Streptomyces crystallinus (DSM 40945, JCM 5067, KCC S-1067)

Name: Streptomyces crystallinus (DSM 40945, JCM 5067, KCC S-1067)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16176

Type strain

Culture col. no. DSM 40945 JCM 5067 KCC S-1067 NRRL (= Lederle T-1384) NRRL B-3629 5 more

NCBI tax ID(s) 68191

Special Collections DSMZ JCM KCTC Wink compendium

History DSMZ <- NRRL (= Lederle T-1384) JCM <-- KCC S-1067 <-- MS 1483 <-- NRRL B-3629 <-- Lederle Labs.; T-1384.

Links

Streptomyces crystallinus DSM 40945 is a bacterium that produces antibiotic compounds.

antibiotic compound production genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49843

DSM 40945,JCM 5067,NRRL B-3629,IFO 15401,NCIMB 12860,KCTC 9717,AS 4.16,NBRC 15401,CGMCC 4.1600

@ref 20215

Last LPSN update 2026-05-29 08:28:43

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces crystallinus

Full scientific name Streptomyces crystallinus Tresner et al. 1961 (Approved Lists 1980)

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125439		95.334
125439		99.46	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9908	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
9908	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)
9908	positive	growth	28
19495	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.912

Spore formation

@ref	Spore formation	Confidence
125439		91.512

Compound production

9908

Compoundhygromycin A

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19495	NaCl	positive	maximum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19495	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
19495	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
19495	28757 ChEBI	fructose	-
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
19495	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
19495	29864 ChEBI	mannitol	-
19495	17268 ChEBI	myo-inositol	+/-
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
19495	16634 ChEBI	raffinose	-
19495	26546 ChEBI	rhamnose	-
19495	17992 ChEBI	sucrose	-
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
19495	18222 ChEBI	xylose	+/-

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
67770	69414 ChEBI	hygromycin A
68368	35581 ChEBI	indole	from API 20E

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
19495	+	+	-	-	-	+	-	+	-	-	+	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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9908	1	Risk group (German classification) According to TRBA 466
19495	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952126v1 assembly for Streptomyces crystallinus JCM 5067	scaffold	GCA_039521265	68191	59.31

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces crystallinus strain JCM 5067 16S ribosomal RNA gene, partial sequence	AY999762	1435	68191
20218	Streptomyces crystallinus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5067	D44436	120	68191
20218	Streptomyces crystallinus gene for 16S rRNA, partial sequence, strain: NBRC 15401	AB184652	1457	68191
124043	Streptomyces crystallinus strain JCM 5067 16S ribosomal RNA gene, partial sequence.	MT760647	683	68191

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3952126v1 assembly for Streptomyces crystallinus JCM 5067
NCBI: GCA_039521265

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.91	no
125439	motility	BacteriaNetⓘ	no	95.33	no
125439	gram_stain	BacteriaNetⓘ	positive	99.46	no
125439	spore_formation	BacteriaNetⓘ	yes	91.51	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Streptomyces cyclosori sp. nov., a novel actinobacterium from the rhizosphere soil of Cyclosorus parasiticus (L.) Farw.	Gao R, Chen Y, Xiao Y, Gao J.	J Antibiot (Tokyo)	10.1038/s41429-025-00857-0	2025
Phylogeny	Streptomyces sanyensis sp. nov., isolated from mangrove sediment.	Sui JL, Xu XX, Qu Z, Wang HL, Lin HP, Xie QY, Ruan JS, Hong K	Int J Syst Evol Microbiol	10.1099/ijs.0.023515-0	2010

References

#9908	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40945
#19495	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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 crystallinus (DSM 40945, JCM 5067, KCC S-1067)

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

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039521265

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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