Strain identifier

BacDive ID: 16133

Type strain: Yes

Species: Streptomyces yokosukanensis

Strain Designation: IPCR B34

Strain history: KCC S-0137 <-- G. Nakamura B-34.

NCBI tax ID(s): 67386 (species)

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General

@ref: 9385

BacDive-ID: 16133

DSM-Number: 40224

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

description: Streptomyces yokosukanensis IPCR B34 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67386
  • Matching level: species

strain history

@refhistory
9385<- E.B. Shirling, ISP <- S. Suzuki, IPCR B34
67770KCC S-0137 <-- G. Nakamura B-34.

doi: 10.13145/bacdive16133.20230509.8.1

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 yokosukanensis
  • full scientific name: Streptomyces yokosukanensis Nakamura 1961 (Approved Lists 1980)

@ref: 9385

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces yokosukanensis

full scientific name: Streptomyces yokosukanensis Nakamura 1961 emend. Nouioui et al. 2018

strain designation: IPCR B34

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
21383Sand yellow10-14 daysISP 2
21383Golden yellow10-14 daysISP 3
21383Honey yellow10-14 daysISP 4
21383Ochre yellow10-14 daysISP 5
21383Sepia brown10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
21383noISP 2
21383yesISP 3Aerial MyceliumBeige
21383yesISP 4Aerial MyceliumBeige
21383yesISP 5Aerial MyceliumBrown beige
21383yesISP 7Aerial MyceliumYellow grey

multimedia

  • @ref: 9385
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40224.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9385GYM 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
21383ISP 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
21383ISP 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:
21383ISP 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
21383ISP 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
21383ISP 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

culture temp

@refgrowthtypetemperaturerange
9385positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9385neburalin
67770Neburalin (9-beta-ribofuranosylpurine)

metabolite utilization

@refChebi-IDmetaboliteutilization activity
2138317234glucose+
2138322599arabinose+
2138317992sucrose-
2138318222xylose+
2138317268myo-inositol+
2138337684mannose-
2138328757fructose+
2138326546rhamnose+
2138316634raffinose+
2138362968cellulose-

enzymes

@refvalueactivityec
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52

API zym

@refAlkaline phosphataseEsteraseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphatasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidase
21383+--++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9385soilJapanJPNAsia
67770SoilJapanJPNAsiaYokosuka, Kanagawa Pref.

isolation source categories

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

Safety information

risk assessment

  • @ref: 9385
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces yokosukanensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4559D44231120ena67386
20218Streptomyces yokosukanensis gene for 16S rRNA, partial sequence, strain: NBRC 13108AB1843191470ena67386
20218Streptomyces yokosukanensis strain NRRL B-3353 16S ribosomal RNA gene, partial sequenceDQ0266521555ena67386

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces yokosukanensis strain DSM 4022467386.3wgspatric67386
66792Streptomyces yokosukanensis DSM 402242775507095draftimg67386
67770Streptomyces yokosukanensis DSM 40224GCA_001514035scaffoldncbi67386

GC content

  • @ref: 67770
  • GC-content: 71.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes87.763no
anaerobicno98.898no
halophileno92.712no
spore-formingyes94.521no
glucose-utilyes90.161yes
thermophileno98.572yes
flagellatedno98.146no
motileno94.973no
aerobicyes89.584no
glucose-fermentno89.931no

External links

@ref: 9385

culture collection no.: DSM 40224, ATCC 25520, CBS 662.69, IFO 13108, ISP 5224, JCM 4137, NBRC 13108, RIA 1300, BCRC 11875, JCM 4559, NRRL B-3353, VKM Ac-1713

straininfo link

  • @ref: 85198
  • straininfo: 92653

literature

  • topic: Phylogeny
  • Pubmed-ID: 18924404
  • title: Isolation and biochemical characterization of delta-aminolevulinic acid dehydratase from Streptomyces yokosukanensis ATCC 25520.
  • authors: Konuk M, Cigerci IH, Aksan S, Korcan SE
  • journal: Prikl Biokhim Mikrobiol
  • year: 2008
  • mesh: Porphobilinogen Synthase/biosynthesis/chemistry/*isolation & purification, Streptomyces/drug effects/*enzymology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9385Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40224)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40224
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
21383Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40224.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
85198Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92653.1StrainInfo: A central database for resolving microbial strain identifiers