Strain identifier

BacDive ID: 15492

Type strain: No

Species: Streptomyces californicus

Strain history: KCC S-0015 <-- T. Yamaguchi (IAM 0003) <-- ATCC 3312 <-- IMRU 3312.

NCBI tax ID(s): 67351 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9241

BacDive-ID: 15492

DSM-Number: 40058

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

description: Streptomyces californicus DSM 40058 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 67351
  • Matching level: species

strain history

@refhistory
9241<- E.B. Shirling, ISP <- S.A. Waksman, IMRU
67770KCC S-0015 <-- T. Yamaguchi (IAM 0003) <-- ATCC 3312 <-- IMRU 3312.

doi: 10.13145/bacdive15492.20230509.8.1

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: 9241

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces puniceus

full scientific name: Streptomyces puniceus Patelski 1951

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.84
69480100positive

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19804yesAerial MyceliumGreyISP 2
19804yesAerial MyceliumGreyISP 3
19804yesAerial MyceliumGreyISP 4
19804yesAerial MyceliumGreyISP 5
19804yesAerial MyceliumGreyISP 6
19804yesAerial MyceliumGreyISP 7

Culture and growth conditions

culture medium

  • @ref: 9241
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
19804positiveoptimum28mesophilic
9241positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19804Formation of spore chains: rectiflixibilis, spore surface: smoothyes
69481yes100
69480yes100

compound production

@refcompound
9241viomycin
20216Griseorhodin
20216Sideromycin

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1980462968cellulose-
1980416634raffinose-
1980426546rhamnose-
1980428757fructose+
1980429864mannitol+
1980417268myo-inositol-
1980418222xylose+
1980417992sucrose-
1980422599arabinose+
1980417234glucose+
6836817634D-glucose+fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
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 TrpINDVPGELGLU
19804+++---++-+++

Isolation, sampling and environmental information

isolation

  • @ref: 9241
  • sample type: soil

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: AB184755
  • 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
92411Risk group (German classification)
198041Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces californicus gene for 16S rRNA, partial sequence, strain: NBRC 12750AB1841161480ena67281
20218Streptomyces californicus gene for 16S rRNA, partial sequence, strain: NBRC 3386AB1847551477ena67281
20218Streptomyces californicus strain IFO 12750 16S ribosomal RNA gene, partial sequenceAY9998371419ena67281
20218Streptomyces californicus strain DSM 40058 16S ribosomal RNA gene, partial sequenceAY9998451420ena67281
20218Streptomyces californicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4567D44236120ena67281
20218Streptomyces californicus strain DSM 40058 16S ribosomal RNA gene, partial sequenceGU383162779ena67281

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces californicus strain FDAARGOS_120967351.14completepatric67351
67770Streptomyces californicus NRRL B-1221GCA_000715715scaffoldncbi67351
67770Streptomyces californicus NRRL B-2098GCA_000717645contigncbi67351
67770Streptomyces californicus NRRL ISP-5058GCA_000716065scaffoldncbi67351

GC content

@refGC-contentmethod
6777070fluorimetric
6777072.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes92.835no
anaerobicno99.046no
halophileno93.853no
spore-formingyes94.516yes
glucose-utilyes88.292no
thermophileno98.67no
flagellatedno98.049no
motileno94.27no
aerobicyes93.559no
glucose-fermentno85.047yes

External links

@ref: 9241

culture collection no.: DSM 40058, ATCC 11896, ATCC 19734, ATCC 3312, CBS 125.20, CBS 354.53, CBS 473.68, ETH 10212, IFO 12750, IFO 3386, IMET 40261, IMRU 3312, IMRU 3313, ISP 5058, JCM 4015, JCM 4567, KCC S-0015, KCC S-0567, NBRC 12750, NBRC 3386, NRRL B-1221, NRRL B-2098, RIA 1015, RIA 63, BCRC 13688, CCM 3016, CGMCC 4.0570, HUT 6049, IFM 1070, KCTC 19939, KCTC 19957, LMG 19309, NBIMCC 1036, NCAIM B.01475, NRRL ISP-5058, VKM Ac-575, VTT E-991421

straininfo link

  • @ref: 84579
  • straininfo: 38299

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
9241Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40058)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40058
19804Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40058.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
84579Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38299.1StrainInfo: A central database for resolving microbial strain identifiers