Strain identifier

BacDive ID: 15261

Type strain: Yes

Species: Streptomyces griseochromogenes

Strain history: KCC S-0039 <-- T. Misato 2A-327.

NCBI tax ID(s): 68214 (species)

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General

@ref: 9600

BacDive-ID: 15261

DSM-Number: 40499

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

description: Streptomyces griseochromogenes DSM 40499 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 68214
  • Matching level: species

strain history

@refhistory
9600<- E.B. Shirling, ISP <- ATCC <- Fukunaga 2A-327
67770KCC S-0039 <-- T. Misato 2A-327.

doi: 10.13145/bacdive15261.20230509.8.1

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 griseochromogenes
  • full scientific name: Streptomyces griseochromogenes Fukunaga 1955 (Approved Lists 1980)

@ref: 9600

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces griseochromogenes

full scientific name: Streptomyces griseochromogenes Fukunaga 1955

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19467Ochre yellow10-14 daysISP 2
19467Ivory10-14 daysISP 3
19467Brown beige10-14 daysISP 4
19467Ivory10-14 daysISP 5
19467Khaki grey10-14 daysISP 6
19467Khaki grey10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19467yesAerial MyceliumOyster white (1013)ISP 2
19467yesAerial MyceliumOyster white (1013)ISP 3
19467yesAerial MyceliumGrey beige (1019)ISP 4
19467noISP 5
19467noISP 6
19467noISP 7

multimedia

  • @ref: 9600
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40499.jpg
  • caption: Medium 84 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9600GYM 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
19467ISP 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
19467ISP 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:
19467ISP 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
19467ISP 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
19467ISP 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
19467ISP 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
9600ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
19467positiveoptimum28mesophilic
9600positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9600blasticidin A
9600blasticidin B
9600blasticidin C
9600blasticidin S
9600cytomycin
9600blasticidin A, B, C
9600toyokamycine
19467Antibiotic A 221
19467Blasticidin H
19467Cytosinine
19467Pentopyranine A
19467Antibiotic SF 701
19467Antibiotic UK 86956
19467Blasticidin A
19467Pentalene
19467Carbazoquinocin
19467Tautomycetin

observation

  • @ref: 67770
  • observation: quinones: MK-9(H8), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1946762968cellulose+
1946716634raffinose+
1946726546rhamnose-
1946728757fructose+
1946729864mannitol+
1946717268myo-inositol+
1946718222xylose-
1946717992sucrose+
1946722599arabinose+
1946717234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770blasticidin Ayes
67770blasticidin Syes15353
67770toyocamycinyes134606
68368acetoinno15688
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
19467+-+-+++++++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19467-+-+-++---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9600soil
67770SoilGazaki, Wakayama Pref.JapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
96001Risk group (German classification)
194671Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces griseochromogenes partial 16S rRNA gene, type strain DSM 40499AJ3109231448ena68214
20218Streptomyces griseochromogenes partial 16S rRNA gene, strain ISP 5499AJ3994911449ena68214
20218Streptomyces griseochromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4764D44343120ena68214
20218Streptomyces griseochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 13413AB1843871474ena68214

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces griseochromogenes ATCC 14511GCA_001542625completencbi68214
66792Streptomyces griseochromogenes DSM 40499GCA_017874495contigncbi68214
66792Streptomyces griseochromogenes strain ATCC 1451168214.3wgspatric68214
66792Streptomyces griseochromogenes strain DSM 4049968214.12wgspatric68214
66792Streptomyces griseochromogenes DSM 404992913531621draftimg68214
66792Streptomyces griseochromogenes ATCC 145112873104240completeimg68214
66792Streptomyces griseochromogenes DSM 404992563366698draftimg68214

GC content

  • @ref: 67770
  • GC-content: 71.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.185no
flagellatedno98.185no
gram-positiveyes88.465no
gram-positiveyes88.465no
anaerobicno99.018no
anaerobicno99.018no
aerobicyes91.298no
aerobicyes91.298no
halophileno93.857no
halophileno93.857no
spore-formingyes94.509no
spore-formingyes94.509no
thermophileno98.094yes
glucose-utilyes89.526no
glucose-utilyes89.526no
motileno93.772no
motileno93.772no
thermophileno98.094yes
glucose-fermentno89.715no
glucose-fermentno89.715no

External links

@ref: 9600

culture collection no.: DSM 40499, ATCC 14511, CBS 714.72, IFO 13413, ISP 5499, JCM 4039, JCM 4764, NBRC 13413, RIA 1374, BCRC 11818, CGMCC 4.1964, IFM 1229, KCTC 9027, NRRL B-12423

straininfo link

  • @ref: 84356
  • straininfo: 45561

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics28342817Complete genome sequence of Streptomyces griseochromogenes ATCC 14511(T), a producer of nucleoside compounds and diverse secondary metabolites.Wu L, Chen G, Feng GJ Biotechnol10.1016/j.jbiotec.2017.03.0172017Antifungal Agents/*metabolism/pharmacology, DNA, Bacterial/analysis/genetics, Fungi/drug effects, Genome, Bacterial/*genetics, Multigene Family/genetics, Nucleosides/*metabolism/pharmacology, Sequence Analysis, DNA, Streptomyces/*chemistry/classification/*genetics/metabolismMetabolism
Cultivation33573182Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria.Schwarz J, Hubmann G, Rosenthal K, Lutz SBiomolecules10.3390/biom110201932021Bacillus amyloliquefaciens/genetics, Culture Media, Data Mining, Deferoxamine/chemistry, Genome, Lysine/analogs & derivatives/chemistry, *Microbial Sensitivity Tests, *Multigene Family, Myxococcales/genetics, Oligopeptides/chemistry, Rhodococcus/genetics, Secondary Metabolism/genetics, Streptomyces/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9600Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40499)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40499
19467Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40499.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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
84356Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45561.1StrainInfo: A central database for resolving microbial strain identifiers