Strain identifier

BacDive ID: 15279

Type strain: Yes

Species: Streptomyces griseorubiginosus

Strain history: KCC S-0481 <-- IFO 13047 <-- SAJ <-- ISP 5469 <-- INA 7712.

NCBI tax ID(s): 67304 (species)

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General

@ref: 9564

BacDive-ID: 15279

DSM-Number: 40469

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

description: Streptomyces griseorubiginosus DSM 40469 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67304
  • Matching level: species

strain history

@refhistory
9564<- E.B. Shirling, ISP <- G.F. Gauze, INA
67770KCC S-0481 <-- IFO 13047 <-- SAJ <-- ISP 5469 <-- INA 7712.

doi: 10.13145/bacdive15279.20230509.8.1

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

  • synonyms

    @refsynonym
    20215Streptomyces phaeoviridis
    20215Streptomyces phaeopurpureus
    20215Actinomyces griseorubiginosus

@ref: 9564

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces griseorubiginosus

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

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.727
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19460Wine red10-14 daysISP 2
19460Carmine red10-14 daysISP 3
19460Black red10-14 daysISP 4
19460Brown beige10-14 daysISP 5
19460Brown beige10-14 daysISP 6
19460Brown beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19460yesAerial MyceliumLight greyISP 2
19460yesAerial MyceliumLight greyISP 3
19460yesAerial MyceliumLight greyISP 4
19460noISP 5
19460noISP 6
19460noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9564GYM 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
19460ISP 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
19460ISP 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:
19460ISP 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
19460ISP 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
19460ISP 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
19460ISP 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
9564ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
19460positiveoptimum28mesophilic
9564positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1946062968cellulose+
1946016634raffinose+
1946026546rhamnose+
1946028757fructose+
1946029864mannitol+
1946017268myo-inositol+
1946018222xylose-
1946017992sucrose+
1946022599arabinose+
1946017234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideyes

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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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
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
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19460++++++++-++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19460+++++++--++

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinentgeographic location
9564soilUSSRAsia
67770Soil (podzol)USSRMoscow

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
95641Risk group (German classification)
194601Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces griseorubiginosus partial 16S rRNA gene, strain ISP 5469AJ3994881449ena67304
20218Streptomyces griseorubiginosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4481D44176120ena67304
20218Streptomyces griseorubiginosus 16S rRNA gene, type strain LMG 19941AJ7813391478ena67304
20218Streptomyces griseorubiginosus gene for 16S rRNA, partial sequence, strain: NBRC 13047AB1842761481ena67304
67770Streptomyces griseorubiginosus strain AS 4.1766 16S ribosomal RNA gene, partial sequenceFJ4059051376ena67304

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces griseorubiginosus strain DSM 4046967304.3wgspatric67304
66792Streptomyces griseorubiginosus DSM 404692775507132draftimg67304
67770Streptomyces griseorubiginosus DSM 40469GCA_001514195scaffoldncbi67304

GC content

@refGC-contentmethod
956470.9sequence analysis
6777070.9genome sequence analysis
6777072.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.165no
anaerobicno99.203no
halophileno95.418no
spore-formingyes93.582no
glucose-utilyes90.168yes
thermophileno99.545no
flagellatedno97.75no
motileno94.61no
aerobicyes93.251no
glucose-fermentno90.181no

External links

@ref: 9564

culture collection no.: DSM 40469, ATCC 23627, ATCC 25459, CBS 692.69, IFO 13047, INA 7712, ISP 5469, NBRC 13047, RIA 1239, JCM 4481, BCRC 12124, CGMCC 4.1766, NRRL B-12384, VKM Ac-1203

straininfo link

  • @ref: 84373
  • straininfo: 38134

literature

  • topic: Phylogeny
  • Pubmed-ID: 22805798
  • title: Taxonomy, purification and chemical characterization of four bioactive compounds from new Streptomyces sp. TN256 strain.
  • authors: Smaoui S, Mathieu F, Elleuch L, Coppel Y, Merlina G, Karray-Rebai I, Mellouli L
  • journal: World J Microbiol Biotechnol
  • DOI: 10.1007/s11274-011-0872-6
  • year: 2011
  • mesh: Anti-Infective Agents/*chemistry/*isolation & purification, Bacterial Typing Techniques, Biological Products/*chemistry/*isolation & purification, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Streptomyces/*chemistry/*classification/genetics/isolation & purification, Tunisia
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9564Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40469)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40469
19460Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40469.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
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
84373Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38134.1StrainInfo: A central database for resolving microbial strain identifiers