Strain identifier

BacDive ID: 16378

Type strain: Yes

Species: Streptomyces africanus

Strain Designation: CPJVR-H

Strain history: DSM 41829 <-- P. R. Meyers CPJVR-H.

NCBI tax ID(s): 231024 (species)

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General

@ref: 10612

BacDive-ID: 16378

DSM-Number: 41829

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

description: Streptomyces africanus CPJVR-H is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 231024
  • Matching level: species

strain history

@refhistory
10612<- P. R. Meyers; CPJVR-H
67770DSM 41829 <-- P. R. Meyers CPJVR-H.

doi: 10.13145/bacdive16378.20230509.8.1

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 africanus
  • full scientific name: Streptomyces africanus Meyers et al. 2004

@ref: 10612

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces africanus

full scientific name: Streptomyces africanus Meyers et al. 2004

strain designation: CPJVR-H

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
18723Cream (9001)10-14 daysISP 2
18723Cream (9001)10-14 daysISP 3
18723Cream (9001)10-14 daysISP 4
18723Cream (9001)10-14 daysISP 5
18723Beige (1001)10-14 daysISP 6
18723Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
18723yesAerial MyceliumAzure blue (5009)ISP 2
18723yesAerial MyceliumAzure blue (5009)ISP 3
18723yesAerial MyceliumAzure blue (5009)ISP 4
18723yesAerial MyceliumWhiteISP 5
18723noISP 6
18723noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10612GYM 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
18723ISP 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
18723ISP 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:
18723ISP 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
18723ISP 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
18723ISP 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
18723ISP 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
10612STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water
10612ROLLED 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

culture temp

@refgrowthtypetemperaturerange
10612positivegrowth28mesophilic
18723positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

enzymes

@refvalueactivityec
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
18723++++++-++++++-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10612soilCape TownSouth AfricaZAFAfrica
67770Suburban garden soilCape TownSouth AfricaZAFAfrica

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
187231German classification
106121Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces africanus gene for 16S rRNA, partial sequence, strain: NBRC 101005AB2499551456ena231024
10612Streptomyces africanus 16S ribosomal RNA gene, partial sequenceAY2089121488ena231024

Genome sequences

  • @ref: 67770
  • description: Streptomyces africanus NRRL B-24243
  • accession: GCA_002150735
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 231024

GC content

  • @ref: 67770
  • GC-content: 73.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.617no
gram-positiveyes88.026no
anaerobicno99.209no
halophileno93.506no
spore-formingyes95.045no
thermophileno97.817yes
glucose-utilyes88.977no
aerobicyes94.53no
glucose-fermentno89.24no
motileno91.871no

External links

@ref: 10612

culture collection no.: DSM 41829, NBRC 101005, NRRL B-24243, JCM 13243

straininfo link

  • @ref: 85432
  • straininfo: 297385

literature

  • topic: Phylogeny
  • Pubmed-ID: 15388706
  • title: Streptomyces africanus sp. nov., a novel streptomycete with blue aerial mycelium.
  • authors: Meyers PR, Goodwin CM, Bennett JA, Aken BL, Price CE, van Rooyen JM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02738-0
  • year: 2004
  • mesh: Antibiosis, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Enterococcus faecium/growth & development, Escherichia coli/growth & development, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/*biosynthesis, Pseudomonas aeruginosa/growth & development, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, South Africa, Spores, Bacterial/cytology, Streptomyces/*classification/cytology/*isolation & purification/physiology/ultrastructure, Temperature
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10612Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41829)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41829
18723Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41829.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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
85432Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297385.1StrainInfo: A central database for resolving microbial strain identifiers