Strain identifier

BacDive ID: 4350

Type strain: Yes

Species: Dickeya dadantii

Strain Designation: B374

Strain history: CIP <- 2005, NCPPB <- strain Hayward B374

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
204038species
1223572strain

strain history

@refhistory
7346<- CFBP <- R. Dadant; B374
118839CIP <- 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
29987negative2 µm0.75 µmrod-shapedyes
69480yes98.381
69480negative99.99
118839negativerod-shapedyes

colony morphology

  • @ref: 118839

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7346REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: 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
37455MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118839CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
118839CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7346positivegrowth30mesophilic
29987positivegrowth36-39mesophilic
29987positiveoptimum37.5mesophilic
37455positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29987facultative anaerobe
118839facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.71

observation

  • @ref: 29987
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2998722599arabinose+carbon source
2998717057cellobiose+carbon source
2998717234glucose+carbon source
2998717716lactose+carbon source
2998725115malate+carbon source
2998715792malonate+carbon source
2998729864mannitol+carbon source
2998737684mannose+carbon source
2998728053melibiose+carbon source
2998717268myo-inositol+carbon source
2998716634raffinose+carbon source
2998717632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117306maltose-builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan+energy source
6836917632nitrate+reduction
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
11883917632nitrate+reduction
11883916301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2998735581indoleyes
6836935581indoleyes
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno
11883935581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
2998735581indole+
6836935581indole+
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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
118839oxidase-
118839alcohol dehydrogenase-1.1.1.1
118839caseinase+3.4.21.50
118839catalase+1.11.1.6
118839lysine decarboxylase-4.1.1.18
118839ornithine decarboxylase-4.1.1.17
118839urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118839-++--++-+-++++--+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7346+---+---++-+++-++++++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7346+++--+-++++++++--++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118839+-++++---++++-+-+/-+---+-++++-+/-++---+---+/-----------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
7346Pelargonium capitatumPelargonium capitatumComorosCOMAfrica
118839Plant, 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

@refpathogenicity plantbiosafety levelbiosafety level comment
7346yes1Risk group (German classification)
1188391Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Dickeya dadantii strain NCPPB 898 16S-23S ribosomal RNA intergenic spacer, partial sequenceKC844733320ena204038
7346Dickeya dadantii strain CFBP 1269 16S ribosomal RNA gene, partial sequenceAF5207071413ena204038

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dickeya dadantii DSM 18020GCA_003049785completencbi204038
66792Dickeya dadantii NCPPB 898GCA_000406145chromosomencbi1223572
66792Dickeya dadantii NCPPB 8981223572.11wgspatric1223572
66792Dickeya dadantii strain DSM 18020204038.21completepatric204038
66792Dickeya dadantii DSM 180202814123163completeimg204038
66792Dickeya dadantii NCPPB 8982558860214draftimg1223572

GC content

@refGC-contentmethod
734659.5high performance liquid chromatography (HPLC)
2998759.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno86no
motileyes89.474yes
flagellatedno54.971no
gram-positiveno98.449yes
anaerobicno96.73yes
aerobicno72.808yes
halophileno92.738no
spore-formingno93.821no
thermophileno99.452yes
glucose-utilyes93.369yes
glucose-fermentyes87.385yes

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014461Transfer 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 LInt J Syst Evol Microbiol10.1099/ijs.0.02791-02005Animals, 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, SerotypingGenetics
Phylogeny21890733Proposal 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 PInt J Syst Evol Microbiol10.1099/ijs.0.035055-02011Bacterial 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 KingdomGenetics
30743366First 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 ZYPlant Dis10.1094/PDIS-06-10-04172010
30764150Bacterial Stem Rot of Oncidium Orchid Caused by a Dickeya sp. (ex Pectobacterium chrysanthemi) in Mainland China.Li B, Qiu W, Fang Y, Xie GLPlant Dis10.1094/PDIS-93-5-0552B2009
32390987Assessment 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 SCFront Microbiol10.3389/fmicb.2020.007512020
35771110First report of Dickeya dadantii causing bacterial soft rot of Thaumatophyllum bipinnatifidum in Taiwan.Wu YM, Wang LH, Chu CCPlant Dis10.1094/PDIS-04-22-0924-PDN2022

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7346Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18020)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18020
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
29987Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126354
37455Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6702
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
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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)
73841Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID111271.1StrainInfo: A central database for resolving microbial strain identifiers
118839Curators of the CIPCollection of Institut Pasteur (CIP 109008)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109008