Strain identifier

BacDive ID: 16384

Type strain: Yes

Species: Streptomyces speibonae

Strain Designation: PK-BLUE

Strain history: CIP <- 2003, P, Meyers, Univ. of Cape Town, Cape Town, South Africa: strain PK-BLUE

NCBI tax ID(s): 195801 (species)

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General

@ref: 10581

BacDive-ID: 16384

DSM-Number: 41797

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

description: Streptomyces speibonae PK-BLUE is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 195801
  • Matching level: species

strain history

@refhistory
10581<- P. Meyers; PK-BLUE
67770DSM 41797 <-- P. R. Meyers strain PK-Blue.
122693CIP <- 2003, P, Meyers, Univ. of Cape Town, Cape Town, South Africa: strain PK-BLUE

doi: 10.13145/bacdive16384.20230509.8.1

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 speibonae
  • full scientific name: Streptomyces speibonae Meyers et al. 2003

@ref: 10581

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces speibonae

full scientific name: Streptomyces speibonae Meyers et al. 2003

strain designation: PK-BLUE

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.804
69480100positive
122693nopositivefilament-shaped

colony morphology

@refcolony colorincubation periodmedium used
18722Leaf green (6002)10-14 daysISP 2
18722Leaf green (6002)10-14 daysISP 3
18722Leaf green (6002)10-14 daysISP 4
18722Leaf green (6002)10-14 daysISP 5
18722Beige (1001)10-14 daysISP 6
18722Leaf green (6002)10-14 daysISP 7
122693

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
18722yesAerial MyceliumSignal grey (7004)ISP 2
18722yesAerial MyceliumSignal grey (7004)ISP 3
18722yesAerial MyceliumSignal grey (7004)ISP 4
18722yesAerial MyceliumWhiteISP 5
18722noISP 6
18722yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10581GYM 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
18722ISP 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
18722ISP 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:
18722ISP 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
18722ISP 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
18722ISP 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
18722ISP 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
33882MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
10581STARCH - 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
122693CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
10581positivegrowth28mesophilic
18722positiveoptimum28mesophilic
33882positivegrowth30mesophilic
67770positivegrowth28mesophilic
122693positivegrowth25-45
122693nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122693
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
122693NaClpositivegrowth0-6 %
122693NaClnogrowth8 %
122693NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12269316947citrate-carbon source
1226934853esculin+hydrolysis
122693606565hippurate-hydrolysis
12269317632nitrate+reduction
12269316301nitrite-reduction
12269317632nitrate+respiration

metabolite production

  • @ref: 122693
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12269315688acetoin-
12269317234glucose-

enzymes

@refvalueactivityec
122693oxidase-
122693beta-galactosidase+3.2.1.23
122693alcohol dehydrogenase-1.1.1.1
122693gelatinase+/-
122693amylase+
122693DNase+
122693caseinase-3.4.21.50
122693catalase+1.11.1.6
122693tween esterase-
122693gamma-glutamyltransferase+2.3.2.2
122693lecithinase-
122693lipase-
122693lysine decarboxylase-4.1.1.18
122693ornithine decarboxylase-4.1.1.17
122693phenylalanine ammonia-lyase-4.3.1.24
122693protease+
122693tryptophan deaminase-
122693urease-3.5.1.5
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+
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
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- FucosidaseControl
18722+++-++---++++-++++-
122693+++-++---++---+-++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122693+++++--+-+++++-+++++++++--+----+++-------------+++----+----+++----------++++---++++++-++++++-++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
10581soilCape TownSouth AfricaZAFAfrica
67770SoilCape TownSouth AfricaZAFAfrica
122693Environment, SoilCape TownSouth AfricaZAFAfrica2000

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
105811Risk group (German classification)
187221German classification
1226931Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
10581Streptomyces speibonae 16S ribosomal RNA gene, partial sequenceAF4527141490ena195801
67770Streptomyces speibonae gene for 16S rRNA, partial sequence, strain: NBRC 100916AB2499611475ena195801

Genome sequences

  • @ref: 67770
  • description: Streptomyces speibonae NRRL B-24240
  • accession: GCA_000715605
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 195801

GC content

@refGC-contentmethod
1058173.4
6777073.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.704no
flagellatedno97.835no
gram-positiveyes90.209no
anaerobicno98.766no
halophileno88.258no
spore-formingyes94.609no
thermophileno96.907yes
glucose-utilyes91.31no
aerobicyes90.141no
glucose-fermentno88.076no

External links

@ref: 10581

culture collection no.: DSM 41797, ATCC BAA 411, CIP 108060, JCM 12682, KCTC 9973, NBRC 101001, NRRL B-24240, BCRC 16379, NBRC 100916

straininfo link

  • @ref: 85434
  • straininfo: 97611

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807203Streptomyces speibonae sp. nov., a novel streptomycete with blue substrate mycelium isolated from South African soil.Meyers PR, Porter DS, Omorogie C, Pule JM, Kwetane TInt J Syst Evol Microbiol10.1099/ijs.0.02341-02003Bacterial Typing Techniques, DNA, Ribosomal/analysis, Melanins/metabolism, Molecular Sequence Data, Phenotype, Pigments, Biological/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South Africa, Spores, Bacterial/physiology, Streptomyces/*classification/genetics/isolation & purification/physiologyMetabolism
Phylogeny30152750Streptomyces caeni sp. nov., isolated from mangrove mud.Huang H, Liu M, Zhong W, Mo K, Zhu J, Zou X, Hu Y, Bao SInt J Syst Evol Microbiol10.1099/ijsem.0.0029162018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitle
10581Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41797)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41797
18722Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41797.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
33882Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5641
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
85434Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97611.1StrainInfo: A central database for resolving microbial strain identifiers
122693Curators of the CIPCollection of Institut Pasteur (CIP 108060)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108060