Strain identifier

BacDive ID: 15105

Type strain: Yes

Species: Streptomyces coeruleorubidus

Strain history: KCC S-0359 <-- IFO 12855 <-- SAJ <-- ISP 5145 <-- INA 12531/54.

NCBI tax ID(s): 116188 (species)

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General

@ref: 9345

BacDive-ID: 15105

DSM-Number: 40145

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

description: Streptomyces coeruleorubidus DSM 40145 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 116188
  • Matching level: species

strain history

@refhistory
9345<- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA
67770KCC S-0359 <-- IFO 12855 <-- SAJ <-- ISP 5145 <-- INA 12531/54.

doi: 10.13145/bacdive15105.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces coeruleorubidus

@ref: 9345

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces coeruleorubidus

full scientific name: Streptomyces coeruleorubidus (Preobrazhenskaya 1957) Pridham et al. 1958

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.555
69480100positive

Culture and growth conditions

culture medium

  • @ref: 9345
  • 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
18545positiveoptimum28mesophilic
9345positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9345daunomycin
20216Rubomycin
67770Rubomycin

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1854517234glucose-
1854522599arabinose+
1854517992sucrose-
1854518222xylose-
1854517268myo-inositol+
1854529864mannitol+
1854528757fructose+
1854526546rhamnose+
1854516634raffinose+
1854562968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
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
18545+++-+++++++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18545+---++----+

Isolation, sampling and environmental information

isolation

  • @ref: 9345
  • sample type: soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185451German classification
93451Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces coeruleorubidus partial 16S rRNA gene, strain ISP 5145AJ3066221451ena116188
20218Streptomyces coeruleorubidus strain ISP 5145 16S ribosomal RNA gene, partial sequenceAY9997191450ena116188

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces coeruleorubidus ATCC 13740GCA_008705135completencbi116188
66792Streptomyces coeruleorubidus JCM 4359GCA_014649455scaffoldncbi116188
66792Streptomyces coeruleorubidus strain ATCC 13740116188.4completepatric116188
66792Streptomyces coeruleorubidus strain JCM 4359116188.5wgspatric116188

GC content

  • @ref: 67770
  • GC-content: 73.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.14no
gram-positiveyes89.197no
anaerobicno99.05no
aerobicyes93.374no
halophileno91.96no
spore-formingyes96.017no
thermophileno98.654no
glucose-utilyes88.197yes
motileno93.01no
glucose-fermentno90.51no

External links

@ref: 9345

culture collection no.: DSM 40145, ATCC 13740, ATCC 23900, CBS 796.68, ETH 24205, IFO 12855, INA 12531/54, ISP 5145, JCM 4359, NBRC 12855, RIA 1132, BCRC 11463, CGMCC 4.1678, IFM 11211, IMET 42060, KCTC 1743, KCTC 1922, NBIMCC 1152, NCIMB 9620, NRRL B-2569, VKM Ac-576

straininfo link

  • @ref: 84211
  • straininfo: 125929

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Cultivation892669Studies on the production of daunomycinone-derived glycosides and related metabolites in Streptomyces coeruleorubidus and Streptomyces peucetius.Blumauerova M, Mateju J, Stajner K, Vanek ZFolia Microbiol (Praha)10.1007/BF028776571977Chromatography, Thin Layer, Culture Media, Daunorubicin/analogs & derivatives/*biosynthesis/isolation & purification, Fermentation, Glycosides/*biosynthesis, Immersion, Streptomyces/*metabolismBiotechnology
Phylogeny21930680Streptomyces shaanxiensis sp. nov., a blue pigment-producing streptomycete from sewage irrigation soil.Lin YB, Wang XY, Fang H, Ma YN, Tang J, Tang M, Wei GHInt J Syst Evol Microbiol10.1099/ijs.0.029959-02011Bacterial Typing Techniques, DNA, Bacterial/genetics, Molecular Sequence Data, *Phylogeny, *Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purificationGenetics
Phylogeny28920834Streptomyces xylanilyticus sp. nov., isolated from soil.Moonmangmee D, Kanchanasin P, Phongsopitanun W, Tanasupawat S, Moonmangmee SInt J Syst Evol Microbiol10.1099/ijsem.0.0022822017Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
35760228Creating diverse glycosides of 2'-hydroxyflavone through microbial glycosylation.Ren J, Barton CD, Zhan JFitoterapia10.1016/j.fitote.2022.1052472022*Flavonoids/chemistry, Glucosides/chemistry, *Glycosides/chemistry, Glycosylation, Molecular Structure, Water

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9345Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40145)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40145
18545Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40145.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
84211Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125929.1StrainInfo: A central database for resolving microbial strain identifiers