Strain identifier

BacDive ID: 16445

Type strain: Yes

Species: Streptomyces rapamycinicus

Strain Designation: AYB-994

Strain history: <- ATCC <- C. Vezina, AY B-994

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

@ref: 10379

BacDive-ID: 16445

DSM-Number: 41530

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

description: Streptomyces rapamycinicus AYB-994 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

NCBI tax idMatching level
1343740strain
1226757species

strain history

  • @ref: 10379
  • history: <- ATCC <- C. Vezina, AY B-994

doi: 10.13145/bacdive16445.20230509.8.1

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 rapamycinicus
  • full scientific name: Streptomyces rapamycinicus Kumar and Goodfellow 2008

@ref: 10379

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces rapamycinicus

full scientific name: Streptomyces rapamycinicus Kumar and Goodfellow 2008

strain designation: AYB-994

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.796
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19820Beige10-14 daysISP 2
19820Beige10-14 daysISP 3
19820Beige10-14 daysISP 4
19820Beige10-14 daysISP 5
19820Beige10-14 daysISP 6
19820Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19820yesAerial MyceliumCreamISP 2
19820yesAerial MyceliumCreamISP 3
19820yesAerial MyceliumWindow greyISP 4
19820yesAerial MyceliumCreamISP 5
19820noISP 6
19820yesAerial MyceliumCreamISP 7

pigmentation

  • @ref: 32383
  • production: no

multimedia

@refmultimedia contentintellectual property rightscaption
10379https://www.dsmz.de/microorganisms/photos/DSM_41530-1.jpg© Leibniz-Institut DSMZ
10379https://www.dsmz.de/microorganisms/photos/DSM_41530.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10379ROLLED 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
10379GYM 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
19820ISP 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
19820ISP 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:
19820ISP 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
19820ISP 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
19820ISP 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
19820ISP 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
10379positivegrowth28mesophilic
19820positiveoptimum28mesophilic
32383positivegrowth10-37

culture pH

  • @ref: 32383
  • ability: positive
  • type: growth
  • pH: 06-10
  • PH range: alkaliphile

Physiology and metabolism

spore formation

@refspore formationconfidence
32383yes
69481yes100
69480yes100

compound production

@refcompound
10379rapamycine
20216Rapamycin

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3238328757fructose+carbon source
3238317234glucose+carbon source
3238317754glycerol+carbon source
3238317306maltose+carbon source
3238329864mannitol+carbon source
3238337684mannose+carbon source
3238316634raffinose+carbon source
3238326546rhamnose+carbon source
3238333942ribose+carbon source
3238317992sucrose+carbon source
3238327082trehalose+carbon source
3238318222xylose+carbon source
323834853esculin+hydrolysis

enzymes

@refvalueactivityec
32383gelatinase+
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
19820+++-+++++++++--+++-

Isolation, sampling and environmental information

isolation

  • @ref: 10379
  • sample type: soil
  • geographic location: Easter island
  • country: Fiji
  • origin.country: FJI
  • continent: Australia and Oceania

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
103791Risk group (German classification)
198201Risk group (German classification)

Sequence information

16S sequences

  • @ref: 10379
  • description: Streptomyces rapamycinicus NRRL:5491 16S ribosomal RNA gene, partial sequence
  • accession: EF408733
  • length: 1448
  • database: ena
  • NCBI tax ID: 1226757

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces rapamycinicus NRRL 5491GCA_003675955contigncbi1343740
66792Streptomyces rapamycinicus NRRL 5491GCA_000418455chromosomencbi1343740
66792Streptomyces rapamycinicus DSM 41530GCA_014205315contigncbi1226757
66792Streptomyces rapamycinicus NRRL 54911343740.8completepatric1343740
66792Streptomyces rapamycinicus strain DSM 415301226757.7wgspatric1226757
66792Streptomyces rapamycinicus NRRL 54912563366593completeimg1343740
66792Streptomyces hygroscopicus NRRL 5491651717164draftimg1343740
66792Streptomyces rapamycinicus DSM 415302873402043draftimg1226757
66792Streptomyces rapamycinicus NRRL 5491GCA_024298965completencbi1343740

GC content

  • @ref: 10379
  • GC-content: 71

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.904no
gram-positiveyes86.127no
anaerobicno99.055no
halophileno91.036no
spore-formingyes95.447yes
thermophileno98.349yes
glucose-utilyes90.284yes
aerobicyes93.351no
flagellatedno97.93no
glucose-fermentno89.868no

External links

@ref: 10379

culture collection no.: DSM 41530, ATCC 29253, IMET 43975, NRRL 5491

straininfo link

  • @ref: 85482
  • straininfo: 39437

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18523180Five new members of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis sp. nov., comb. nov., Streptomyces himastatinicus sp. nov., Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp. nov. and Streptomyces ruanii sp. nov.Kumar Y, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.65408-02008Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA, Species Specificity, Streptomyces/*classification/genetics/physiologyGenetics
Phylogeny19684315Streptomyces iranensis sp. nov., isolated from soil.Hamedi J, Mohammadipanah F, Klenk HP, Potter G, Schumann P, Sproer C, von Jan M, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/ijs.0.015339-02009Base Sequence, Molecular Sequence Data, Phenotype, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification/physiologyGenetics
Genetics23929477Draft Genome Sequence of Streptomyces rapamycinicus Strain NRRL 5491, the Producer of the Immunosuppressant Rapamycin.Baranasic D, Gacesa R, Starcevic A, Zucko J, Blazic M, Horvat M, Gjuracic K, Fujs S, Hranueli D, Kosec G, Cullum J, Petkovic HGenome Announc10.1128/genomeA.00581-132013
Genetics25035323Draft Genome Sequence of Streptomyces iranensis.Horn F, Schroeckh V, Netzker T, Guthke R, Brakhage AA, Linde JGenome Announc10.1128/genomeA.00616-142014
Metabolism25424695Characterization of negative regulatory genes for the biosynthesis of rapamycin in Streptomyces rapamycinicus and its application for improved production.Yoo YJ, Hwang JY, Shin HL, Cui H, Lee J, Yoon YJJ Ind Microbiol Biotechnol10.1007/s10295-014-1546-92014Gene Deletion, *Gene Expression Regulation, Bacterial, *Genes, Bacterial, *Genes, Regulator, Multigene Family, Sirolimus/*metabolism, Streptomyces/*genetics/metabolismBiotechnology
Genetics27800124Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer.Komaki H, Ichikawa N, Oguchi A, Hamada M, Harunari E, Kodani S, Fujita N, Igarashi YStand Genomic Sci10.1186/s40793-016-0207-12016
Enzymology28277818Extraction of rapamycin (sirolimus) from Streptomyces rapamycinicus using ultrasound.More AS, Gadalkar S, Rathod VKPrep Biochem Biotechnol10.1080/10826068.2017.13036092017Anti-Bacterial Agents/*isolation & purification, Chemical Fractionation/*methods, Sirolimus/*isolation & purification, Sonication/*methods, Streptomyces/*chemistryPhylogeny
Metabolism35717543Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin.Jo HG, Adidjaja JJ, Kim DK, Park BS, Lee N, Cho BK, Kim HU, Oh MKSci Rep10.1038/s41598-022-14199-62022Bacterial Proteins/metabolism, Genomics, Multigene Family, *Sirolimus/metabolism, *Streptomyces/genetics/metabolismGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
10379Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41530)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41530
19820Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41530.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)
32383Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2860928776041
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)
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
85482Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39437.1StrainInfo: A central database for resolving microbial strain identifiers