Strain identifier

BacDive ID: 15215

Type strain: Yes

Species: Streptomyces gancidicus

Strain history: KCC S-0171 <-- IFM 1024 (AAK-84).

NCBI tax ID(s): 68204 (species)

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General

@ref: 9899

BacDive-ID: 15215

DSM-Number: 40935

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

description: Streptomyces gancidicus DSM 40935 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 68204
  • Matching level: species

strain history

@refhistory
9899<- NRRL
67770KCC S-0171 <-- IFM 1024 (AAK-84).

doi: 10.13145/bacdive15215.20230509.8.1

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 gancidicus
  • full scientific name: Streptomyces gancidicus Suzuki 1957 (Approved Lists 1980)

@ref: 9899

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces gancidicus

full scientific name: Streptomyces gancidicus Suzuki 1957

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18681Brown10-14 daysISP 2
18681Colorless10-14 daysISP 3
18681Brown10-14 daysISP 4
18681Brown10-14 daysISP 5
18681Yellow10-14 daysISP 6
18681Brown10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
18681yesAerial MyceliumGreyISP 2
18681yesAerial MyceliumGreyISP 3
18681yesAerial MyceliumGreyISP 4
18681yesAerial MyceliumGreyISP 5
18681noISP 6
18681yesAerial MyceliumGreyISP 7

multimedia

  • @ref: 9899
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40935.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9899GYM 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
18681ISP 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
18681ISP 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:
18681ISP 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
18681ISP 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
18681ISP 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
18681ISP 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
9899ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
9899STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf

culture temp

@refgrowthtypetemperaturerange
18681positiveoptimum28mesophilic
9899positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 18681
  • spore description: Formation of spore chains (spirales)(Sp), spore surface spiny
  • spore formation: yes

compound production

@refcompound
9899gancidin-complex (components A and W)
18681Cyclo(leucylprolyl), diketopiperazine antibiotic
67770Gancidin

halophily

  • @ref: 18681
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1868117234glucose+
1868122599arabinose+
1868117992sucrose-
1868118222xylose+
1868117268myo-inositol+
1868129864mannitol+
1868128757fructose+
1868126546rhamnose+
1868116634raffinose-
1868162968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan+energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleyes
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18681++----+++++

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil
  • geographic location: Jiyugaoka, Tokyo
  • country: Japan
  • origin.country: JPN
  • continent: Asia

taxonmaps

  • @ref: 69479
  • File name: preview.99_6264.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_91;97_97;98_1662;99_6264&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AY999919
  • Sequence Identity:
  • Total samples: 166
  • soil counts: 112
  • aquatic counts: 2
  • animal counts: 49
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186811German classification
98991Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces gancidicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4171D44022121ena68204
20218Streptomyces gancidicus gene for 16S rRNA, partial sequence, strain: NBRC 15412AB1846601457ena68204
20218Streptomyces gancidicus strain NRRL B-1872 16S ribosomal RNA gene, partial sequenceAY9999191377ena68204

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces gancidicus JCM 4171GCA_014649055scaffoldncbi68204
66792Streptomyces gancidicus strain JCM 417168204.7wgspatric68204

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.671no
gram-positiveyes90.272no
anaerobicno99.211no
aerobicyes93.642no
halophileno91.85no
spore-formingyes96.835yes
glucose-utilyes89.015yes
thermophileno98.477yes
motileno94.451no
glucose-fermentno89.405no

External links

@ref: 9899

culture collection no.: DSM 40935, IFM 1024, JCM 4171, KCC S-0171, NRRL B-1872, CGMCC 4.1971, IFO 15412, KCTC 19062, NBRC 15412, NCIMB 12858

straininfo link

  • @ref: 84313
  • straininfo: 49839

literature

  • topic: Phylogeny
  • Pubmed-ID: 29158025
  • title: Oligomycins A and E, major bioactive secondary metabolites produced by Streptomyces sp. strain HG29 isolated from a Saharan soil.
  • authors: Khebizi N, Boudjella H, Bijani C, Bouras N, Klenk HP, Pont F, Mathieu F, Sabaou N
  • journal: J Mycol Med
  • DOI: 10.1016/j.mycmed.2017.10.007
  • year: 2017
  • mesh: Africa, Northern, Algeria, Antifungal Agents/pharmacology, Fermentation, Fungi/classification/drug effects/isolation & purification/pathogenicity, Mass Spectrometry, Microbial Sensitivity Tests, Oligomycins/*chemistry/isolation & purification/pharmacology, Phylogeny, RNA, Ribosomal, 16S/genetics, Secondary Metabolism, Sequence Analysis, DNA, Soil/*chemistry, *Soil Microbiology, Streptomyces/*chemistry/classification/genetics/*isolation & purification
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9899Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40935)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40935
18681Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40935.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
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
84313Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49839.1StrainInfo: A central database for resolving microbial strain identifiers