Strain identifier
BacDive ID: 4346
Type strain:
Species: Dickeya chrysanthemi
Strain Designation: EC17
Strain history: <- CIP <- NCPPB <- W. Burkholder, EC17
NCBI tax ID(s): 1223569 (strain), 556 (species)
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 id | Matching level |
---|---|
556 | species |
1223569 | strain |
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
@ref synonym 20215 Pectobacterium chrysanthemi 20215 Erwinia 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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 98.238 | |
69480 | 99.985 | negative |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
1800 | positive | growth | 30 | mesophilic |
54451 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 54451
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 95 |
69480 | no | 99.918 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 30849 | L-arabinose | + | fermentation |
68368 | 27613 | amygdalin | + | fermentation |
68368 | 28053 | melibiose | + | fermentation |
68368 | 17992 | sucrose | + | fermentation |
68368 | 62345 | L-rhamnose | + | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | + | fermentation |
68368 | 16899 | D-mannitol | + | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | + | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | + | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | yes |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | + | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pectobacterium chrysanthemi strain ATCC 11663(Type strain) 16S-23S intergenic spacer region and tRNA-Glu gene, complete sequence | AF232681 | 356 | ena | 556 |
20218 | Erwinia chrysanthemi 16S ribosomal RNA gene, partial sequence | U80200 | 1458 | ena | 556 |
20218 | Erwinia chrysanthemi 16S rRNA gene (strain DSM 4610) | AJ233412 | 1496 | ena | 556 |
20218 | Erwinia chrysanthemi partial 16S rRNA gene, type strain DSM 4610T, clone 1 | HG515378 | 1528 | ena | 556 |
20218 | Erwinia chrysanthemi partial 16S rRNA gene, type strain DSM 4610T, clone 2 | HG515379 | 1528 | ena | 556 |
20218 | Erwinia chrysanthemi LMG 2804 16S ribosomal RNA | Z96093 | 1497 | ena | 556 |
20218 | Erwinia chrysanthemi strain NCPPB 402 16S-23S ribosomal RNA intergenic spacer, partial sequence | KC844732 | 319 | ena | 556 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dickeya chrysanthemi NCPPB 402 | GCA_000406105 | chromosome | ncbi | 1223569 |
66792 | Dickeya chrysanthemi NCPPB 402 | 1223569.8 | wgs | patric | 1223569 |
66792 | Dickeya chrysanthemi NCPPB 402 | 2558860220 | draft | img | 1223569 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 95 | no |
motile | yes | 91.047 | no |
flagellated | no | 54.013 | no |
gram-positive | no | 98.408 | no |
anaerobic | no | 96.968 | yes |
aerobic | yes | 54.024 | yes |
halophile | no | 92.914 | no |
spore-forming | no | 93.532 | no |
thermophile | no | 99.428 | yes |
glucose-util | yes | 93.839 | no |
glucose-ferment | yes | 91.257 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1800 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4610) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4610 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
54451 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 38766) | https://www.ccug.se/strain?id=38766 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68368 | Automatically annotated from API 20E | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
73837 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13658.1 | StrainInfo: A central database for resolving microbial strain identifiers |