Streptomyces pathocidini (DSM 40799, ATCC 14510, BCRC 12331)

Name: Streptomyces pathocidini (DSM 40799, ATCC 14510, BCRC 12331)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14968

Type strain

Strain Designation B-28, BK-513

Culture col. no. DSM 40799 ATCC 14510 BCRC 12331 CCRC 12331 CGMCC 4.1633 10 more

NCBI tax ID(s) 1650571

Special Collections DSMZ JCM KCTC CIP

History <- H.D. Tresner, BK-513 KCC S-0166 <-- S. Suzuki B-28. CIP <- 1995, JCM <- KCC <- S. Suzuki: strain B-28

Links

Streptomyces pathocidini B-28 is an obligate aerobe, Gram-positive, rod-shaped bacterium that produces antibiotic compounds and was isolated from Soil.

antibiotic compound production Gram-positive rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 36101

ATCC 14510,CIP 104431,JCM 4166,DSM 40799,CCRC 12331,IFO 13812,VKM Ac-598,KCTC 9671,AS 4.1633,NBRC 13812,BCRC 12331,CGMCC 4.1633,NRRL B-24287

@ref 20215

Last LPSN update 2026-02-09 11:21:33

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces pathocidini

Full scientific name Streptomyces pathocidini (Nagatsu et al. 1962) Labeda et al. 2014

Synonyms (1)

Streptomyces albus subsp. pathocidicus

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121630	positive	rod-shaped
125438			90.5
125438	positive		90.035

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
9805	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
41379	MEDIUM 122 - for Streptomyces		Distilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.000 g);Starch maize (10.000 g)
9805	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
121630	CIP Medium 122	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
9805	positive	growth	28
41379	positive	growth	30
67770	positive	growth	28
121630	positive	growth	30-45

Physiology and metabolism

Oxygen tolerance

121630

Oxygen toleranceobligate aerobe

Compound production

@ref	Compound
9805	blasticidin S
9805	pathocidin-(8-azaguanine)
9805	restriction endonuclease SpaI (_XhoI)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121630	4853 ChEBI	esculin	-	hydrolysis
121630	17234 ChEBI	glucose	+	fermentation
121630	17632 ChEBI	nitrate	-	reduction
121630	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite
67770	63486 ChEBI	8-azaguanine
67770	15353 ChEBI	blasticidin S
121630	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
121630	alcohol dehydrogenase	-	1.1.1.1
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
121630	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
121630	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121630	caseinase	-	3.4.21.50
121630	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121630	DNase	+
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
121630	gelatinase	+/-
121630	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121630	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
121630	ornithine decarboxylase	-	4.1.1.17
121630	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
121630	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
121630	-	+	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121630	not determinedn.d.	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type
67770	Soil
121630	Environment, Soil

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9805	1	Risk group (German classification) According to TRBA 466
121630	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID
67770	ASM141849v1 assembly for Streptomyces pathocidini NRRL B-24287	scaffold	GCA_001418495	2690316220	1650571

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Streptomyces albus subsp. pathocidicus strain JCM 4166 16S ribosomal RNA gene, partial sequence	AY999806	1431		1650571
9805	Streptomyces albus subsp. pathocidicus gene for 16S rRNA, partial sequence, strain: NBRC 13812	AB184501	1467		1650571

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces pathocidini NRRL B-24287
NCBI: GCA_001418495.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.04	no
125438	anaerobic	anaerobicⓘ	no	98.77	yes
125438	aerobic	aerobicⓘ	yes	89.70	yes
125438	spore-forming	spore-formingⓘ	yes	89.20	no
125438	thermophilic	thermophileⓘ	no	94.92	yes
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Recent Developments and Challenges in the Enzymatic Formation of Nitrogen-Nitrogen Bonds.	Angeli C, Atienza-Sanz S, Schroder S, Hein A, Li Y, Argyrou A, Osipyan A, Terholsen H, Schmidt S.	ACS Catal	10.1021/acscatal.4c05268	2025
Metabolism	Nitric oxide as a source for bacterial triazole biosynthesis.	Zhao G, Guo YY, Yao S, Shi X, Lv L, Du YL.	Nat Commun	10.1038/s41467-020-15420-8	2020
	Draft Genome Sequence of Streptomyces morookaense DSM 40503, an 8-Azaguanine-Producing Strain.	Hei Y, Li Z, Zhou Y, Hu C, Gao JM, Qi J.	Microbiol Resour Announc	10.1128/mra.00518-20	2020
	Promiscuity of lanthipeptide enzymes: new challenges and applications.	Garcia-Ausencio C, Guzman-Chavez F, Rodriguez-Sanoja R, Sanchez S.	World J Microbiol Biotechnol	10.1007/s11274-025-04505-5	2025
	In vitro and in vivo production and split-intein mediated ligation (SIML) of circular bacteriocins.	Pena N, Bland MJ, Sevillano E, Munoz-Atienza E, Lafuente I, Bakkoury ME, Cintas LM, Hernandez PE, Gabant P, Borrero J.	Front Microbiol	10.3389/fmicb.2022.1052686	2022
	Class V Lanthipeptide Cyclase Directs the Biosynthesis of a Stapled Peptide Natural Product.	Pei ZF, Zhu L, Sarksian R, van der Donk WA, Nair SK.	J Am Chem Soc	10.1021/jacs.2c06808	2022
Metabolism	Cell wall glycopolymers of Streptomyces albus, Streptomyces albidoflavus and Streptomyces pathocidini.	Shashkov AS, Streshinskaya GM, Tul'skaya EM, Senchenkova SN, Baryshnikova LM, Dmitrenok AS, Ostash BE, Fedorenko VA	Antonie Van Leeuwenhoek	10.1007/s10482-016-0691-8	2016
Phylogeny	Streptomyces tremellae sp. nov., isolated from a culture of the mushroom Tremella fuciformis.	Wen ZQ, Chen B, Li X, Li BB, Li CH, Huang QH, Zhang QH, Dai WH, Jiang YJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001464	2016
Phylogeny	Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov.	Labeda DP, Doroghazi JR, Ju KS, Metcalf WW	Int J Syst Evol Microbiol	10.1099/ijs.0.058107-0	2013

References

#9805	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40799
#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 )
#41379	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#121630	Collection of Institut Pasteur ; Curators of the CIP; CIP 104431
#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 )
#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 pathocidini (DSM 40799, ATCC 14510, BCRC 12331)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Metabolite utilization

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001418495

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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