Strain identifier

BacDive ID: 15099

Type strain: Yes

Species: Streptomyces cirratus

Strain Designation: 12.090

Strain history: KCC S-0738 <-- IFO 13398 <-- SAJ <-- ISP 5479 <-- ATCC 14699 <-- Bristol-Banyu Res. Inst.; 12090.

NCBI tax ID(s): 68187 (species)

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General

@ref: 9572

BacDive-ID: 15099

DSM-Number: 40479

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

description: Streptomyces cirratus 12.090 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 68187
  • Matching level: species

strain history

@refhistory
9572<- E.B. Shirling, ISP <- ATCC <- Bristol-Banyu Res. Inst., 12.090
67770KCC S-0738 <-- IFO 13398 <-- SAJ <-- ISP 5479 <-- ATCC 14699 <-- Bristol-Banyu Res. Inst.; 12090.

doi: 10.13145/bacdive15099.20230509.8.1

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 cirratus
  • full scientific name: Streptomyces cirratus Koshiyama et al. 1963 (Approved Lists 1980)

@ref: 9572

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces cirratus

full scientific name: Streptomyces cirratus Koshiyama et al. 1963

strain designation: 12.090

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.427
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19462Brown beige10-14 daysISP 2
19462Brown beige10-14 daysISP 3
19462Brown beige10-14 daysISP 4
19462Beige10-14 daysISP 5
19462Beige10-14 daysISP 6
19462Brown beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19462yesAerial MyceliumCream (9001)ISP 2
19462yesAerial MyceliumLight grey (7035)ISP 3
19462yesAerial MyceliumLight grey (7035)ISP 4
19462noISP 5
19462noISP 6
19462noISP 7

multimedia

  • @ref: 9572
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40479.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9572GYM 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
19462ISP 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
19462ISP 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:
19462ISP 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
19462ISP 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
19462ISP 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
19462ISP 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
9572ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
19462positiveoptimum28mesophilic
9572positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9572cirramycin A
9572cirramycin B
9572cirramycin A, B
19462Antibiotic A 6888X
19462Cirramycin A
19462Antrimycin
19462Pheganomycin
67770Cirramycins A and B

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1946262968cellulose+
1946216634raffinose-
1946226546rhamnose-
1946228757fructose+
1946229864mannitol-
1946217268myo-inositol-
1946218222xylose-
1946217992sucrose-
1946222599arabinose+
1946217234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

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
19462+++++++++++-+-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19462+++++-+--++

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_163.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_144;99_163&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AY999794
  • Sequence Identity:
  • Total samples: 26399
  • soil counts: 19336
  • aquatic counts: 1680
  • animal counts: 1702
  • plant counts: 3681

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
95721Risk group (German classification)
194621Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces cirratus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4738D44322120ena68187
20218Streptomyces cirratus gene for 16S rRNA, partial sequence, strain: NBRC 13398AB1843771456ena68187
20218Streptomyces cirratus strain NRRL B-3250 16S ribosomal RNA gene, partial sequenceAY9997941493ena68187

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces cirratus JCM 4738GCA_014650775contigncbi68187
66792Streptomyces cirratus strain JCM 473868187.4wgspatric68187

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes89.288no
anaerobicno98.897no
halophileno95.484no
spore-formingyes93.03no
glucose-utilyes92.459yes
thermophileno97.454yes
flagellatedno97.858no
aerobicyes89.159no
glucose-fermentno89.452no
motileno94.72no

External links

@ref: 9572

culture collection no.: DSM 40479, ATCC 14699, CBS 699.72, IFO 13398, ISP 5479, JCM 4738, NBRC 13398, RIA 1359, BCRC 16208, CGMCC 4.1679, KCTC 9709, NRRL B-3250, VKM Ac-620, VTT E-052935

straininfo link

  • @ref: 84206
  • straininfo: 36155

literature

  • topic: Pathogenicity
  • Pubmed-ID: 20560349
  • title: [Exploiting bioactive Enediynes from marine microbe based on activity and gene screening].
  • authors: Pei G, Dai H, Ren B, Liu X, Zhang L
  • journal: Wei Sheng Wu Xue Bao
  • year: 2010
  • mesh: Enediynes/*pharmacology, Genes, Bacterial/drug effects, *Marine Biology, Molecular Sequence Data, Multigene Family/*drug effects/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9572Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40479)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40479
19462Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40479.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
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
84206Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36155.1StrainInfo: A central database for resolving microbial strain identifiers