Strain identifier

BacDive ID: 15568

Type strain: Yes

Species: Streptomyces rubiginosohelvolus

Strain history: KCC S-0415 <-- IFO 12912 <-- SAJ <-- ISP 5176 <-- INA 10/53.

NCBI tax ID(s): 67362 (species)

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General

@ref: 9369

BacDive-ID: 15568

DSM-Number: 40176

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

description: Streptomyces rubiginosohelvolus DSM 40176 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67362
  • Matching level: species

strain history

@refhistory
9369<- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA
67770KCC S-0415 <-- IFO 12912 <-- SAJ <-- ISP 5176 <-- INA 10/53.

doi: 10.13145/bacdive15568.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces rubiginosohelvolus

@ref: 9369

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces rubiginosohelvolus

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

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.843
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19418Yellow10-14 daysISP 2
19418Yellow10-14 daysISP 3
19418Yellow10-14 daysISP 4
19418Yellow10-14 daysISP 5
19418Yellow10-14 daysISP 6
19418Yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19418yesAerial MyceliumYellowISP 2
19418yesAerial MyceliumWhiteISP 3
19418yesAerial MyceliumYellowISP 4
19418yesAerial MyceliumWhiteISP 5
19418noISP 6
19418yesAerial MyceliumYellowISP 7

multimedia

  • @ref: 9369
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40176.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9369GYM 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
19418ISP 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
19418ISP 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:
19418ISP 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
19418ISP 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
19418ISP 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
19418ISP 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
9369ROLLED 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

culture temp

@refgrowthtypetemperaturerange
19418positiveoptimum28mesophilic
9369positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19418Formation of spore chains: rectiflixibilis,spore surface: smoothyes
69481yes100
69480yes100

halophily

  • @ref: 19418
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1941862968cellulose-
1941816634raffinose-
1941826546rhamnose+
1941828757fructose+
1941829864mannitol+
1941817268myo-inositol-
1941818222xylose-
1941817992sucrose-
1941822599arabinose+
1941817234glucose+
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
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
19418+++++++++++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19418-++++-+--++

Isolation, sampling and environmental information

isolation

  • @ref: 9369
  • sample type: soil

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: AB184240
  • 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
93691Risk group (German classification)
194181Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces rubiginosohelvolus gene for 16S rRNA, partial sequenceAB122740564ena67362
20218Streptomyces rubiginosohelvolus strain IFO 12912 16S ribosomal RNA gene, partial sequenceAY9998641420ena67362
20218Streptomyces rubiginosohelvolus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4415D44129120ena67362
20218Streptomyces rubiginosohelvolus gene for 16S rRNA, partial sequence, strain: NBRC 12912AB1842401481ena67362
20218Streptomyces rubiginosohelvolus 16S ribosomal RNA gene, partial sequenceKC355420704ena67362

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces rubiginosohelvolus JCM 4415GCA_014649875scaffoldncbi67362
66792Streptomyces rubiginosohelvolus strain JCM 441567362.3wgspatric67362

GC content

  • @ref: 67770
  • GC-content: 69
  • method: fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.831no
gram-positiveyes91.64no
anaerobicno99.136no
aerobicyes93.442no
halophileno91.883no
spore-formingyes94.235yes
glucose-utilyes88.654yes
thermophileno98.645yes
motileno93.961no
glucose-fermentno86.87no

External links

@ref: 9369

culture collection no.: DSM 40176, ATCC 19926, ATCC 23960, CBS 943.68, ETH 28494, IFO 12912, INA 10/53, ISP 5176, JCM 4415, KCC S-0415, NBRC 12912, RIA 1136, BCRC 13780, CGMCC 4.1752, KCTC 19970, NRRL B-5425, VKM Ac-1072

straininfo link

  • @ref: 84655
  • straininfo: 389359

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9369Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40176)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40176
19418Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40176.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
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
84655Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389359.1StrainInfo: A central database for resolving microbial strain identifiers