Strain identifier

BacDive ID: 15108

Type strain: Yes

Species: Streptomyces collinus

Strain Designation: Ist 301

Strain history: KCC S-0361 <-- IFO 12759 <-- SAJ <-- ISP 5129 <-- P. Wilde Ist 301.

NCBI tax ID(s): 42684 (species)

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General

@ref: 9332

BacDive-ID: 15108

DSM-Number: 40129

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

description: Streptomyces collinus Ist 301 is a mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 42684
  • Matching level: species

strain history

@refhistory
9332<- ATCC <- E.B. Shirling, ISP <- P. Wilde, Ist 301
67770KCC S-0361 <-- IFO 12759 <-- SAJ <-- ISP 5129 <-- P. Wilde Ist 301.

doi: 10.13145/bacdive15108.20230509.8.1

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 collinus
  • full scientific name: Streptomyces collinus Lindenbein 1952 (Approved Lists 1980)

@ref: 9332

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces collinus

full scientific name: Streptomyces collinus Lindenbein 1952

strain designation: Ist 301

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19406Dahlia yellow10-14 daysISP 2
19406Dahlia yellow10-14 daysISP 3
19406Beige10-14 daysISP 4
19406Beige10-14 daysISP 5
19406Brown beige10-14 daysISP 6
19406Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19406yesAerial MyceliumCreamISP 2
19406yesAerial MyceliumLight greyISP 3
19406yesAerial MyceliumCreamISP 4
19406noISP 5
19406noISP 6
19406noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
9332https://www.dsmz.de/microorganisms/photos/DSM_40129-1.jpg© Leibniz-Institut DSMZ
9332https://www.dsmz.de/microorganisms/photos/DSM_40129.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9332GYM 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
19406ISP 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
19406ISP 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:
19406ISP 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
19406ISP 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
19406ISP 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
19406ISP 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
19406positiveoptimum28mesophilic
9332positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

compound production

@refcompound
9332collinomycin
9332rubromycine

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1940662968cellulose+
1940616634raffinose+
1940626546rhamnose+
1940628757fructose-
1940629864mannitol-
1940617268myo-inositol+
1940618222xylose-
1940617992sucrose-
1940622599arabinose-
1940617234glucose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770collinomycinyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideyes16136

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
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
19406++++++++-++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19406+++++++--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
9332soilIstein, hillside of stone quarry at Bärengraben (47° 40' N, 7° 33' E)GermanyDEUEurope47.66677.55
67770SoilBadenGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_408.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_91;97_97;98_106;99_408&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AJ306623
  • Sequence Identity:
  • Total samples: 50
  • soil counts: 30
  • animal counts: 18
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
93321Risk group (German classification)
194061Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces collinus partial 16S rRNA gene, strain DSM 40129AJ3066231448ena42684
20218Streptomyces collinus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4361D44078121ena42684
20218Streptomyces collinus 16S ribosomal RNA gene, partial sequenceKC355417861ena42684
9332Streptomyces collinus gene for 16S rRNA, partial sequence, strain: NBRC 12759AB1841231459ena42684

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces collinus strain DSM 4012942684.9wgspatric42684
66792Streptomyces collinus DSM 401292867977797draftimg42684
66792Streptomyces collinus DSM 20122563366695draftimg42684
66792Streptomyces collinus DSM 20122563366694draftimg42684

GC content

  • @ref: 67770
  • GC-content: 70.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes90.081no
anaerobicno99.034no
halophileno93.115no
spore-formingyes95.471no
glucose-utilyes89.84yes
aerobicyes91.868no
flagellatedno98.124no
motileno94.49no
thermophileno98.336no
glucose-fermentno90.287no

External links

@ref: 9332

culture collection no.: DSM 40129, ATCC 19743, CBS 482.68, DSM 2012, ETH 24318, IFO 12759, ISP 5129, JCM 4361, RIA 1024, BCRC 11465, CGMCC 4.1623, KCTC 9713, NBRC 12759, NRRL B-5412, VKM Ac-710

straininfo link

  • @ref: 84214
  • straininfo: 37092

literature

  • Pubmed-ID: 34198933
  • title: Scaffold Hopping of alpha-Rubromycin Enables Direct Access to FDA-Approved Cromoglicic Acid as a SARS-CoV-2 M(Pro) Inhibitor.
  • authors: Alhadrami HA, Sayed AM, Al-Khatabi H, Alhakamy NA, Rateb ME
  • journal: Pharmaceuticals (Basel)
  • DOI: 10.3390/ph14060541
  • year: 2021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9332Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40129)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40129
19406Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40129.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
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
84214Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID37092.1StrainInfo: A central database for resolving microbial strain identifiers