Strain identifier

BacDive ID: 16058

Type strain: Yes

Species: Streptomyces tubercidicus

Strain Designation: IPCR 585

Strain history: KCC S-0054 <-- S. Suzuki 585.

NCBI tax ID(s): 47759 (species)

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General

@ref: 9415

BacDive-ID: 16058

DSM-Number: 40261

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

description: Streptomyces tubercidicus IPCR 585 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 47759
  • Matching level: species

strain history

@refhistory
9415<- E.B. Shirling, ISP <- S. Suzuki, IPCR, 585
67770KCC S-0054 <-- S. Suzuki 585.

doi: 10.13145/bacdive16058.20230509.8.1

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 tubercidicus
  • full scientific name: Streptomyces tubercidicus Nakamura 1961 (Approved Lists 1980)

@ref: 9415

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces tubercidicus

full scientific name: Streptomyces tubercidicus Nakamura 1961

strain designation: IPCR 585

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no96.631
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9415GYM 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
9415ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
9415positivegrowth28mesophilic
18573positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9415tubercidin
20216Tubercidin
20216Endonuclease Stu I
67770Endonuclease

halophily

  • @ref: 18573
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1857317234glucose+
1857322599arabinose-
1857317992sucrose+
1857318222xylose-
1857317268myo-inositol+
1857329864mannitol+
1857328757fructose+
1857326546rhamnose-
1857316634raffinose+
1857362968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777048267tubercidinyes
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 TrpINDVPGEL
18573+-+-+-+--++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9415soilJapanJPNAsia
67770SoilJapanJPNAsiaMobara, Chiba Pref.

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94151Risk group (German classification)
185731German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces tubercidicus strain AS 4.1414 16S ribosomal RNA gene, partial sequenceFJ4061121362ena47759
20218Streptomyces tubercidicus 16S rRNA gene, type strain DSM 40261TAJ6216121498ena47759
20218Streptomyces tubercidicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4558D44230121ena47759
20218Streptomyces tubercidicus gene for 16S rRNA, partial sequence, strain: NBRC 13090AB1843041452ena47759

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces tubercidicus strain NBRC 1309047759.3wgspatric47759
67770Streptomyces tubercidicus NBRC 13090GCA_009811635contigncbi47759
66792Streptomyces tubercidicus DSM 40261GCA_027497495completencbi47759

GC content

  • @ref: 67770
  • GC-content: 70.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.445no
flagellatedno98.168no
gram-positiveyes89.384no
anaerobicno99.303no
aerobicyes92.873no
halophileno88.658no
spore-formingyes96.303no
glucose-fermentno91.912no
thermophileno97.507yes
glucose-utilyes91.715yes

External links

@ref: 9415

culture collection no.: DSM 40261, ATCC 25502, CBS 644.69, IFO 13090, ISP 5261, JCM 4054, NBRC 13090, RIA 1282, BCRC 11886, CECT 3272, CGMCC 4.1414, IFM 1064, IMET 43517, JCM 4558, KCTC 9109, LMG 19361, MTCC 1820, NRRL B-5440, VKM Ac-1073

straininfo link

  • @ref: 85131
  • straininfo: 14117

literature

  • topic: Metabolism
  • Pubmed-ID: 30153835
  • title: Discovery and characterization of the tubercidin biosynthetic pathway from Streptomyces tubercidicus NBRC 13090.
  • authors: Liu Y, Gong R, Liu X, Zhang P, Zhang Q, Cai YS, Deng Z, Winkler M, Wu J, Chen W
  • journal: Microb Cell Fact
  • DOI: 10.1186/s12934-018-0978-8
  • year: 2018
  • mesh: Streptomyces/*metabolism, Synthetic Biology/*methods, Tubercidin/biosynthesis/*metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9415Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40261)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40261
18573Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40261.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
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
85131Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14117.1StrainInfo: A central database for resolving microbial strain identifiers