Strain identifier

BacDive ID: 15496

Type strain: No

Species: Streptomyces californicus

Strain Designation: MS 1484, PD A 5014a

Strain history: KCC S-1068 <-- MS 1484 <-- NRRL 2423 <-- Parke, Davis & Co.; PD 04833.

NCBI tax ID(s): 67351 (species)

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General

@ref: 9902

BacDive-ID: 15496

DSM-Number: 40938

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

description: Streptomyces californicus MS 1484 is a mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 67351
  • Matching level: species

strain history

@refhistory
9902<- NRRL
67770KCC S-1068 <-- MS 1484 <-- NRRL 2423 <-- Parke, Davis & Co.; PD 04833.

doi: 10.13145/bacdive15496.20230509.8.1

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 californicus
  • full scientific name: Streptomyces californicus (Waksman and Curtis 1916) Waksman and Henrici 1948 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Actinomyces californicus
    20215Streptomyces floridae

@ref: 9902

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces puniceus

full scientific name: Streptomyces puniceus Patelski 1951

strain designation: MS 1484, PD A 5014a

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.412
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
18682Red brown (8012)10-14 daysISP 2
18682Brown10-14 daysISP 3
18682Violet10-14 daysISP 4
18682Red10-14 daysISP 5
18682Brown10-14 daysISP 6
18682Violet10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
18682yesAerial MyceliumWhiteISP 2
18682yesAerial MyceliumWhiteISP 3
18682yesAerial MyceliumWhiteISP 4
18682yesAerial MyceliumWhiteISP 5
18682noISP 6
18682yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9902GYM 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
18682ISP 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
18682ISP 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:
18682ISP 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
18682ISP 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
18682ISP 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
18682ISP 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
9902ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
18682positiveoptimum28mesophilic
9902positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
18682Formation of spore chains (rectiflixibilis), spore surface smoothno
69481yes100
69480yes100

compound production

@refcompound
9902viomycin
18682Viomycin

halophily

  • @ref: 18682
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1868217234glucose+
1868222599arabinose-
1868217992sucrose-
1868218222xylose-
1868217268myo-inositol-
1868229864mannitol+
1868228757fructose+
1868226546rhamnose-
1868216634raffinose+
1868262968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777015782viomycinyes
6836815688acetoinno
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18682++++--++--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9902soil
67770SoilFLUSAUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_135.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_120;99_135&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AY999916
  • Sequence Identity:
  • Total samples: 4030
  • soil counts: 2441
  • aquatic counts: 286
  • animal counts: 1009
  • plant counts: 294

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186821German classification
99021Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces floridae gene for 16S rRNA, partial sequence, strain: NBRC 15405AB1846561477ena68201
20218Streptomyces floridae strain NRRL 2423 16S ribosomal RNA gene, partial sequenceAY9999161424ena68201
20218Streptomyces floridae gene for 16S ribosomal RNA, partial sequence, strain: JCM 5068D44437120ena68201
20218Streptomyces floridae strain DSM 40938 16S ribosomal RNA gene, partial sequenceGU383177779ena68201

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces floridae strain NRRL 242368201.3wgspatric67351
66792Streptomyces californicus NRRL 24232767802092draftimg67351
67770Streptomyces californicus NRRL 2423GCA_000717665contigncbi67351

GC content

  • @ref: 67770
  • GC-content: 72.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes92.155no
anaerobicno98.893no
halophileno92.552no
spore-formingyes93.648yes
glucose-utilyes88.359yes
thermophileno98.69no
flagellatedno97.804no
motileno94.238no
aerobicyes93.355no
glucose-fermentno84.584no

External links

@ref: 9902

culture collection no.: DSM 40938, IFO 15405, ISP 5618, JCM 5068, KCC S-1068, NBRC 15405, NCIB 9345, NCIMB 12830, NRRL 2423, PD 04833, CGMCC 4.1972, MTCC 2534, NBIMCC 3334, NCIMB 9345

straininfo link

  • @ref: 84582
  • straininfo: 386981

literature

  • topic: Phylogeny
  • Pubmed-ID: 21148669
  • title: Streptomyces sundarbansensis sp. nov., an actinomycete that produces 2-allyloxyphenol.
  • authors: Arumugam M, Mitra A, Pramanik A, Saha M, Gachhui R, Mukherjee J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.028258-0
  • year: 2010
  • mesh: Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Phenols/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Streptomyces/*classification/genetics/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9902Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40938)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40938
18682Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40938.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
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
84582Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID386981.1StrainInfo: A central database for resolving microbial strain identifiers