Strain identifier

BacDive ID: 4346

Type strain: Yes

Species: Dickeya chrysanthemi

Strain Designation: EC17

Strain history: <- CIP <- NCPPB <- W. Burkholder, EC17

NCBI tax ID(s): 1223569 (strain), 556 (species)

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

@ref: 1800

BacDive-ID: 4346

DSM-Number: 4610

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

description: Dickeya chrysanthemi EC17 is an aerobe, mesophilic, motile plant pathogen that was isolated from Chrysanthemum morifolium.

NCBI tax id

NCBI tax idMatching level
556species
1223569strain

strain history

  • @ref: 1800
  • history: <- CIP <- NCPPB <- W. Burkholder, EC17

doi: 10.13145/bacdive4346.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Pectobacteriaceae
  • genus: Dickeya
  • species: Dickeya chrysanthemi
  • full scientific name: Dickeya chrysanthemi (Burkholder et al. 1953) Samson et al. 2005
  • synonyms

    @refsynonym
    20215Pectobacterium chrysanthemi
    20215Erwinia chrysanthemi

@ref: 1800

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Dickeya

species: Dickeya chrysanthemi

full scientific name: Dickeya chrysanthemi (Burkholder et al. 1953) Samson et al. 2005

strain designation: EC17

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.238
6948099.985negative

multimedia

  • @ref: 1800
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_4610.jpg
  • caption: DSM 4610 on medium 1 at 28 °C
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

  • @ref: 1800
  • name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1a
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
1800positivegrowth30mesophilic
54451positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 54451
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no95
69480no99.918

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole+

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
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 TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1800++--+---+--+++-+++++-

Isolation, sampling and environmental information

isolation

  • @ref: 54451
  • sample type: Chrysanthemum morifolium
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7297.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_451;97_1020;98_1203;99_7297&stattab=map
  • Last taxonomy: Dickeya chrysanthemi
  • 16S sequence: HG515379
  • Sequence Identity:
  • Total samples: 66
  • soil counts: 2
  • aquatic counts: 16
  • animal counts: 45
  • plant counts: 3

Safety information

risk assessment

  • @ref: 1800
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pectobacterium chrysanthemi strain ATCC 11663(Type strain) 16S-23S intergenic spacer region and tRNA-Glu gene, complete sequenceAF232681356ena556
20218Erwinia chrysanthemi 16S ribosomal RNA gene, partial sequenceU802001458ena556
20218Erwinia chrysanthemi 16S rRNA gene (strain DSM 4610)AJ2334121496ena556
20218Erwinia chrysanthemi partial 16S rRNA gene, type strain DSM 4610T, clone 1HG5153781528ena556
20218Erwinia chrysanthemi partial 16S rRNA gene, type strain DSM 4610T, clone 2HG5153791528ena556
20218Erwinia chrysanthemi LMG 2804 16S ribosomal RNAZ960931497ena556
20218Erwinia chrysanthemi strain NCPPB 402 16S-23S ribosomal RNA intergenic spacer, partial sequenceKC844732319ena556

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dickeya chrysanthemi NCPPB 402GCA_000406105chromosomencbi1223569
66792Dickeya chrysanthemi NCPPB 4021223569.8wgspatric1223569
66792Dickeya chrysanthemi NCPPB 4022558860220draftimg1223569

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileyes91.047no
flagellatedno54.013no
gram-positiveno98.408no
anaerobicno96.968yes
aerobicyes54.024yes
halophileno92.914no
spore-formingno93.532no
thermophileno99.428yes
glucose-utilyes93.839no
glucose-fermentyes91.257no

External links

@ref: 1800

culture collection no.: CCUG 38766, LMG 2804, DSM 4610, ATCC 11663, CIP 82.99, DAR 35625, NCPPB 402, PDDCC 5703

straininfo link

  • @ref: 73837
  • straininfo: 13658

literature

  • Pubmed-ID: 30769513
  • title: Bacterial Stem Rot of Poinsettia Caused by a Dickeya sp. (Pectobacterium chrysanthemi) in China.
  • authors: Rungnapha K, Yu SH, Xie GL
  • journal: Plant Dis
  • DOI: 10.1094/PDIS-92-7-1135B
  • year: 2008

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1800Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4610)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4610
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
54451Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38766)https://www.ccug.se/strain?id=38766
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)
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
73837Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13658.1StrainInfo: A central database for resolving microbial strain identifiers