Strain identifier

BacDive ID: 15112

Type strain: Yes

Species: Streptomyces corchorusii

Strain history: KCC S-0286 <-- NCIB 9476 <-- K. Ahmad and A. M. Bhuiyan.

NCBI tax ID(s): 1903 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 9471

BacDive-ID: 15112

DSM-Number: 40340

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

description: Streptomyces corchorusii DSM 40340 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1903
  • Matching level: species

strain history

@refhistory
9471<- E.B. Shirling, ISP <- NCIB <- K. Ahmad, Dacca University
67770KCC S-0286 <-- NCIB 9476 <-- K. Ahmad and A. M. Bhuiyan.

doi: 10.13145/bacdive15112.20230509.8.1

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 corchorusii
  • full scientific name: Streptomyces corchorusii Ahmad and Bhuiyan 1958 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces chibaensis

@ref: 9471

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces corchorusii

full scientific name: Streptomyces corchorusii Ahmad and Bhuiyan 1958 emend. Lanoot et al. 2005 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.613
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19440Dahlia yellow10-14 daysISP 2
19440Lemon yellow10-14 daysISP 3
19440Beige10-14 daysISP 4
19440Lemon yellow10-14 daysISP 5
19440Lemon yellow10-14 daysISP 6
19440Dahlia yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19440yesAerial MyceliumCreamISP 2
19440yesAerial MyceliumLight greyISP 3
19440yesAerial MyceliumLight greyISP 4
19440noISP 5
19440noISP 6
19440noISP 7

multimedia

  • @ref: 9471
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40340.jpg
  • caption: Medium 84 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9471ROLLED 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
9471GYM 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
19440ISP 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
19440ISP 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:
19440ISP 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
19440ISP 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
19440ISP 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
19440ISP 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
19440positiveoptimum28mesophilic
9471positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9471anti-fungal antibiotic
9471restriction endonuclease ScoAI
20216Antifungal antibiotics against jute pathogens
67770Antifungal antibiotic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1944062968cellulose+
1944016634raffinose+
1944026546rhamnose+
1944028757fructose+
1944029864mannitol+
1944017268myo-inositol+
1944018222xylose-
1944017992sucrose+
1944022599arabinose+
1944017234glucose+
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
19440+++-++-+-++++-+++++

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19440+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9471soilArichola, near Dacca
67770SoilArichola near DaccaBangladeshBGDAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94711Risk group (German classification)
194401Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces corchorusii gene for 16S ribosomal RNA, partial sequence, strain: JCM 4467D44162120ena1903
20218Streptomyces corchorusii strain KCTC 9715 16S ribosomal RNA gene, partial sequenceAY9998041419ena1903
9471Streptomyces corchorusii gene for 16S rRNA, partial sequence, strain: NBRC 13032AB1842671471ena1903

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces corchorusii strain DSM 403401903.3wgspatric1903
66792Streptomyces corchorusii DSM 403402775507096draftimg1903
67770Streptomyces corchorusii DSM 40340GCA_001514055scaffoldncbi1903

GC content

  • @ref: 67770
  • GC-content: 72
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.147no
gram-positiveyes88.828no
anaerobicno99.121no
aerobicyes93.147no
halophileno94.732no
spore-formingyes95.486no
glucose-utilyes88.638no
flagellatedno97.843no
thermophileno98.565yes
glucose-fermentno89.513no

External links

@ref: 9471

culture collection no.: DSM 40340, ATCC 25444, CBS 677.69, IFO 13032, ISP 5340, JCM 4286, KCC S-0286, NBRC 13032, NCIB 9476, RIA 1224, BCRC 11821, CGMCC 4.1592, JCM 4467, KCTC 9715, LMG 20488, NCIMB 9476, NCIMB 9979, NRRL B-12289, VKM Ac-1906

straininfo link

  • @ref: 84218
  • straininfo: 38552

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23645019Streptomyces kebangsaanensis sp. nov., an endophytic actinomycete isolated from an ethnomedicinal plant, which produces phenazine-1-carboxylic acid.Sarmin NIM, Tan GYA, Franco CMM, Edrada-Ebel R, Latip J, Zin NMInt J Syst Evol Microbiol10.1099/ijs.0.047878-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Malaysia, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phenazines/metabolism, *Phylogeny, Plants, Medicinal/*microbiology, Portulaca/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny25491896Streptomyces lactacystinicus sp. nov. and Streptomyces cyslabdanicus sp. nov., producing lactacystin and cyslabdan, respectively.Take A, Matsumoto A, Omura S, Takahashi YJ Antibiot (Tokyo)10.1038/ja.2014.1622014Acetylcysteine/*analogs & derivatives/metabolism, Anti-Bacterial Agents/*metabolism, DNA, Bacterial/genetics, Diterpenes/*metabolism, Gene Expression Regulation, Bacterial/physiology, Phylogeny, Species Specificity, Streptomyces/*classification/*metabolism/ultrastructureMetabolism
Phylogeny30816228Streptomyces monashensis sp. nov., a novel mangrove soil actinobacterium from East Malaysia with antioxidative potential.Law JW, Ser HL, Ab Mutalib NS, Saokaew S, Duangjai A, Khan TM, Chan KG, Goh BH, Lee LHSci Rep10.1038/s41598-019-39592-62019Antineoplastic Agents/isolation & purification/metabolism/*pharmacology, Antioxidants/isolation & purification/metabolism/*pharmacology, Bacterial Typing Techniques, Base Composition, Cell Survival/drug effects, DNA, Bacterial/isolation & purification, HCT116 Cells, Humans, Malaysia, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/genetics/isolation & purification/*metabolism, Superoxides/antagonists & inhibitorsEnzymology
Phylogeny35597859Streptomyces spinosus sp. nov. and Streptomyces shenzhenensis subsp. oryzicola subsp. nov. endophytic actinobacteria isolated from Jasmine rice and their genome mining for potential as antibiotic producers and plant growth promoters.Kaewkla O, Sukpanoa S, Suriyachadkun C, Chamroensaksi N, Chumroenphat T, Franco CMMAntonie Van Leeuwenhoek10.1007/s10482-022-01741-92022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9471Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40340)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40340
19440Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40340.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
84218Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38552.1StrainInfo: A central database for resolving microbial strain identifiers