Strain identifier
BacDive ID: 4350
Type strain:
Species: Dickeya dadantii
Strain Designation: B374
Strain history: CIP <- 2005, NCPPB <- strain Hayward B374
NCBI tax ID(s): 1223572 (strain), 204038 (species)
General
@ref: 7346
BacDive-ID: 4350
DSM-Number: 18020
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, plant pathogen
description: Dickeya dadantii B374 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from Pelargonium capitatum.
NCBI tax id
NCBI tax id | Matching level |
---|---|
204038 | species |
1223572 | strain |
strain history
@ref | history |
---|---|
7346 | <- CFBP <- R. Dadant; B374 |
118839 | CIP <- 2005, NCPPB <- strain Hayward B374 |
doi: 10.13145/bacdive4350.20230509.8.1
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 dadantii
- full scientific name: Dickeya dadantii Samson et al. 2005
@ref: 7346
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Pectobacteriaceae
genus: Dickeya
species: Dickeya dadantii
full scientific name: Dickeya dadantii Samson et al. 2005 emend. Brady et al. 2012
strain designation: B374
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 | 98.381 | ||||
69480 | negative | 99.99 | ||||
118839 | negative | rod-shaped | yes |
colony morphology
- @ref: 118839
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7346 | REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) | yes | https://mediadive.dsmz.de/medium/535b | Name: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water |
37455 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
118839 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
118839 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7346 | positive | growth | 30 | mesophilic |
29987 | positive | growth | 36-39 | mesophilic |
29987 | positive | optimum | 37.5 | mesophilic |
37455 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29987 | facultative anaerobe |
118839 | facultative anaerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.71
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 | 17057 | cellobiose | + | carbon source |
29987 | 17234 | glucose | + | carbon source |
29987 | 17716 | lactose | + | 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 |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | + | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | + | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | + | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | + | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 30849 | L-arabinose | + | builds acid from |
68371 | 17108 | D-arabinose | + | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | + | builds acid from |
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | + | fermentation |
68369 | 27897 | tryptophan | + | energy source |
68369 | 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 |
118839 | 17632 | nitrate | + | reduction |
118839 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
29987 | 35581 | indole | yes |
68369 | 35581 | indole | yes |
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | yes |
68368 | 16136 | hydrogen sulfide | no |
118839 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
29987 | 35581 | indole | + | |
68369 | 35581 | indole | + | |
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
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 |
118839 | oxidase | - | |
118839 | alcohol dehydrogenase | - | 1.1.1.1 |
118839 | caseinase | + | 3.4.21.50 |
118839 | catalase | + | 1.11.1.6 |
118839 | lysine decarboxylase | - | 4.1.1.18 |
118839 | ornithine decarboxylase | - | 4.1.1.17 |
118839 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118839 | - | + | + | - | - | + | + | - | + | - | + | + | + | + | - | - | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7346 | + | - | - | - | + | - | - | - | + | + | - | + | + | + | - | + | + | + | + | + | + |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7346 | + | + | + | - | - | + | - | + | + | + | + | + | + | + | + | - | - | + | + | - | + |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118839 | + | - | + | + | + | + | - | - | - | + | + | + | + | - | + | - | +/- | + | - | - | - | + | - | + | + | + | + | - | +/- | + | + | - | - | - | + | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent |
---|---|---|---|---|---|
7346 | Pelargonium capitatum | Pelargonium capitatum | Comoros | COM | Africa |
118839 | Plant, Host plant, Pelargonium capitatum |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Shrub (Scrub)
taxonmaps
- @ref: 69479
- File name: preview.99_2933.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_451;97_1020;98_1353;99_2933&stattab=map
- Last taxonomy: Dickeya dadantii
- 16S sequence: AF520707
- Sequence Identity:
- Total samples: 42
- soil counts: 2
- aquatic counts: 8
- animal counts: 17
- plant counts: 15
Safety information
risk assessment
@ref | pathogenicity plant | biosafety level | biosafety level comment |
---|---|---|---|
7346 | yes | 1 | Risk group (German classification) |
118839 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Dickeya dadantii strain NCPPB 898 16S-23S ribosomal RNA intergenic spacer, partial sequence | KC844733 | 320 | ena | 204038 |
7346 | Dickeya dadantii strain CFBP 1269 16S ribosomal RNA gene, partial sequence | AF520707 | 1413 | ena | 204038 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dickeya dadantii DSM 18020 | GCA_003049785 | complete | ncbi | 204038 |
66792 | Dickeya dadantii NCPPB 898 | GCA_000406145 | chromosome | ncbi | 1223572 |
66792 | Dickeya dadantii NCPPB 898 | 1223572.11 | wgs | patric | 1223572 |
66792 | Dickeya dadantii strain DSM 18020 | 204038.21 | complete | patric | 204038 |
66792 | Dickeya dadantii DSM 18020 | 2814123163 | complete | img | 204038 |
66792 | Dickeya dadantii NCPPB 898 | 2558860214 | draft | img | 1223572 |
GC content
@ref | GC-content | method |
---|---|---|
7346 | 59.5 | high performance liquid chromatography (HPLC) |
29987 | 59.5 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 86 | no |
motile | yes | 89.474 | yes |
flagellated | no | 54.971 | no |
gram-positive | no | 98.449 | yes |
anaerobic | no | 96.73 | yes |
aerobic | no | 72.808 | yes |
halophile | no | 92.738 | no |
spore-forming | no | 93.821 | no |
thermophile | no | 99.452 | yes |
glucose-util | yes | 93.369 | yes |
glucose-ferment | yes | 87.385 | yes |
External links
@ref: 7346
culture collection no.: DSM 18020, LMG 25991, NCPPB 898, CFBP 1269, CIP 109008, ICMP 1544, Hayward B374
straininfo link
- @ref: 73841
- straininfo: 111271
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 |
Phylogeny | 21890733 | Proposal to reclassify Brenneria quercina (Hildebrand and Schroth 1967) Hauben et al. 1999 into a new genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov. and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii. | Brady CL, Cleenwerck I, Denman S, Venter SN, Rodriguez-Palenzuela P, Coutinho TA, De Vos P | Int J Syst Evol Microbiol | 10.1099/ijs.0.035055-0 | 2011 | Bacterial Proteins/genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enterobacteriaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phylogeny, Plant Diseases/microbiology, Quercus/microbiology, RNA, Ribosomal, 16S/genetics, Spain, United Kingdom | Genetics |
30743366 | First Report of Bacterial Stem and Root Rot of Sweetpotato Caused by a Dickeya sp. (Erwinia chrysanthemi) in China. | Huang LF, Fang BP, Luo ZX, Chen JY, Zhang XJ, Wang ZY | Plant Dis | 10.1094/PDIS-06-10-0417 | 2010 | |||
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 | |||
32390987 | Assessment of a Potential Role of Dickeya dadantii DSM 18020 as a Pectinase Producer for Utilization in Poultry Diets Based on in silico Analyses. | Dittoe DK, Barabote RD, Rothrock MJ, Ricke SC | Front Microbiol | 10.3389/fmicb.2020.00751 | 2020 | |||
35771110 | First report of Dickeya dadantii causing bacterial soft rot of Thaumatophyllum bipinnatifidum in Taiwan. | Wu YM, Wang LH, Chu CC | Plant Dis | 10.1094/PDIS-04-22-0924-PDN | 2022 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
7346 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18020) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18020 | ||||
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 | ||
37455 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6702 | |||||
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 | ||||||
68369 | Automatically annotated from API 20NE | ||||||
68371 | Automatically annotated from API 50CH acid | ||||||
68382 | Automatically annotated from API zym | ||||||
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) | ||||
73841 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID111271.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
118839 | Curators of the CIP | Collection of Institut Pasteur (CIP 109008) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109008 |