Name: Streptomyces yogyakartensis C4R3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16355

Type strain:

Species: Streptomyces yogyakartensis

Strain Designation: C4R3

Culture col. no.: DSM 41766, NCIMB 13681, JCM 11448, MTCC 6924, NBRC 100779

Strain history: NCIMB 13681 <-- M. Goodfellow C4R3.

NCBI tax ID(s): 114692 (species)

SI-ID 50109

DSM 41766, NCIMB 13681, JCM 11448, NBRC 100779, NRRL B-24280

Special Collections

Section

Streptomyces yogyakartensis C4R3 is a bacterium that builds an aerial mycelium and was isolated from soil around the rhizosphere of Paraserianthes falcataria.

16S sequence
Bacteria

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 yogyakartensis**
	Full Scientific Name (LPSN)	Streptomyces yogyakartensis Sembiring et al. 2001

Information on morphological and physiological properties Morphology

[Ref.: #69298]	Colony color	Grey beige (1019)
[Ref.: #69298]	Cultivation medium used	ISP 6

[Ref.: #69298]	Colony color	Grey beige (1019)
[Ref.: #69298]	Cultivation medium used	suter with tyrosine

[Ref.: #69298]	Colony color	Light ivory (1015)
[Ref.: #69298]	Cultivation medium used	ISP 2

[Ref.: #69298]	Colony color	Light ivory (1015)
[Ref.: #69298]	Cultivation medium used	suter without tyrosine

[Ref.: #69298]	Colony color	Ochre brown (8001)
[Ref.: #69298]	Cultivation medium used	ISP 7

[Ref.: #69298]	Colony color	Sand yellow (1002)
[Ref.: #69298]	Cultivation medium used	ISP 5

[Ref.: #69298]	Pigment production	yes
[Ref.: #69298]	Pigment name	Melanin
[Ref.: #69298]	Pigment production	yes
[Ref.: #69298]	Pigmentation color	Beige (1001), sand yellow (1002), ochre brown (8001)
[Ref.: #69298]	Pigment name	soluble pigment

[Ref.: #69298]	Multicellular complex forming ability	yes
[Ref.: #69298]	Multicellular complex name	Aerial mycelium
[Ref.: #69298]	Multicellular complex color	Cream (9001), signal white (9003)
[Ref.: #69298]	Medium Name (multicellularity)	ISP 2

[Ref.: #69298]	Multicellular complex forming ability	yes
[Ref.: #69298]	Multicellular complex name	Aerial mycelium
[Ref.: #69298]	Multicellular complex color	Signal white (9003),stone grey (7030)
[Ref.: #69298]	Medium Name (multicellularity)	ISP 3

[Ref.: #69298]	Multicellular complex forming ability	yes
[Ref.: #69298]	Multicellular complex name	Aerial mycelium
[Ref.: #69298]	Multicellular complex color	Signal white (9003), stone grey (7030)
[Ref.: #69298]	Medium Name (multicellularity)	ISP 4

[Ref.: #69298]	Multicellular complex forming ability	yes
[Ref.: #69298]	Multicellular complex name	Aerial mycelium
[Ref.: #69298]	Multicellular complex color	Mouse grey (7005)
[Ref.: #69298]	Medium Name (multicellularity)	ISP 5

[Ref.: #69298]	Multicellular complex forming ability	no
[Ref.: #69298]	Multicellular complex name	Aerial mycelium
[Ref.: #69298]	Medium Name (multicellularity)	ISP 6

[Ref.: #69298]	Multicellular complex forming ability	yes
[Ref.: #69298]	Multicellular complex name	Aerial mycelium
[Ref.: #69298]	Multicellular complex color	Traffic white (9016)
[Ref.: #69298]	Medium Name (multicellularity)	ISP 7

[Ref.: #69298]	Multicellular complex forming ability	yes
[Ref.: #69298]	Multicellular complex name	Aerial mycelium
[Ref.: #69298]	Multicellular complex color	Oyster white (1013)
[Ref.: #69298]	Medium Name (multicellularity)	suter with tyrosine

[Ref.: #69298]	Multicellular complex forming ability	no
[Ref.: #69298]	Multicellular complex name	Aerial mycelium
[Ref.: #69298]	Medium Name (multicellularity)	suter without tyrosine

Multimedia content

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Caption:

Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)

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Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

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Caption:

Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69298]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

Information on culture and growth conditions Culture and growth conditions

[Ref.: #10555]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #10555]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #10555]			growth	28 °C
[Ref.: #67770]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69298]		NaCl		growth	0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69298]	arabinose ChEBI	+	growth
[Ref.: #69298]	cellulose ChEBI	-	growth
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #69298]	fructose ChEBI	+	growth
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #69298]	glucose ChEBI	+	growth
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #69298]	inositol ChEBI	+	growth
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69298]	mannose ChEBI	+	growth
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #69298]	raffinose ChEBI	+	growth
[Ref.: #69298]	rhamnose ChEBI	+	growth
[Ref.: #69298]	sucrose ChEBI	+	growth
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #69298]	xylose ChEBI	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne, API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68379]	alpha-glucosidase	+	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68379]	beta-galactosidase	+	3.2.1.23	* from API Coryne, API zym
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API Coryne, API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #69298]	3792	-	-	-	+	-	+	+	+	+	-	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #69298]	5976	not determinedn.d.	+	+/-	-	-	+	+	+/-	+	+	+	+	+	+	-	-	+/-	+	+	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #10555]	Sample type/isolated from	soil around the rhizosphere of Paraserianthes falcataria
[Ref.: #10555]	Host species	Paraserianthes falcataria
[Ref.: #10555]	Geographic location (country and/or sea, region)	Java, Yogyakarta
[Ref.: #10555]	Country	Indonesia
[Ref.: #10555]	Country ISO 3 Code	IDN
[Ref.: #10555]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Non-rhizosphere soil adjacent to a stand of the tropical legume, Paraserianthes falcataria
[Ref.: #67770]	Host species	Paraserianthes falcataria
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yogyakarta
[Ref.: #67770]	Country	Indonesia
[Ref.: #67770]	Country ISO 3 Code	IDN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

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Global distribution of 16S sequence HQ244470 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	65
Soil Samples	635
Animal Samples	94
Plant Samples	40
Total Samples	834

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

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Biosafety level

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 sp. C4R3 (S3) partial 16S rRNA gene	AJ391827	1481	GenBank ENA	114692 tax ID	*
[Ref.: #20218]	Streptomyces yogyakartensis strain DSM 41766 16S ribosomal RNA gene, partial sequence	HQ244470	1376	GenBank ENA	114692 tax ID	*
[Ref.: #20218]	Streptomyces yogyakartensis gene for 16S rRNA, partial sequence, strain: NBRC 100779	AB249942	1482	GenBank ENA	114692 tax ID	*

Availability in culture collections External links

[Ref.: #10555]

Culture collection no.

DSM 41766, NCIMB 13681, JCM 11448, MTCC 6924, NBRC 100779

[Ref.: #85410]

SI-ID 50109

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Streptomyces antioxidans sp. nov., a Novel Mangrove Soil Actinobacterium with Antioxidative and Neuroprotective Potentials.	Ser HL, Tan LT, Palanisamy UD, Abd Malek SN, Yin WF, Chan KG, Goh BH, Lee LH	Front Microbiol	10.3389/fmicb.2016.00899	2016	*
Phylogeny	Streptomyces iranensis sp. nov., isolated from soil.	Hamedi J, Mohammadipanah F, Klenk HP, Potter G, Schumann P, Sproer C, von Jan M, Kroppenstedt RM	Int J Syst Evol Microbiol	10.1099/ijs.0.015339-0	2009	*

References

#10555

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 41766

#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;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69298

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 .

#85410

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-ID50109.1 )

* These data were automatically processed and therefore are not curated

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