Strain identifier

BacDive ID: 15063

Type strain: Yes

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)

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

@refhistory
9212<- E.B. Shirling, ISP <- H. Tresner, Lederle Labs, T-3018
67770KCC 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

    @refsynonym
    20215Streptomyces asterosporus
    20215Streptomyces 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

@refmotilityconfidencegram stain
69480no91.517
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19385Black grey10-14 daysISP 2
19385Beige10-14 daysISP 3
19385Black grey10-14 daysISP 4
19385Beige10-14 daysISP 5
19385Beige10-14 daysISP 6
19385Brown beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19385noISP 2
19385noISP 3
19385noISP 4
19385noISP 5
19385noISP 6
19385noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9212GYM 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
19385ISP 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
19385ISP 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:
19385ISP 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
19385ISP 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
19385ISP 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
19385ISP 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
9212ROLLED 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
19385positiveoptimum28mesophilic
9212positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 9212
  • compound: nucleocidin

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1938562968cellulose+
1938516634raffinose+
1938526546rhamnose-
1938528757fructose+
1938529864mannitol+
1938517268myo-inositol+
1938518222xylose-
1938517992sucrose+
1938522599arabinose+
1938517234glucose+
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
67770166872nucleocidinyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
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
19385++++++++-++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVP
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

@refbiosafety levelbiosafety level comment
92121Risk group (German classification)
193851Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces calvus strain ISP 5010 16S ribosomal RNA gene, partial sequenceAY9997801495ena67282
20218Streptomyces calvus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4628D44275121ena67282
20218Streptomyces calvus gene for 16S rRNA, partial sequence, strain: NBRC 13200AB1843291474ena67282

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces calvus CECT 3271GCA_014138735scaffoldncbi67282
66792Streptomyces calvus JCM 4326GCA_014649315scaffoldncbi67282
66792Streptomyces calvus strain CECT 327167282.12wgspatric67282
66792Streptomyces calvus strain JCM 432667282.13wgspatric67282
66792Streptomyces calvus CECT 32712863276171draftimg67282
67770Streptomyces calvus T3018GCA_006782915contigncbi67282

GC content

  • @ref: 67770
  • GC-content: 72.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.881no
flagellatedno97.806no
gram-positiveyes87.664no
anaerobicno98.92no
aerobicyes92.743no
halophileno90.392no
spore-formingyes96.135no
glucose-utilyes89.427yes
thermophileno97.853yes
glucose-fermentno89.707no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism26374477Biosynthesis 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 DLChembiochem10.1002/cbic.2015004022015Adenosine/*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
32110306Two 3'-O-beta-glucosylated nucleoside fluorometabolites related to nucleocidin in Streptomyces calvus.Feng X, Bello D, Lowe PT, Clark J, O'Hagan DChem Sci10.1039/c9sc03374b2019
Metabolism32333627Role 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 AChembiochem10.1002/cbic.2020001422020Peptide Biosynthesis, Nucleic Acid-Independent, Protein Conformation, Streptomyces/*chemistry/metabolism
Phylogeny34382927Proposal 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 JInt J Syst Evol Microbiol10.1099/ijsem.0.0049552021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9212Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40010)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40010
19385Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40010.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
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
84169Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45538.1StrainInfo: A central database for resolving microbial strain identifiers