Strain identifier

BacDive ID: 15046

Type strain: Yes

Species: Streptomyces badius

Strain Designation: 1203/53

Strain history: KCC S-0350 <-- IFO 12745 <-- SAJ <-- ISP 5139 <-- INA 1203/53.

NCBI tax ID(s): 1941 (species)

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General

@ref: 9341

BacDive-ID: 15046

DSM-Number: 40139

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

description: Streptomyces badius 1203/53 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1941
  • Matching level: species

strain history

@refhistory
9341<- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA, 1203/53
67770KCC S-0350 <-- IFO 12745 <-- SAJ <-- ISP 5139 <-- INA 1203/53.

doi: 10.13145/bacdive15046.20230509.8.1

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 badius
  • full scientific name: Streptomyces badius (Kudrina 1957) Pridham et al. 1958 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces badius

@ref: 9341

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces badius

full scientific name: Streptomyces badius (Kudrina 1957) Pridham et al. 1958

strain designation: 1203/53

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.134
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19408Brown10-14 daysISP 2
19408Dark brown10-14 daysISP 3
19408Brown10-14 daysISP 4
19408Brown10-14 daysISP 5
19408Brown10-14 daysISP 6
19408Brown10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19408yesAerial MyceliumGreyISP 2
19408yesAerial MyceliumGrey/YellowISP 3
19408yesAerial MyceliumGrey/YellowISP 4
19408yesAerial MyceliumYellowISP 5
19408yesAerial MyceliumYellow/GreyISP 6
19408yesAerial MyceliumGreyISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9341GYM 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
19408ISP 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
19408ISP 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:
19408ISP 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
19408ISP 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
19408ISP 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
19408ISP 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
19408positiveoptimum28mesophilic
9341positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19408Formation of spore chains: rectifilibrilis, spore surface: smoothyes
69481yes91
69480yes100

compound production

@refcompound
9341cutinase
20216Antibiotic agent
20216Antifungal agent

halophily

  • @ref: 19408
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1940862968cellulose-
1940816634raffinose-
1940826546rhamnose-
1940828757fructose-
1940829864mannitol-
1940817268myo-inositol-
1940818222xylose-
1940817992sucrose-
1940822599arabinose+
1940817234glucose+
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
19408++--+-++-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9341soilKaukasusRussiaRUSEurope
67770SoilRussiaRUS

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_135.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_120;99_135&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AY999783
  • Sequence Identity:
  • Total samples: 4030
  • soil counts: 2441
  • aquatic counts: 286
  • animal counts: 1009
  • plant counts: 294

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
93411Risk group (German classification)
194081Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces badius gene for 16S ribosomal RNA, partial sequence, strain: JCM 4350D44068120ena1941
20218Streptomyces badius gene for 16S rRNA, partial sequence, strain: NBRC 12745AB1841141474ena1941
20218Streptomyces badius strain NRRL B-2567 16S ribosomal RNA gene, partial sequenceAY9997831496ena1941

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces badius JCM 4350GCA_014649415scaffoldncbi1941
66792Streptomyces badius strain JCM 43501941.9wgspatric1941

GC content

  • @ref: 67770
  • GC-content: 70
  • method: fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes91no
flagellatedno98.073no
gram-positiveyes91.021no
anaerobicno99.277no
aerobicyes95.055no
halophileno91.439no
spore-formingyes93.842no
glucose-utilyes88.083yes
thermophileno99.115no
motileno93.911no
glucose-fermentno86.292no

External links

@ref: 9341

culture collection no.: DSM 40139, ATCC 19729, ATCC 19888, CBS 468.68, IFO 12745, ISP 5139, NBRC 12745, RIA 1010, JCM 4350, BCRC 13759, CGMCC 4.1406, HAMBI 1008, IMET 43089, INA 1203/53, LMG 19353, NBIMCC 3320, NCIMB 13011, NRRL B-2567, VKM Ac-735

straininfo link

  • @ref: 84152
  • straininfo: 13357

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9341Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40139)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40139
19408Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40139.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
84152Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13357.1StrainInfo: A central database for resolving microbial strain identifiers