Strain identifier

BacDive ID: 16355

Type strain: Yes

Species: Streptomyces yogyakartensis

Strain Designation: C4R3

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

NCBI tax ID(s): 114692 (species)

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General

@ref: 10555

BacDive-ID: 16355

DSM-Number: 41766

keywords: 16S sequence, Bacteria

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

NCBI tax id

  • NCBI tax id: 114692
  • Matching level: species

strain history

@refhistory
10555<- M. Goodfellow, Univ. Newcastle; C4R3
67770NCIMB 13681 <-- M. Goodfellow C4R3.

doi: 10.13145/bacdive16355.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces yogyakartensis
  • full scientific name: Streptomyces yogyakartensis Sembiring et al. 2001

@ref: 10555

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces yogyakartensis

full scientific name: Streptomyces yogyakartensis Sembiring et al. 2001

strain designation: C4R3

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
69298Grey beige (1019)ISP 6
69298Grey beige (1019)suter with tyrosine
69298Light ivory (1015)ISP 2
69298Light ivory (1015)suter without tyrosine
69298Ochre brown (8001)ISP 7
69298Sand yellow (1002)ISP 5

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69298yesAerial myceliumCream (9001), signal white (9003)ISP 2
69298yesAerial myceliumSignal white (9003),stone grey (7030)ISP 3
69298yesAerial myceliumSignal white (9003), stone grey (7030)ISP 4
69298yesAerial myceliumMouse grey (7005)ISP 5
69298noAerial myceliumISP 6
69298yesAerial myceliumTraffic white (9016)ISP 7
69298yesAerial myceliumOyster white (1013)suter with tyrosine
69298noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
69298yesMelanin
69298yessoluble pigmentBeige (1001), sand yellow (1002), ochre brown (8001)

multimedia

@refmultimedia contentcaptionintellectual property rights
69298DSM_41766_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69298DSM_41766_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10555GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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
10555ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: 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
10555STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperature
10555positivegrowth28
67770positivegrowth28

Physiology and metabolism

halophily

  • @ref: 69298
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6929822599arabinose+growth
6929862968cellulose-growth
6929828757fructose+growth
6929817234glucose+growth
6929817268inositol+growth
6929837684mannose+growth
6929816634raffinose+growth
6929826546rhamnose+growth
6929817992sucrose+growth
6929818222xylose+growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69298---+-++++-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69298++/---+++/-++++++--+/-++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
10555soil around the rhizosphere of Paraserianthes falcatariaParaserianthes falcatariaJava, YogyakartaIndonesiaIDNAsia
67770Non-rhizosphere soil adjacent to a stand of the tropical legume, Paraserianthes falcatariaParaserianthes falcatariaYogyakartaIndonesiaIDNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_359.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_103;97_110;98_303;99_359&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: HQ244470
  • Sequence Identity:
  • Total samples: 834
  • soil counts: 635
  • aquatic counts: 65
  • animal counts: 94
  • plant counts: 40

Safety information

risk assessment

  • @ref: 10555
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces sp. C4R3 (S3) partial 16S rRNA geneAJ3918271481nuccore114692
20218Streptomyces yogyakartensis strain DSM 41766 16S ribosomal RNA gene, partial sequenceHQ2444701376nuccore114692
20218Streptomyces yogyakartensis gene for 16S rRNA, partial sequence, strain: NBRC 100779AB2499421482nuccore114692

External links

@ref: 10555

culture collection no.: DSM 41766, NCIMB 13681, JCM 11448, MTCC 6924, NBRC 100779

straininfo link

  • @ref: 85410
  • straininfo: 50109

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19684315Streptomyces iranensis sp. nov., isolated from soil.Hamedi J, Mohammadipanah F, Klenk HP, Potter G, Schumann P, Sproer C, von Jan M, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/ijs.0.015339-02009Base Sequence, Molecular Sequence Data, Phenotype, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny27379040Streptomyces 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 LHFront Microbiol10.3389/fmicb.2016.008992016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10555Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41766)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41766
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69298Wink, J.https://cdn.dsmz.de/wink/DSM%2041766.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
85410Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50109.1StrainInfo: A central database for resolving microbial strain identifiers