Strain identifier
BacDive ID: 4351
Type strain:
Species: Dickeya dianthicola
Strain history: <- CFBP <- R. A. Lelliott; CN 26
NCBI tax ID(s): 1223568 (strain), 204039 (species)
General
@ref: 7273
BacDive-ID: 4351
DSM-Number: 18054
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, plant pathogen
description: Dickeya dianthicola DSM 18054 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from Dianthus caryophyllus.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1223568 | strain |
204039 | species |
strain history
- @ref: 7273
- history: <- CFBP <- R. A. Lelliott; CN 26
doi: 10.13145/bacdive4351.20230509.8.1
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 dianthicola
- full scientific name: Dickeya dianthicola Samson et al. 2005
@ref: 7273
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Pectobacteriaceae
genus: Dickeya
species: Dickeya dianthicola
full scientific name: Dickeya dianthicola Samson et al. 2005
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29987 | negative | 2 µm | 0.75 µm | rod-shaped | yes | |
69480 | yes | 98.423 | ||||
69480 | negative | 99.985 |
Culture and growth conditions
culture medium
- @ref: 7273
- 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 |
---|---|---|---|---|
7273 | positive | growth | 30 | mesophilic |
29987 | positive | optimum | 36 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 29987
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.825 |
observation
- @ref: 29987
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29987 | 22599 | arabinose | + | carbon source |
29987 | 17234 | glucose | + | carbon source |
29987 | 25115 | malate | + | carbon source |
29987 | 15792 | malonate | + | carbon source |
29987 | 29864 | mannitol | + | carbon source |
29987 | 37684 | mannose | + | carbon source |
29987 | 28053 | melibiose | + | carbon source |
29987 | 17268 | myo-inositol | + | carbon source |
29987 | 16634 | raffinose | + | carbon source |
29987 | 17632 | nitrate | + | reduction |
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 |
---|---|---|---|
29987 | 35581 | indole | yes |
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | yes |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
29987 | 35581 | indole | + | |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7273 | + | + | - | - | + | - | - | - | + | + | - | + | + | - | - | + | + | + | + | + | - |
Isolation, sampling and environmental information
isolation
- @ref: 7273
- sample type: Dianthus caryophyllus
- host species: Dianthus caryophyllus
- country: United Kingdom
- origin.country: GBR
- continent: Europe
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
Safety information
risk assessment
- @ref: 7273
- 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 | Dickeya dianthicola strain NCPPB 453 16S-23S ribosomal RNA intergenic spacer, partial sequence | KC844729 | 339 | ena | 204039 |
7273 | Dickeya dianthicola strain CFBP 1200 16S ribosomal RNA gene, partial sequence | AF520708 | 1427 | ena | 204039 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dickeya dianthicola NCPPB 453 | GCA_000365305 | chromosome | ncbi | 1223568 |
66792 | Dickeya dianthicola NCPPB 453 | 1223568.13 | wgs | patric | 1223568 |
66792 | Dickeya dianthicola NCPPB 453 | 2551306377 | draft | img | 1223568 |
GC content
- @ref: 29987
- GC-content: 59.5
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.219 | yes |
flagellated | yes | 52.52 | no |
gram-positive | no | 98.228 | no |
anaerobic | no | 97.128 | yes |
aerobic | no | 51.759 | no |
halophile | no | 94.251 | no |
spore-forming | no | 92.279 | no |
glucose-util | yes | 92.97 | yes |
thermophile | no | 99.358 | yes |
glucose-ferment | yes | 89.523 | yes |
External links
@ref: 7273
culture collection no.: DSM 18054, CFBP 1200, ICMP 6427, LMG 2485, NCPPB 453, CN 26
straininfo link
- @ref: 73842
- straininfo: 10989
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16014461 | Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. | Samson R, Legendre JB, Christen R, Saux MF, Achouak W, Gardan L | Int J Syst Evol Microbiol | 10.1099/ijs.0.02791-0 | 2005 | Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Dickeya chrysanthemi/*classification/genetics/physiology, Enterobacteriaceae/*classification/genetics/physiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rabbits, Serotyping | Genetics |
30764150 | Bacterial Stem Rot of Oncidium Orchid Caused by a Dickeya sp. (ex Pectobacterium chrysanthemi) in Mainland China. | Li B, Qiu W, Fang Y, Xie GL | Plant Dis | 10.1094/PDIS-93-5-0552B | 2009 | |||
33200972 | First Report of Dickeya dianthicola causing blackleg on New Guinea Impatiens (Impatiens hawkeri) in New York State, USA. | Liu Y, Vasiu S, Daughtrey ML, Filiatrault M | Plant Dis | 10.1094/PDIS-09-20-2020-PDN | 2020 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
7273 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18054) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18054 | ||||
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 | ||
29987 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 26354 | ||
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 | ||||||
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 | ||||
73842 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10989.1 | StrainInfo: A central database for resolving microbial strain identifiers |