Strain identifier
BacDive ID: 16445
Type strain:
Species: Streptomyces rapamycinicus
Strain Designation: AYB-994
Strain history: <- ATCC <- C. Vezina, AY B-994
NCBI tax ID(s): 1343740 (strain), 1226757 (species)
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 id | Matching level |
---|---|
1343740 | strain |
1226757 | species |
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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 92.796 | |
69480 | 100 | positive |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19820 | Beige | 10-14 days | ISP 2 |
19820 | Beige | 10-14 days | ISP 3 |
19820 | Beige | 10-14 days | ISP 4 |
19820 | Beige | 10-14 days | ISP 5 |
19820 | Beige | 10-14 days | ISP 6 |
19820 | Beige | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
19820 | yes | Aerial Mycelium | Cream | ISP 2 |
19820 | yes | Aerial Mycelium | Cream | ISP 3 |
19820 | yes | Aerial Mycelium | Window grey | ISP 4 |
19820 | yes | Aerial Mycelium | Cream | ISP 5 |
19820 | no | ISP 6 | ||
19820 | yes | Aerial Mycelium | Cream | ISP 7 |
pigmentation
- @ref: 32383
- production: no
multimedia
@ref | multimedia content | intellectual property rights | caption |
---|---|---|---|
10379 | https://www.dsmz.de/microorganisms/photos/DSM_41530-1.jpg | © Leibniz-Institut DSMZ | |
10379 | https://www.dsmz.de/microorganisms/photos/DSM_41530.jpg | © Leibniz-Institut DSMZ | Medium 65 28°C |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
10379 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: 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 |
10379 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | 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 |
19820 | ISP 2 | yes | Name: 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 | |
19820 | ISP 3 | yes | Name: 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: | |
19820 | ISP 4 | yes | Name: 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 | |
19820 | ISP 5 | yes | Name: 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 | |
19820 | ISP 6 | yes | Name: 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 | |
19820 | ISP 7 | yes | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
10379 | positive | growth | 28 | mesophilic |
19820 | positive | optimum | 28 | mesophilic |
32383 | positive | growth | 10-37 |
culture pH
- @ref: 32383
- ability: positive
- type: growth
- pH: 06-10
- PH range: alkaliphile
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
32383 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
compound production
@ref | compound |
---|---|
10379 | rapamycine |
20216 | Rapamycin |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32383 | 28757 | fructose | + | carbon source |
32383 | 17234 | glucose | + | carbon source |
32383 | 17754 | glycerol | + | carbon source |
32383 | 17306 | maltose | + | carbon source |
32383 | 29864 | mannitol | + | carbon source |
32383 | 37684 | mannose | + | carbon source |
32383 | 16634 | raffinose | + | carbon source |
32383 | 26546 | rhamnose | + | carbon source |
32383 | 33942 | ribose | + | carbon source |
32383 | 17992 | sucrose | + | carbon source |
32383 | 27082 | trehalose | + | carbon source |
32383 | 18222 | xylose | + | carbon source |
32383 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32383 | gelatinase | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | + | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- 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
@ref | biosafety level | biosafety level comment |
---|---|---|
10379 | 1 | Risk group (German classification) |
19820 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces rapamycinicus NRRL 5491 | GCA_003675955 | contig | ncbi | 1343740 |
66792 | Streptomyces rapamycinicus NRRL 5491 | GCA_000418455 | chromosome | ncbi | 1343740 |
66792 | Streptomyces rapamycinicus DSM 41530 | GCA_014205315 | contig | ncbi | 1226757 |
66792 | Streptomyces rapamycinicus NRRL 5491 | 1343740.8 | complete | patric | 1343740 |
66792 | Streptomyces rapamycinicus strain DSM 41530 | 1226757.7 | wgs | patric | 1226757 |
66792 | Streptomyces rapamycinicus NRRL 5491 | 2563366593 | complete | img | 1343740 |
66792 | Streptomyces hygroscopicus NRRL 5491 | 651717164 | draft | img | 1343740 |
66792 | Streptomyces rapamycinicus DSM 41530 | 2873402043 | draft | img | 1226757 |
66792 | Streptomyces rapamycinicus NRRL 5491 | GCA_024298965 | complete | ncbi | 1343740 |
GC content
- @ref: 10379
- GC-content: 71
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 92.904 | no |
gram-positive | yes | 86.127 | no |
anaerobic | no | 99.055 | no |
halophile | no | 91.036 | no |
spore-forming | yes | 95.447 | yes |
thermophile | no | 98.349 | yes |
glucose-util | yes | 90.284 | yes |
aerobic | yes | 93.351 | no |
flagellated | no | 97.93 | no |
glucose-ferment | no | 89.868 | no |
External links
@ref: 10379
culture collection no.: DSM 41530, ATCC 29253, IMET 43975, NRRL 5491
straininfo link
- @ref: 85482
- straininfo: 39437
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18523180 | Five 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 M | Int J Syst Evol Microbiol | 10.1099/ijs.0.65408-0 | 2008 | Bacterial 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/physiology | Genetics |
Phylogeny | 19684315 | Streptomyces iranensis sp. nov., isolated from soil. | Hamedi J, Mohammadipanah F, Klenk HP, Potter G, Schumann P, Sproer C, von Jan M, Kroppenstedt RM | Int J Syst Evol Microbiol | 10.1099/ijs.0.015339-0 | 2009 | Base Sequence, Molecular Sequence Data, Phenotype, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification/physiology | Genetics |
Genetics | 23929477 | Draft 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 H | Genome Announc | 10.1128/genomeA.00581-13 | 2013 | ||
Genetics | 25035323 | Draft Genome Sequence of Streptomyces iranensis. | Horn F, Schroeckh V, Netzker T, Guthke R, Brakhage AA, Linde J | Genome Announc | 10.1128/genomeA.00616-14 | 2014 | ||
Metabolism | 25424695 | Characterization 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 YJ | J Ind Microbiol Biotechnol | 10.1007/s10295-014-1546-9 | 2014 | Gene Deletion, *Gene Expression Regulation, Bacterial, *Genes, Bacterial, *Genes, Regulator, Multigene Family, Sirolimus/*metabolism, Streptomyces/*genetics/metabolism | Biotechnology |
Genetics | 27800124 | Draft 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 Y | Stand Genomic Sci | 10.1186/s40793-016-0207-1 | 2016 | ||
Enzymology | 28277818 | Extraction of rapamycin (sirolimus) from Streptomyces rapamycinicus using ultrasound. | More AS, Gadalkar S, Rathod VK | Prep Biochem Biotechnol | 10.1080/10826068.2017.1303609 | 2017 | Anti-Bacterial Agents/*isolation & purification, Chemical Fractionation/*methods, Sirolimus/*isolation & purification, Sonication/*methods, Streptomyces/*chemistry | Phylogeny |
Metabolism | 35717543 | Comparative 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 MK | Sci Rep | 10.1038/s41598-022-14199-6 | 2022 | Bacterial Proteins/metabolism, Genomics, Multigene Family, *Sirolimus/metabolism, *Streptomyces/genetics/metabolism | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
10379 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41530) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-41530 | |||
19820 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM41530.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20216 | Curators of the HKI | http://www.leibniz-hki.de/de/ | Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) | |||
32383 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28609 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
85482 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39437.1 | StrainInfo: A central database for resolving microbial strain identifiers |