Strain identifier

BacDive ID: 15486

Type strain: Yes

Species: Streptomyces prunicolor

Strain history: KCC S-0508 <-- IFO 13075 <-- SAJ <-- ISP 5335 <-- INA 8805/64.

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General

@ref: 9467

BacDive-ID: 15486

DSM-Number: 40335

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive

description: Streptomyces prunicolor DSM 40335 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
67348species
1312234strain

strain history

@refhistory
9467<- E.B. Shirling, ISP <- G.F. Gauze, INA
67770KCC S-0508 <-- IFO 13075 <-- SAJ <-- ISP 5335 <-- INA 8805/64.

doi: 10.13145/bacdive15486.20230509.8.1

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 prunicolor
  • full scientific name: Streptomyces prunicolor (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Actinomyces prunicolor

@ref: 9467

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces prunicolor

full scientific name: Streptomyces prunicolor (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19439Yellow10-14 daysISP 2
19439Yellow10-14 daysISP 3
19439Yellow10-14 daysISP 4
19439Yellow10-14 daysISP 5
1943910-14 daysISP 6
19439Yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19439yesAerial MyceliumWhite/YellowISP 2
19439yesAerial MyceliumWhiteISP 3
19439yesAerial MyceliumWhiteISP 4
19439yesAerial MyceliumWhiteISP 5
19439noISP 6
19439yesAerial MyceliumWhiteISP 7

multimedia

  • @ref: 9467
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40335.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9467GYM 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
19439ISP 2yesName: 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
19439ISP 3yesName: 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:
19439ISP 4yesName: 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
19439ISP 5yesName: 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
19439ISP 6yesName: 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
19439ISP 7yesName: 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
9467ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
19439positiveoptimum28mesophilic
9467positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19439Formation of spore chains: rectiflixibilis, spore surface: smoothyes
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1943916634raffinose+/-
1943926546rhamnose+
1943928757fructose+
1943929864mannitol+
1943917268myo-inositol+
1943918222xylose+
1943917992sucrose-
1943922599arabinose+
1943917234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase+4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19439++----++-++

Isolation, sampling and environmental information

isolation

  • @ref: 9467
  • sample type: soil
  • country: USSR
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_940.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_118;99_940&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: DQ026659
  • Sequence Identity:
  • Total samples: 63
  • soil counts: 48
  • aquatic counts: 4
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94671Risk group (German classification)
194391Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces prunicolor gene for 16S ribosomal RNA, partial sequence, strain: JCM 4508D44198120ena1312234
20218Streptomyces prunicolor gene for 16S rRNA, partial sequence, strain: NBRC 13075AB1842941479ena1312234
20218Streptomyces prunicolor NBRC 13075 strain NRRL B-12281 16S ribosomal RNA gene, partial sequenceDQ0266591494ena1312234

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces prunicolor NBRC 130751312234.3wgspatric1312234
66792Streptomyces prunicolor NBRC 130752565956830draftimg1312234
67770Streptomyces prunicolor NBRC 13075GCA_000367365contigncbi1312234

GC content

  • @ref: 67770
  • GC-content: 69.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.435no
gram-positiveyes88.887no
anaerobicno99.028no
halophileno94.396no
spore-formingyes91.744yes
glucose-utilyes89.141yes
flagellatedno97.486no
thermophileno99.6yes
aerobicyes91.69no
glucose-fermentno87.934no

External links

@ref: 9467

culture collection no.: DSM 40335, ATCC 25487, CBS 915.69, IFO 13075, INA 8805/64, ISP 5335, NBRC 13075, RIA 1267, JCM 4508, BCRC 15146, CGMCC 4.1413, IMET 43129, KACC 20018, LMG 19311, NBIMCC 3317, NCIMB 9978, NRRL B-12281, PCM 2370, VKM Ac-992

straininfo link

  • @ref: 84573
  • straininfo: 13332

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24690912Streptomyces hokutonensis sp. nov., a novel actinomycete isolated from the strawberry root rhizosphere.Yamamura H, Ashizawa H, Hamada M, Hosoyama A, Komaki H, Otoguro M, Tamura T, Hayashi Y, Nakagawa Y, Ohtsuki T, Fujita N, Ui S, Hayakawa MJ Antibiot (Tokyo)10.1038/ja.2014.202014DNA, Bacterial/genetics, Fatty Acids/metabolism, Fragaria/metabolism/*microbiology, Japan, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizosphere, Streptomyces/*classification/genetics/isolation & purificationMetabolism
Phylogeny24812360Streptomyces graminifolii sp. nov., isolated from bamboo (Sasa borealis) litter.Lee HJ, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.056895-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sasa/*microbiology, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9467Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40335)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40335
19439Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40335.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
84573Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13332.1StrainInfo: A central database for resolving microbial strain identifiers