Strain identifier

BacDive ID: 16101

Type strain: Yes

Species: Streptomyces violarus

Strain history: KCC S-0534 <-- IFO 13104 <-- SAJ <-- ISP 5205 <-- INMI 1212.

NCBI tax ID(s): 67380 (species)

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General

@ref: 9378

BacDive-ID: 16101

DSM-Number: 40205

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive, antibiotic compound production

description: Streptomyces violarus DSM 40205 is a spore-forming, mesophilic, Gram-positive bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67380
  • Matching level: species

strain history

@refhistory
9378<- E.B. Shirling, ISP <- N.A. Krassilnikov, INMI
67770KCC S-0534 <-- IFO 13104 <-- SAJ <-- ISP 5205 <-- INMI 1212.

doi: 10.13145/bacdive16101.20230509.8.1

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 violarus
  • full scientific name: Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Actinomyces violarus

@ref: 9378

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces violarus

full scientific name: Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

  • @ref: 9378
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
9378positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9378antibiotic 12-12
9378antibiotic 452-7
9378rhodomycine
9378violarin B

Isolation, sampling and environmental information

isolation

@refsample type
9378soil
67770Soil

isolation source categories

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

Safety information

risk assessment

  • @ref: 9378
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces violarus partial 16S rRNA gene, strain ISP 5205AJ3994771447ena67380
20218Streptomyces violarus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4534D44219120ena67380
20218Streptomyces violarus gene for 16S rRNA, partial sequence, strain: NBRC 13104AB1843161474ena67380

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces violarus CECT 3237GCA_014191845scaffoldncbi67380
66792Streptomyces violarus JCM 4534GCA_014650255scaffoldncbi67380
66792Streptomyces violarus strain CECT 323767380.3wgspatric67380
66792Streptomyces violarus strain JCM 453467380.4wgspatric67380
66792Streptomyces violarus CECT 32372824309123draftimg67380

GC content

  • @ref: 67770
  • GC-content: 74.7
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.477no
gram-positiveyes88.49no
anaerobicno99.108no
aerobicyes92.882no
halophileno93.155no
spore-formingyes94.664no
glucose-utilyes90.142no
thermophileno98.471yes
motileno92.729no
glucose-fermentno89.787no

External links

@ref: 9378

culture collection no.: DSM 40205, ATCC 15891, ATCC 25516, CBS 658.69, IFO 13104, ISP 5205, JCM 4534, KCC S-0534, KCTC 9788, NBRC 13104, NRRL B-5432, RIA 1296, RIA 157, VKM Ac-528, NIHJ 493, BCRC 13791, CCT 5007, CECT 3237, CGMCC 4.1772, INMI 1212

straininfo link

  • @ref: 85167
  • straininfo: 83034

literature

  • topic: Pathogenicity
  • Pubmed-ID: 29457331
  • title: A strain of Streptomyces sp. isolated from rhizospheric soil of Crataegus oxycantha producing nalidixic acid, a synthetic antibiotic.
  • authors: Arora N, Kumar S, Satti NK, Ali A, Gupta P, Katoch M
  • journal: J Appl Microbiol
  • DOI: 10.1111/jam.13736
  • year: 2018
  • mesh: Anti-Bacterial Agents/*biosynthesis/chemistry/pharmacology, Cell Line, Transformed, Cell Survival/drug effects, Crataegus/*growth & development, Escherichia coli/drug effects, Humans, Nalidixic Acid/chemistry/*metabolism/pharmacology, Phylogeny, Plant Extracts, Pseudomonas aeruginosa/drug effects, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/classification/genetics/*isolation & purification/*metabolism
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9378Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40205)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40205
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/
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
85167Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID83034.1StrainInfo: A central database for resolving microbial strain identifiers