Strain identifier

BacDive ID: 16108

Type strain: Yes

Species: Streptomyces viridiviolaceus

Strain history: KCC S-0855 <-- IFO 13359 <-- SAJ <-- ISP 5280 <-- INA 5276/56.

NCBI tax ID(s): 68282 (species)

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General

@ref: 9431

BacDive-ID: 16108

DSM-Number: 40280

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

description: Streptomyces viridiviolaceus DSM 40280 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from Soil.

NCBI tax id

  • NCBI tax id: 68282
  • Matching level: species

strain history

@refhistory
9431<- E.B. Shirling, ISP <- G.F. Gauze, INA
67770KCC S-0855 <-- IFO 13359 <-- SAJ <-- ISP 5280 <-- INA 5276/56.

doi: 10.13145/bacdive16108.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces viridiviolaceus

@ref: 9431

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces viridiviolaceus

full scientific name: Streptomyces viridiviolaceus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.806
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19431Brown10-14 daysISP 2
19431Yellow10-14 daysISP 3
19431Violett10-14 daysISP 4
19431Orange10-14 daysISP 5
19431Brown10-14 daysISP 6
19431Yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19431yesAerial MyceliumGreyISP 2
19431yesAerial MyceliumGreyISP 3
19431yesAerial MyceliumGreyISP 4
19431yesAerial MyceliumGreyISP 5
19431noISP 6
19431yesAerial MyceliumGreyISP 7

multimedia

  • @ref: 9431
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40280.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9431GYM 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
19431ISP 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
19431ISP 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:
19431ISP 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
19431ISP 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
19431ISP 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
19431ISP 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
9431ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
9431positivegrowth28mesophilic
19431positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19431Formation of spore chains: spira, spore surface: spiny to hairyyes
69481yes100
69480yes100

halophily

  • @ref: 19431
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1943162968cellulose-
1943116634raffinose-
1943126546rhamnose-
1943128757fructose+
1943129864mannitol+
1943117268myo-inositol-
1943118222xylose+/-
1943117992sucrose-
1943122599arabinose+
1943117234glucose+
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
19431+-----+--++

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94311Risk group (German classification)
194311Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces viridiviolaceus strain IFO 13359 16S ribosomal RNA gene, partial sequenceAY9998541420ena68282
20218Streptomyces viridiviolaceus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4855D44408120ena68282
20218Streptomyces viridiviolaceus gene for 16S rRNA, partial sequence, strain: NBRC 13359AB1843501471ena68282

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces viridiviolaceus JCM 4855GCA_014650995scaffoldncbi68282
66792Streptomyces viridiviolaceus strain JCM 485568282.3wgspatric68282

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.783no
gram-positiveyes88.376no
anaerobicno99.133no
aerobicyes93.294no
halophileno91.204no
spore-formingyes94.851yes
thermophileno97.95yes
glucose-utilyes89.795yes
motileno94.352no
glucose-fermentno89.651no

External links

@ref: 9431

culture collection no.: DSM 40280, ATCC 27478, CBS 660.72, IFO 13359, INA 5276/56, ISP 5280, NBRC 13359, RIA 1320, JCM 4855, BCRC 12457, CGMCC 4.1775, KCTC 19976, NRRL B-12182, VKM Ac-587

straininfo link

  • @ref: 85174
  • straininfo: 39022

literature

  • topic: Phylogeny
  • Pubmed-ID: 35412082
  • title: Streptomyces griseicoloratus sp. nov., isolated from soil in cotton fields in Xinjiang, China.
  • authors: Xing L, Xia YY, Zhang QY, Xia ZF, Wan CX, Zhang LL, Luo XX
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-022-02818-9
  • year: 2022
  • mesh: DNA, Bacterial/genetics, Fatty Acids/chemistry, Gossypium, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Soil Microbiology, *Streptomyces
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9431Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40280)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40280
19431Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40280.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
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
85174Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39022.1StrainInfo: A central database for resolving microbial strain identifiers