Strain identifier

BacDive ID: 16335

Type strain: Yes

Species: Streptomyces echinoruber

Strain history: KCC S-1016 <-- NRRL 8144 <-- Hoffmann-La Roche Inc.; X14077.

NCBI tax ID(s): 68898 (species)

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General

@ref: 10478

BacDive-ID: 16335

DSM-Number: 41696

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

description: Streptomyces echinoruber DSM 41696 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 68898
  • Matching level: species

strain history

@refhistory
10478<- NRRL <- Hoffmann-La-Roche Inc., X14077
67770KCC S-1016 <-- NRRL 8144 <-- Hoffmann-La Roche Inc.; X14077.

doi: 10.13145/bacdive16335.20230509.8.1

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 echinoruber
  • full scientific name: Streptomyces echinoruber Palleroni et al. 1981

@ref: 10478

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces echinoruber

full scientific name: Streptomyces echinoruber Palleroni et al. 1981

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
18713Red10-14 daysISP 2
18713Red10-14 daysISP 3
18713Red10-14 daysISP 4
18713Red10-14 daysISP 5
18713Brown10-14 daysISP 6

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
18713yesAerial MyceliumGreyISP 2
18713yesAerial MyceliumGreyISP 3
18713yesAerial MyceliumGreyISP 4
18713yesAerial MyceliumWhiteISP 5
18713noISP 6
18713yesAerial MyceliumGreyISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10478GYM 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
18713ISP 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
18713ISP 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:
18713ISP 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
18713ISP 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
18713ISP 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
10478ROLLED 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
18713positiveoptimum28mesophilic
67770positivegrowth28mesophilic
10478positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
18713Formation of spore chains (retinaculiapetri), spore surface spinyyes
69481yes100
69480yes100

compound production

@refcompound
10478rubrolone
18713Rubrolone

halophily

  • @ref: 18713
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
67770140148rubroloneyes
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
18713++-----+-++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
10478soilArgentinaARGMiddle and South America
67770SoilArgentinaARGMiddle and South America

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
104781Risk group (German classification)
187131German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces echinoruber gene for 16S ribosomal RNA, partial sequence, strain: JCM 5016D44426120ena68898
20218Streptomyces echinoruber strain NBRC 14238 16S ribosomal RNA gene, partial sequenceKC1392521466ena68898

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces echinoruber JCM 5016GCA_014651135scaffoldncbi68898
66792Streptomyces echinoruber strain JCM 501668898.3wgspatric68898

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.971no
gram-positiveyes92.571no
anaerobicno98.936no
aerobicyes88.944no
halophileno92.563no
spore-formingyes96.558no
thermophileno95.697yes
glucose-utilyes88.645no
motileno92.951no
glucose-fermentno90.075no

External links

@ref: 10478

culture collection no.: DSM 41696, IFO 14238, JCM 5016, KCC S-0516, NBRC 14238, NCIMB 12831, NRRL 8144, BCRC 16859, CGMCC 4.1707, KCTC 9725, KCTC 9776

straininfo link

  • @ref: 85390
  • straininfo: 307492

literature

  • topic: Phylogeny
  • Pubmed-ID: 738965
  • title: Production of a novel red pigment, rubrolone, by Streptomyces echinoruber sp. nov. I. Taxonomy, fermentation and partial purification.
  • authors: Palleroni NJ, Reichelt KE, Mueller D, Epps R, Tabenkin B, Bull DN, Schuep W, Berger J
  • journal: J Antibiot (Tokyo)
  • DOI: 10.7164/antibiotics.31.1218
  • year: 1978
  • mesh: Animals, Anti-Bacterial Agents, Bacteria/drug effects, Drug Stability, Fermentation, Mice, Pigments, Biological/*biosynthesis/isolation & purification/pharmacology, Spores, Bacterial, Streptomyces/*classification/cytology/metabolism
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10478Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41696)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41696
18713Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41696.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
85390Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID307492.1StrainInfo: A central database for resolving microbial strain identifiers