Strain identifier

BacDive ID: 16077

Type strain: Yes

Species: Streptomyces violaceochromogenes

Strain history: KCC S-0530 <-- IFO 13100 <-- SAJ <-- ISP 5181 <-- T. P. Preobrazhenskaya INA 425.

NCBI tax ID(s): 67377 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9245

BacDive-ID: 16077

DSM-Number: 40181

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

description: Streptomyces violaceochromogenes DSM 40181 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67377
  • Matching level: species

strain history

@refhistory
9245<- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA
67770KCC S-0530 <-- IFO 13100 <-- SAJ <-- ISP 5181 <-- T. P. Preobrazhenskaya INA 425.

doi: 10.13145/bacdive16077.20230509.8.1

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 violaceochromogenes
  • full scientific name: Streptomyces violaceochromogenes (Ryabova and Preobrazhenskaya 1957) Pridham 1970 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Actinomyces violaceochromogenes

@ref: 9245

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces violaceochromogenes

full scientific name: Streptomyces violaceochromogenes (Ryabova and Preobrazhenskaya 1957) Pridham 1970

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.071
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19419Brown10-14 daysISP 2
19419Yellow10-14 daysISP 3
19419Brown10-14 daysISP 4
19419Yellow10-14 daysISP 5
19419Yellow10-14 daysISP 6
19419Brown10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19419yesAerial MyceliumWhiteISP 2
19419yesAerial MyceliumGreyISP 3
19419yesAerial MyceliumGreyISP 4
19419yesAerial MyceliumGreyISP 5
19419noISP 6
19419yesAerial MyceliumGreyISP 7

multimedia

  • @ref: 9245
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40181.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9245GYM 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
19419ISP 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
19419ISP 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:
19419ISP 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
19419ISP 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
19419ISP 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
19419ISP 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
9245positivegrowth28mesophilic
19419positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19419Formation of spore chains: retinaculiapetri, spore surface: smoothyes
69481yes100
69480yes100

halophily

  • @ref: 19419
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1941962968cellulose-
1941916634raffinose-
1941926546rhamnose-
1941928757fructose-
1941929864mannitol-
1941917268myo-inositol-
1941918222xylose-
1941917992sucrose-
1941922599arabinose-
1941917234glucose+
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19419+----+-+-+-

Isolation, sampling and environmental information

isolation

  • @ref: 9245
  • sample type: soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
92451Risk group (German classification)
194191Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces sp. NTG2 gene for 16S ribosomal RNA, partial sequenceAB9205731252ena1571709
20218Streptomyces sp. NTG5 gene for 16S ribosomal RNA, partial sequenceAB9205761286ena1571712
20218Streptomyces sp. NTGn11 gene for 16S ribosomal RNA, partial sequenceAB9205781303ena1571714
20218Streptomyces sp. NTHn1 gene for 16S ribosomal RNA, partial sequenceAB9205791306ena1571715
20218Streptomyces sp. NTHn2 gene for 16S ribosomal RNA, partial sequenceAB9205801312ena1571716
20218Streptomyces sp. NTM2 gene for 16S ribosomal RNA, partial sequenceAB9205831297ena1571719
20218Streptomyces sp. MTMn4 gene for 16S ribosomal RNA, partial sequenceAB9205851279ena1571721
20218Streptomyces sp. NTRH1 gene for 16S ribosomal RNA, partial sequenceAB9205861287ena1571722
20218Streptomyces violaceochromogenes strain IFO 13100 16S ribosomal RNA gene, partial sequenceAY9998671425ena67377
20218Streptomyces violaceochromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4530D44215121ena67377
20218Streptomyces violaceochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 13100AB1843121477ena67377

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces violaceochromogenes JCM 4530GCA_014650235scaffoldncbi67377
66792Streptomyces violaceochromogenes strain JCM 453067377.3wgspatric67377

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.081no
gram-positiveyes89.643no
anaerobicno99.049no
aerobicyes92.163no
halophileno93.571no
spore-formingyes95.045yes
glucose-utilyes90.208yes
thermophileno98.18yes
motileno93.741no
glucose-fermentno90.544no

External links

@ref: 9245

culture collection no.: DSM 40181, ATCC 19932, ATCC 25512, CBS 654.69, IFO 13100, INA 425, ISP 5181, NBRC 13100, RIA 1292, JCM 4530, CGMCC 4.1753, KCTC 19974, NRRL B-5427, VKM Ac-581

straininfo link

  • @ref: 85147
  • straininfo: 45813

literature

  • topic: Pathogenicity
  • Pubmed-ID: 30797881
  • title: Nybomycin-producing Streptomyces isolated from carpenter ant Camponotus vagus.
  • authors: Zakalyukina YV, Birykov MV, Lukianov DA, Shiriaev DI, Komarova ES, Skvortsov DA, Kostyukevich Y, Tashlitsky VN, Polshakov VI, Nikolaev E, Sergiev PV, Osterman IA
  • journal: Biochimie
  • DOI: 10.1016/j.biochi.2019.02.010
  • year: 2019
  • mesh: Animals, Anti-Bacterial Agents/*pharmacology, Ants, Cell Survival, Cells, Cultured, DNA, Bacterial/genetics, Escherichia coli/drug effects/*growth & development, Fibroblasts/*cytology/drug effects, Humans, Lung Neoplasms/drug therapy/*pathology, Phylogeny, Quinolones/pharmacology, RNA, Ribosomal, 16S/genetics, Streptomyces/isolation & purification/*metabolism
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9245Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40181)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40181
19419Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40181.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
85147Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45813.1StrainInfo: A central database for resolving microbial strain identifiers