Strain identifier

BacDive ID: 15096

Type strain: Yes

Species: Streptomyces cinnabarinus

Strain history: KCC S-0463 <-- IFO 13028 <-- SAJ <-- ISP 5467 <-- INA 1242.

NCBI tax ID(s): 67287 (species)

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General

@ref: 9562

BacDive-ID: 15096

DSM-Number: 40467

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

description: Streptomyces cinnabarinus DSM 40467 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil of hot climate area.

NCBI tax id

  • NCBI tax id: 67287
  • Matching level: species

strain history

@refhistory
9562<- E.B. Shirling, ISP <- G.F. Gauze, INA
67770KCC S-0463 <-- IFO 13028 <-- SAJ <-- ISP 5467 <-- INA 1242.

doi: 10.13145/bacdive15096.20230509.8.1

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 cinnabarinus
  • full scientific name: Streptomyces cinnabarinus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces cinnabarinus

@ref: 9562

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces cinnabarinus

full scientific name: Streptomyces cinnabarinus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.476
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19459Brown red10-14 daysISP 2
19459Salmon red10-14 daysISP 3
19459Salmon red10-14 daysISP 4
19459Salmon red10-14 daysISP 5
19459Olive drab10-14 daysISP 6
19459Salmon red10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19459yesAerial MyceliumCreamISP 2
19459yesAerial MyceliumCreamISP 3
19459yesAerial MyceliumCreamISP 4
19459yesAerial MyceliumISP 5
19459noISP 6
19459yesAerial MyceliumISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9562GYM 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
19459ISP 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
19459ISP 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:
19459ISP 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
19459ISP 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
19459ISP 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
19459ISP 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
9562ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
19459positiveoptimum28mesophilic
9562positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1945962968cellulose+
1945916634raffinose+
1945926546rhamnose+
1945928757fructose+
1945929864mannitol+
1945917268myo-inositol+
1945918222xylose-
1945917992sucrose+
1945922599arabinose+
1945917234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideyes

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
19459++++++++-++-+-++-++

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19459-+--++---++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.country
9562soil of hot climate area
67770SoilRussiaRUS

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Climate#Hot

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
95621Risk group (German classification)
194591Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces cinnabarinus partial 16S rRNA gene, strain ISP 5467AJ3994871448ena67287
20218Streptomyces cinnabarinus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4463D44159120ena67287
20218Streptomyces cinnabarinus gene for 16S rRNA, partial sequence, strain: NBRC 13028AB1842661476ena67287
20218Streptomyces cinnabarinus strain NRRL B-12382 16S ribosomal RNA gene, partial sequenceDQ0266401493ena67287

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
67770Streptomyces cinnabarinus NRRL B-12382GCA_000715615scaffoldncbi67287
66792Streptomyces cinnabarinus DSM 40467GCA_027270315completencbi67287

GC content

@refGC-contentmethod
6777070.7genome sequence analysis
6777070.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.913no
gram-positiveyes89.606no
anaerobicno98.931no
aerobicyes92.344no
halophileno93.414no
spore-formingyes94.889no
glucose-fermentno87.773no
thermophileno99.074yes
glucose-utilyes89.738yes
motileno94.077no

External links

@ref: 9562

culture collection no.: DSM 40467, ATCC 23617, CBS 671.69, IFO 13028, INA 1242, ISP 5467, NBRC 13028, RIA 1220, JCM 4463, ATCC 25440, BCRC 15162, CGMCC 4.1590, NRRL B-12382, PCM 2311, VKM Ac-1904

straininfo link

@refstraininfo
8420238129
8420362733

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25663029Streptomyces fractus sp. nov., a novel streptomycete isolated from the gut of a South African termite.Rohland J, Meyers PRAntonie Van Leeuwenhoek10.1007/s10482-015-0404-82015Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Gastrointestinal Tract/microbiology, Isoptera/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, South Africa, Streptomyces/*classification/genetics/*isolation & purificationGenetics
Phylogeny29227220Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov.Landwehr W, Kampfer P, Glaeser SP, Ruckert C, Kalinowski J, Blom J, Goesmann A, Mack M, Schumann P, Atasayar E, Hahnke RL, Rohde M, Martin K, Stadler M, Wink JInt J Syst Evol Microbiol10.1099/ijsem.0.0025192017Bacterial Typing Techniques, DNA, Bacterial/genetics, Philippines, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9562Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40467)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40467
19459Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40467.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
84202Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38129.1StrainInfo: A central database for resolving microbial strain identifiers
84203Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62733.1StrainInfo: A central database for resolving microbial strain identifiers