-content (mol%)	Method
67770	73.5	genome sequence analysis

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Aromatic side-chain crosslinking in RiPP biosynthesis.	Kandy SK, Pasquale MA, Chekan JR.	Nat Chem Biol	10.1038/s41589-024-01795-y	2025
	Biotechnological applications of S-adenosyl-methionine-dependent methyltransferases for natural products biosynthesis and diversification.	Zhang C, Sultan SA, T R, Chen X.	Bioresour Bioprocess	10.1186/s40643-021-00425-y	2021
Enzymology	Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products.	Adrover-Castellano ML, Schmidt JJ, Sherman DH.	ChemCatChem	10.1002/cctc.202001886	2021
Metabolism	Elucidation of a carboxylate O-methyltransferase NcmP in nocamycin biosynthetic pathway.	Mo X, Gui C, Wang Q.	Bioorg Med Chem Lett	10.1016/j.bmcl.2017.08.010	2017
	Cryptic Cerulenin Rearrangement in Ketosynthase Covalent Inhibition.	Jiang Z, Chen JA, Mohamed OG, Huynh J, Chen A, Tripathi A, La Clair JJ, Burkart MD.	J Am Chem Soc	10.1021/jacs.4c05938	2024
	Mutagenetic analysis of the biosynthetic pathway of tetramate bripiodionen bearing 3-(2H-pyran-2-ylidene)pyrrolidine-2,4-dione skeleton.	Zang H, Cheng Y, Li M, Zhou L, Hong LL, Deng H, Lin HW, Zhou Y.	Microb Cell Fact	10.1186/s12934-024-02364-7	2024
	Photocobilins integrate B₁₂ and bilin photochemistry for enzyme control.	Zhang S, Jeffreys LN, Poddar H, Yu Y, Liu C, Patel K, Johannissen LO, Zhu L, Cliff MJ, Yan C, Schiro G, Weik M, Sakuma M, Levy CW, Leys D, Heyes DJ, Scrutton NS.	Nat Commun	10.1038/s41467-024-46995-1	2024
Genetics	A panoramic view of the genomic landscape of the genus Streptomyces.	Nikolaidis M, Hesketh A, Frangou N, Mossialos D, Van de Peer Y, Oliver SG, Amoutzias GD.	Microb Genom	10.1099/mgen.0.001028	2023
Genetics	Diverse Cone-Snail Species Harbor Closely Related Streptomyces Species with Conserved Chemical and Genetic Profiles, Including Polycyclic Tetramic Acid Macrolactams.	Quezada M, Licona-Cassani C, Cruz-Morales P, Salim AA, Marcellin E, Capon RJ, Barona-Gomez F.	Front Microbiol	10.3389/fmicb.2017.02305	2017
	A Novel Protein Elicitor BAR11 From Saccharothrix yanglingensis Hhs.015 Improves Plant Resistance to Pathogens and Interacts With Catalases as Targets.	Zhang Y, Yan X, Guo H, Zhao F, Huang L.	Front Microbiol	10.3389/fmicb.2018.00700	2018
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Enzymology	Novel dTDP-l-Rhamnose Synthetic Enzymes (RmlABCD) From Saccharothrix syringae CGMCC 4.1716 for One-Pot Four-Enzyme Synthesis of dTDP-l-Rhamnose.	Yang S, An X, Gu G, Yan Z, Jiang X, Xu L, Xiao M	Front Microbiol	10.3389/fmicb.2021.772839	2021
Enzymology	Short-Chain Dehydrogenase NcmD Is Responsible for the C-10 Oxidation of Nocamycin F in Nocamycin Biosynthesis.	Mo X, Zhang H, Du F, Yang S	Front Microbiol	10.3389/fmicb.2020.610827	2020
	Complete Genome of Nocamycin-Producing Strain Saccharothrix syringae NRRL B-16468 Reveals the Biosynthetic Potential for Secondary Metabolites.	Mo X, Yang S	Curr Microbiol	10.1007/s00284-020-02272-0	2020
Metabolism	Identification of nocamycin biosynthetic gene cluster from Saccharothrix syringae NRRL B-16468 and generation of new nocamycin derivatives by manipulating gene cluster.	Mo X, Shi C, Gui C, Zhang Y, Ju J, Wang Q	Microb Cell Fact	10.1186/s12934-017-0718-5	2017
Phylogeny	Saccharothrix xinjiangensis sp. nov., a pyrene-degrading actinomycete isolated from Tianchi Lake, Xinjiang, China.	Hu YT, Zhou PJ, Zhou YG, Liu ZH, Liu SJ.	Int J Syst Evol Microbiol	10.1099/ijs.0.63143-0	2004

References

#11365	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43886
#19974	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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68369	Automatically annotated from API 20NE .
#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 .
#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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Saccharothrix syringae (DSM 43886, ATCC 51364, IFO 14523)

Name and taxonomic classification

Morphology

Colony morphology

Multicellular morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Compound production

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_009498035

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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