Name: Dickeya dadantii subsp. dieffenbachiae DSM 18013
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4349

Type strain:

Species: Dickeya dadantii subsp. dieffenbachiae

Culture col. no.: DSM 18013, CFBP 2051, CIP 109104, ICPB ED102, NCPPB 2976

Strain history: <- CFBP <- L. A. Mac Fadden

NCBI tax ID(s): 1223574 (strain), 204040 (subspecies)

SI-ID 111273

CFBP 2051, NCPPB 2976, BCRC 13198, CCRC 13198, ICMP 1568, DSM 18013, CIP 109104, CFBP 1246, LMG 25992

Section

Dickeya dadantii subsp. dieffenbachiae DSM 18013 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from Dieffenbachia sp..

Gram-negative
motile
rod-shaped
facultative anaerobe
mesophilic
plant pathogen
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Pectobacteriaceae*
	Genus	*Dickeya*
	Species	**Dickeya dadantii subsp. dieffenbachiae**
	Full Scientific Name (LPSN)	Dickeya dadantii subsp. dieffenbachiae (Samson et al. 2005) Brady et al. 2012

Synonym

Dickeya dieffenbachiae

Information on morphological and physiological properties Morphology

[Ref.: #29987]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.987

[Ref.: #29987]	Cell length	2 µm

[Ref.: #29987]	Cell width	0.75 µm

[Ref.: #29987]	Cell shape	rod-shaped

[Ref.: #29987]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.419

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7332]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #7332]

Culture medium growth

[Ref.: #7332]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7332]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7332]	growth	28 °C
[Ref.: #29987]	growth	36-39 °C
[Ref.: #29987]	optimum	37.5 °C

[Ref.: #7332]	Temperature range	mesophilic
[Ref.: #29987]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29987]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %97
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.687

[Ref.: #29987]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29987]	arabinose ChEBI	+	carbon source
[Ref.: #29987]	glucose ChEBI	+	carbon source
[Ref.: #29987]	malate ChEBI	+	carbon source
[Ref.: #29987]	malonate ChEBI	+	carbon source
[Ref.: #29987]	mannitol ChEBI	+	carbon source
[Ref.: #29987]	mannose ChEBI	+	carbon source
[Ref.: #29987]	myo-inositol ChEBI	+	carbon source
[Ref.: #29987]	nitrate ChEBI	+	reduction

	Metabolite production	Metabolite	Production
[Ref.: #29987]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #29987]		indole ChEBI	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7332]	Sample type/isolated from	Dieffenbachia sp.
[Ref.: #7332]	Host species	Dieffenbachia
[Ref.: #7332]	Country	USA
[Ref.: #7332]	Country ISO 3 Code	USA
[Ref.: #7332]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF520712 (>99% sequence identity) for Dickeya from Microbeatlas

Aquatic Samples	1
Soil Samples	2
Animal Samples	29
Plant Samples	12
Total Samples	44

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7332]	Pathogenicity (plant)	yes
[Ref.: #7332]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7332]	Dickeya dieffenbachiae strain CFBP 2051 16S ribosomal RNA gene, partial sequence	AF520712	1434	ENA	204040 tax ID
[Ref.: #20218]	Dickeya dadantii subsp. dieffenbachiae strain NCPPB 2976 16S-23S ribosomal RNA intergenic spacer, partial sequence	KC844736	319	ENA	204040 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dickeya dadantii subsp. dieffenbachiae NCPPB 2976	GCA_000406185	chromosome	GenBank	1223574 tax ID	*
[Ref.: #66792]	Dickeya dadantii subsp. dieffenbachiae NCPPB 2976	1223574.11	wgs	PATRIC	1223574 tax ID	*
[Ref.: #66792]	Dickeya dadantii dieffenbachiae NCPPB 2976	2558860213	draft	JGI IMG/M	1223574 tax ID	*

[Ref.: #29987]

GC-content

57.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Dickeya dadantii subsp. dieffenbachiae NCPPB 2976 NCPPB 2976 NCBI: GCA_000406185.1
[Ref.: #69481]	spore-forming	no	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Dickeya dadantii subsp. dieffenbachiae NCPPB 2976 NCPPB 2976 NCBI: GCA_000406185.1
[Ref.: #69480]	motile	yes	91.099	yes
[Ref.: #69480]	flagellated	yes	56.045	no
[Ref.: #69480]	gram-positive	no	98.565	yes
[Ref.: #69480]	anaerobic	no	97.156	no
[Ref.: #69480]	aerobic	no	62.961	no
[Ref.: #69480]	halophile	no	93.825	no
[Ref.: #69480]	spore-forming	no	92.879	no
[Ref.: #69480]	thermophile	no	99.441	yes
[Ref.: #69480]	glucose-util	yes	93.837	yes
[Ref.: #69480]	glucose-ferment	yes	90.348	no

Availability in culture collections External links

[Ref.: #7332]

Culture collection no.

DSM 18013, CFBP 2051, CIP 109104, ICPB ED102, NCPPB 2976

[Ref.: #73840]

SI-ID 111273

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Phylogeny	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	*

References

#7332

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18013

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#29987

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26354 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#73840

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID111273.1 )

#26354

IJSEM 1415 2005 ( DOI 10.1099/ijs.0.02791-0 , PubMed 16014461 )

* These data were automatically processed and therefore are not curated

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Dickeya dadantii subsp. dieffenbachiae NCPPB 2976 NCPPB 2976

Dickeya dadantii subsp. dieffenbachiae NCPPB 2976 NCPPB 2976

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