Strain identifier

BacDive ID: 7289

Type strain: Yes

Species: Clavibacter michiganensis

Strain Designation: S 05, SO5

Strain history: ICMP 2550 <-- D. W. Dye CC31 <-- ICPB CM177 <-- Z. Klement SO5.

NCBI tax ID(s): 28447 (species)

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General

@ref: 12537

BacDive-ID: 7289

DSM-Number: 46364

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, plant pathogen

description: Clavibacter michiganensis S 05 is a mesophilic plant pathogen that was isolated from Lycopersicon lycopersicum.

NCBI tax id

  • NCBI tax id: 28447
  • Matching level: species

strain history

@refhistory
12537<- IMET <- LMG <- PDDCC <- D. Dye <- ICPB <- Z. Klement, SO5
67770ICMP 2550 <-- D. W. Dye CC31 <-- ICPB CM177 <-- Z. Klement SO5.

doi: 10.13145/bacdive7289.20230509.8.1

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 michiganensis
  • full scientific name: Clavibacter michiganensis corrig. (Smith 1910) Davis et al. 1984

  • synonyms

    @refsynonym
    20215Bacterium michiganense
    20215Clavibacter michiganense
    20215Corynebacterium michiganense

@ref: 12537

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Clavibacter

species: Clavibacter michiganensis

full scientific name: Clavibacter michiganensis (Smith 1910) Davis et al. 1984 emend. Nouioui et al. 2018

strain designation: S 05, SO5

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.917
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12537R2A 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
12537TRYPTICASE 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
12537positivegrowth25mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

murein

  • @ref: 12537
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

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

Isolation, sampling and environmental information

isolation

@refsample typesampling datecountryorigin.countrycontinenthost species
47797Lycopersicon lycopersicum1957HungaryHUNEurope
67770Tomato (Lycopercicon esculentum)HungaryHUNEuropeLycopercicon esculentum

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_730.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_446;97_510;98_586;99_730&stattab=map
  • Last taxonomy: Clavibacter michiganensis
  • 16S sequence: X77435
  • Sequence Identity:
  • Total samples: 54773
  • soil counts: 15732
  • aquatic counts: 10493
  • animal counts: 18473
  • plant counts: 10075

Safety information

risk assessment

  • @ref: 12537
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clavibacter michiganensis subsp. michiganensis partial 16S rRNA gene, type strain DSM 46364AM4106961471ena33013
20218Clavibacter michiganensis subsp. michiganensis strain ICMP 2550 16S-23S ribosomal RNA intergenic spacer, partial sequenceFJ205139516ena33013
20218Clavibacter michiganensis subsp. michiganensis partial 16S rRNA gene, strain LMG7333TFR728336452ena33013
20218Clavibacter michiganensis subsp. michiganensis strain LMG 7333 16S ribosomal RNA gene, partial sequenceJN6032771359ena33013
20218Clavibacter michiganensis subsp. michiganensis strain LMG 7333 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceJN603289773ena33013
20218Clavibacter michiganensis michiganensis LGM 7333 16S-23S rRNA spacer regionU09380481ena28447
20218Clavibacter michiganensis michiganensis LMG 7333 16S rRNAU097621491ena28447
12537Clavibacter michiganensis strain DSM 46364 16S ribosomal RNA, partial sequenceNR_1150401471nuccore28447
67770C.michiganense (DSM 46364) 16S rRNA geneX774351471ena28447

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clavibacter michiganensis subsp. michiganensis33013.123wgspatric33013
66792Clavibacter michiganensis subsp. michiganensis strain CFBP 499933013.190wgspatric33013
66792Clavibacter michiganensis CFBP 49992846599232draftimg28447
67770Clavibacter michiganensis VKM Ac-1403GCA_900168345scaffoldncbi28447
67770Clavibacter michiganensis subsp. michiganensis LMG 7333GCA_002240575contigncbi33013
67770Clavibacter michiganensis subsp. michiganensis CFBP 4999GCA_003697295scaffoldncbi33013
66792Clavibacter michiganensis LMG7333GCA_021216655completencbi28447
66792Clavibacter michiganensis strain LMG733328447.208completepatric28447

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno98.016no
gram-positiveyes93.952no
anaerobicno99.252no
aerobicyes92.757no
halophileno83.025no
spore-formingno95.682no
motileno90.659no
thermophileno99.128yes
glucose-utilyes86.91no
glucose-fermentno90.802no

External links

@ref: 12537

culture collection no.: CCUG 23363, CIP 104846, DSM 46364, ICPB CM 177, IMET 11518, LMG 7333, NCPPB 2979, PDDCC 2550, JCM 9665, CFBP 2352, CFBP 4999, ICMP 2550, IMSNU 21316, KACC 20122, KCCM 41108, VKM Ac-1403, VTT E-97058

straininfo link

  • @ref: 76739
  • straininfo: 386953

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics28935724Genome Sequences for Multiple Clavibacter Strains from Different Subspecies.Li XS, Yuan XKGenome Announc10.1128/genomeA.00721-172017
Enzymology30345870Functional Characterization of Two Cellulase Genes in the Gram-Positive Pathogenic Bacterium Clavibacter michiganensis for Wilting in Tomato.Hwang IS, Oh EJ, Lee HB, Oh CSMol Plant Microbe Interact10.1094/MPMI-08-18-0227-R2019*Actinobacteria/enzymology/genetics, *Cellulase/genetics/metabolism, *Lycopersicon esculentum/microbiology, *Plant Diseases/microbiology, Protein Sorting Signals/genetics/physiology, Virulence/geneticsMetabolism
30769542First Report of Bacterial Canker of Tomato Caused by Clavibacter michiganensis subsp. michiganensis in Korea.Myung IS, Kim DG, An SH, Lee YK, Kim WGPlant Dis10.1094/PDIS-92-10-1472A2008
33524890Novel galactofuranan and pyruvylated galactomannan in the cell wall of Clavibacter michiganensis subsp. michiganensis VKM Ac-1403(T).Kim D, Shashkov AS, Dmitrenok AS, Potekhina NV, Senchenkova SN, Dorofeeva LV, Evtushenko LI, Tul'skaya EMCarbohydr Res10.1016/j.carres.2021.1082472021Carbohydrate Conformation, Cell Wall/*chemistry, Clavibacter/chemistry/cytology, Polysaccharides/*chemistry
35178040Comparative Genome Analyses of Clavibacter michiganensis Type Strain LMG7333(T) Reveal Distinct Gene Contents in Plasmids From Other Clavibacter Species.Oh EJ, Hwang IS, Park IW, Oh CSFront Microbiol10.3389/fmicb.2021.7933452022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12537Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46364)https://www.dsmz.de/collection/catalogue/details/culture/DSM-46364
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
47797Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23363)https://www.ccug.se/strain?id=23363
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/
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
76739Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID386953.1StrainInfo: A central database for resolving microbial strain identifiers