Strain identifier
BacDive ID: 15063
Type strain:
Species: Streptomyces calvus
Strain Designation: T-3018
Strain history: KCC S-0326 <-- Y. Okami (NIHJ 517) <-- H. Tresner T-3018.
NCBI tax ID(s): 67282 (species)
General
@ref: 9212
BacDive-ID: 15063
DSM-Number: 40010
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces calvus T-3018 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from Soil.
NCBI tax id
- NCBI tax id: 67282
- Matching level: species
strain history
@ref | history |
---|---|
9212 | <- E.B. Shirling, ISP <- H. Tresner, Lederle Labs, T-3018 |
67770 | KCC S-0326 <-- Y. Okami (NIHJ 517) <-- H. Tresner T-3018. |
doi: 10.13145/bacdive15063.20230509.8.1
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 calvus
- full scientific name: Streptomyces calvus Backus et al. 1957 (Approved Lists 1980)
synonyms
@ref synonym 20215 Streptomyces asterosporus 20215 Streptomyces aureorectus
@ref: 9212
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces calvus
full scientific name: Streptomyces calvus Backus et al. 1957
strain designation: T-3018
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 91.517 | |
69480 | 100 | positive |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19385 | Black grey | 10-14 days | ISP 2 |
19385 | Beige | 10-14 days | ISP 3 |
19385 | Black grey | 10-14 days | ISP 4 |
19385 | Beige | 10-14 days | ISP 5 |
19385 | Beige | 10-14 days | ISP 6 |
19385 | Brown beige | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19385 | no | ISP 2 |
19385 | no | ISP 3 |
19385 | no | ISP 4 |
19385 | no | ISP 5 |
19385 | no | ISP 6 |
19385 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9212 | 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 |
19385 | 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 | |
19385 | 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: | |
19385 | 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 | |
19385 | 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 | |
19385 | 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 | |
19385 | 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 | |
9212 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19385 | positive | optimum | 28 | mesophilic |
9212 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
compound production
- @ref: 9212
- compound: nucleocidin
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
19385 | 62968 | cellulose | + | |
19385 | 16634 | raffinose | + | |
19385 | 26546 | rhamnose | - | |
19385 | 28757 | fructose | + | |
19385 | 29864 | mannitol | + | |
19385 | 17268 | myo-inositol | + | |
19385 | 18222 | xylose | - | |
19385 | 17992 | sucrose | + | |
19385 | 22599 | arabinose | + | |
19385 | 17234 | glucose | + | |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | + | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | + | degradation |
68368 | 25094 | lysine | + | degradation |
68368 | 29016 | arginine | + | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
67770 | 166872 | nucleocidin | yes |
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | + | 3.5.1.5 |
68368 | ornithine decarboxylase | + | 4.1.1.17 |
68368 | lysine decarboxylase | + | 4.1.1.18 |
68368 | arginine dihydrolase | + | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19385 | + | + | + | + | + | + | + | + | - | + | + | + | + | - | + | + | + | + | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP |
---|---|---|---|---|---|---|---|---|---|---|
19385 | + | + | + | + | + | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Soil
- geographic location: Dinepur
- country: India
- origin.country: IND
- continent: Asia
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
9212 | 1 | Risk group (German classification) |
19385 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces calvus strain ISP 5010 16S ribosomal RNA gene, partial sequence | AY999780 | 1495 | ena | 67282 |
20218 | Streptomyces calvus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4628 | D44275 | 121 | ena | 67282 |
20218 | Streptomyces calvus gene for 16S rRNA, partial sequence, strain: NBRC 13200 | AB184329 | 1474 | ena | 67282 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces calvus CECT 3271 | GCA_014138735 | scaffold | ncbi | 67282 |
66792 | Streptomyces calvus JCM 4326 | GCA_014649315 | scaffold | ncbi | 67282 |
66792 | Streptomyces calvus strain CECT 3271 | 67282.12 | wgs | patric | 67282 |
66792 | Streptomyces calvus strain JCM 4326 | 67282.13 | wgs | patric | 67282 |
66792 | Streptomyces calvus CECT 3271 | 2863276171 | draft | img | 67282 |
67770 | Streptomyces calvus T3018 | GCA_006782915 | contig | ncbi | 67282 |
GC content
- @ref: 67770
- GC-content: 72.4
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 93.881 | no |
flagellated | no | 97.806 | no |
gram-positive | yes | 87.664 | no |
anaerobic | no | 98.92 | no |
aerobic | yes | 92.743 | no |
halophile | no | 90.392 | no |
spore-forming | yes | 96.135 | no |
glucose-util | yes | 89.427 | yes |
thermophile | no | 97.853 | yes |
glucose-ferment | no | 89.707 | no |
External links
@ref: 9212
culture collection no.: DSM 40010, ATCC 13382, ATCC 23890, CBS 676.68, IFO 13200, ISP 5010, JCM 4326, JCM 4628, NBRC 13200, RIA 1103, BCRC 11859, CBS 350.62, CECT 3271, CGMCC 4.1691, IFM 1093, NCIMB 12240, NRRL B-2399, VKM Ac-1185
straininfo link
- @ref: 84169
- straininfo: 45538
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 26374477 | Biosynthesis of the Fluorinated Natural Product Nucleocidin in Streptomyces calvus Is Dependent on the bldA-Specified Leu-tRNA(UUA) Molecule. | Zhu XM, Hackl S, Thaker MN, Kalan L, Weber C, Urgast DS, Krupp EM, Brewer A, Vanner S, Szawiola A, Yim G, Feldmann J, Bechthold A, Wright GD, Zechel DL | Chembiochem | 10.1002/cbic.201500402 | 2015 | Adenosine/*analogs & derivatives/analysis/biosynthesis/chemistry, Bacterial Proteins/genetics/*metabolism, Biological Products/analysis/chemistry/*metabolism, Chromatography, High Pressure Liquid, Fluorine/chemistry, Halogenation, Mass Spectrometry, Multigene Family, Open Reading Frames/genetics, Purine-Nucleoside Phosphorylase/genetics/metabolism, RNA, Transfer, Leu/genetics/*metabolism, Streptomyces/genetics/*metabolism | |
32110306 | Two 3'-O-beta-glucosylated nucleoside fluorometabolites related to nucleocidin in Streptomyces calvus. | Feng X, Bello D, Lowe PT, Clark J, O'Hagan D | Chem Sci | 10.1039/c9sc03374b | 2019 | |||
Metabolism | 32333627 | Role of Two Exceptional trans Adenylation Domains and MbtH-like Proteins in the Biosynthesis of the Nonribosomal Peptide WS9324A from Streptomyces calvus ATCC 13382. | Bernhardt M, Berman S, Zechel D, Bechthold A | Chembiochem | 10.1002/cbic.202000142 | 2020 | Peptide Biosynthesis, Nucleic Acid-Independent, Protein Conformation, Streptomyces/*chemistry/metabolism | |
Phylogeny | 34382927 | Proposal of Streptomyces aureorectus (ex Taig et al. 1969) Taig and Solovieva 1986 as a later heterotypic synonym of Streptomyces calvus Backus et al. 1957 (Approved Lists 1980) on the basis of a polyphasic taxonomic approach. | Li K, Hu S, Wang Y, Guo Y, Zhou M, Tang X, Gao J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004955 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9212 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40010) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40010 | |||
19385 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40010.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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
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 | |||
84169 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45538.1 | StrainInfo: A central database for resolving microbial strain identifiers |