Strain identifier

BacDive ID: 7294

Type strain: Yes

Species: Clavibacter sepedonicus

Strain Designation: C-1

Strain history: ICMP 2535 <-- D. W. Dye CB5 <-- ICPB CS101 <-- H. N. Racicot C1.

NCBI tax ID(s): 31964 (subspecies)

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General

@ref: 9053

BacDive-ID: 7294

DSM-Number: 20744

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive, plant pathogen

description: Clavibacter sepedonicus C-1 is a mesophilic, Gram-positive plant pathogen that was isolated from Solanum tuberosum.

NCBI tax id

  • NCBI tax id: 31964
  • Matching level: subspecies

strain history

@refhistory
9053<- ATCC <- NCPPB <- ICPB <- H.N. Racicot, C-1
67770ICMP 2535 <-- D. W. Dye CB5 <-- ICPB CS101 <-- H. N. Racicot C1.

doi: 10.13145/bacdive7294.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Clavibacter
  • species: Clavibacter sepedonicus
  • full scientific name: Clavibacter sepedonicus (Spieckermann and Kotthoff 1914) Li et al. 2018

  • synonyms

    @refsynonym
    20215Corynebacterium sepedonicum
    20215Bacterium sepedonicum
    20215Corynebacterium michiganense subsp. sepedonicum
    20215Clavibacter michiganensis subsp. sepedonicus
    20215Clavibacter sepedonicus
    20215Clavibacter michiganense subsp. sepedonicus
    20215Clavibacter michiganense subsp. sepedonicum
    20215Clavibacter michiganensis subsp. sepedonicum

@ref: 9053

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Clavibacter

species: Clavibacter sepedonicus

full scientific name: Clavibacter sepedonicus (Spieckermann and Kotthoff 1914) Li et al. 2018

strain designation: C-1

type strain: yes

Morphology

cell morphology

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9053R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
9053TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
9053positivegrowth25mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.946

observation

  • @ref: 67770
  • observation: quinones: MK-9

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
9053Solanum tuberosumSolanum tuberosum
47885Solanum tuberosum,ringrot
67770Potato (Solanum tuberosum)Solanum tuberosumCanadaCANNorth America

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

  • @ref: 9053
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clavibacter michiganensis subsp. sepedonicus partial 16S rRNA gene, type strain DSM 20744AM4106941492ena31964
20218Clavibacter michiganensis subsp. sepedonicus partial 16S rRNA gene, strain LMG2889TFR728289445ena31964
20218Clavibacter michiganensis sepedonicus LMG 2889 16S-23S rRNA spacer regionU09382470ena28447
20218Clavibacter michiganensis strain LMG 2889 16S ribosomal RNA, partial sequenceU097641492ena28447
20218Clavibacter michiganensis subsp. sepedonicus strain Ac-1405 16S-23S ribosomal RNA intergenic spacer, partial sequenceHQ394204445ena31964

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clavibacter michiganensis subsp. sepedonicus ATCC 33113GCA_000069225completencbi31964
66792Clavibacter michiganensis subsp. sepedonicus strain ATCC 3311331964.42plasmidpatric31964
66792Clavibacter michiganensis subsp. sepedonicus strain ATCC 3311331964.41plasmidpatric31964
66792Clavibacter michiganensis subsp. sepedonicus strain ATCC 3311331964.6completepatric31964
66792Clavibacter michiganensis sepedonicus ATCC 33113642555124completeimg31964

GC content

  • @ref: 67770
  • GC-content: 72.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.281no
flagellatedno97.793no
gram-positiveyes94.219no
anaerobicno99.3no
aerobicyes91.934no
halophileno84.223no
spore-formingno93.48no
thermophileno98.339yes
glucose-utilyes86.591no
glucose-fermentno90.492no

External links

@ref: 9053

culture collection no.: DSM 20744, ATCC 33113, ICPB CS101, NCPPB 2137, CCUG 23908, LMG 2889, CIP 104844, JCM 9667, CECT 4886, CFBP 2049, ICMP 2535, KACC 20123, KCCM 41286, VKM Ac-1405

straininfo link

  • @ref: 76744
  • straininfo: 1833

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9053Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20744)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20744
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
47885Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23908)https://www.ccug.se/strain?id=23908
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
76744Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1833.1StrainInfo: A central database for resolving microbial strain identifiers