Dickeya chrysanthemi (CCUG 38766, LMG 2804, DSM 4610)

Name: Dickeya chrysanthemi (CCUG 38766, LMG 2804, DSM 4610)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4346

Type strain

Strain Designation EC17

Culture col. no. CCUG 38766 LMG 2804 DSM 4610 ATCC 11663 CIP 82.99 4 more

NCBI tax ID(s) 1223569 556

Special Collections DSMZ CCUG CIP

History <- CIP <- NCPPB <- W. Burkholder, EC17

Links

Dickeya chrysanthemi EC17 is an aerobe plant pathogen that was isolated from Chrysanthemum morifolium.

aerobe plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 13658

LMG 2804,ATCC 11663,ICMP 5703,NCPPB 402,PDDCC 5703,CCUG 38766,NBIMCC 2332,DSM 4610,CIP 82.99,KCTC 2569,CFBP 2048,NCAIM B.01392,BCRC 12849,CCRC 12849,KACC 10062

@ref 20215

Last LPSN update 2026-02-09 11:18:42

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 (2)

Pectobacterium chrysanthemi
Erwinia chrysanthemi

BacDive ID	Other strains from **Dickeya chrysanthemi** (1)	Type strain
4347	D. chrysanthemi EC 16, DSM 30177, ATCC 11662

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99

Multimedia

@ref:	1800
multimedia content:	DSM_4610.jpg
multimedia.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
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1800	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)		Medium recipe at MediaDive	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 (°C)
1800	positive	growth	30
54451	positive	growth	30

Physiology and metabolism

Oxygen tolerance

54451

Oxygen toleranceaerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	+	fermentation	from API 20E
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	+	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	+	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		+	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
1800	+	+	-	-	+	-	-	-	+	-	-	+	+	+	-	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
54451	Chrysanthemum morifolium	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence HG515379 (>99% sequence identity) for Dickeya chrysanthemi from Microbeatlas

Aquatic Samples	16
Soil Samples	2
Animal Samples	45
Plant Samples	3
Total Samples	66

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
1800		1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Dickeya chrysanthemi NCPPB 402	complete			2558860220	1223569	94.81
66792	DCH402_1.0 assembly for Dickeya chrysanthemi NCPPB 402	chromosome	GCA_000406105	1223569.8	2962773892	1223569	72.58

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Pectobacterium chrysanthemi strain ATCC 11663(Type strain) 16S-23S intergenic spacer region and tRNA-Glu gene, complete sequence	AF232681	356	556
20218	Erwinia chrysanthemi 16S ribosomal RNA gene, partial sequence	U80200	1458	556
20218	Erwinia chrysanthemi 16S rRNA gene (strain DSM 4610)	AJ233412	1496	556
20218	Erwinia chrysanthemi LMG 2804 16S ribosomal RNA	Z96093	1497	556
20218	Erwinia chrysanthemi strain NCPPB 402 16S-23S ribosomal RNA intergenic spacer, partial sequence	KC844732	319	556
124043	Dickeya chrysanthemi strain NCPPB 402 16S ribosomal RNA gene, partial sequence.	KY190327	999	556

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dickeya chrysanthemi NCPPB 402
PATRIC: 1223569.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	61.10	no
125439	gram_stain	BacteriaNetⓘ	negative	87.00	no
125439	motility	BacteriaNetⓘ	yes	69.70	no
125439	spore_formation	BacteriaNetⓘ	no	77.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dickeya chrysanthemi NCPPB 402 NCPPB 402
NCBI: GCA_000406105.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	96.28	no
125438	aerobic	aerobicⓘ	no	72.08	no
125438	spore-forming	spore-formingⓘ	no	85.95	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	80.12	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Species of Dickeya and Pectobacterium Isolated during an Outbreak of Blackleg and Soft Rot of Potato in Northeastern and North Central United States.	Curland RD, Mainello A, Perry KL, Hao J, Charkowski AO, Bull CT, McNally RR, Johnson SB, Rosenzweig N, Secor GA, Larkin RP, Gugino BK, Ishimaru CA.	Microorganisms	10.3390/microorganisms9081733	2021
	First Report of Stem Rot on Potato Caused by Dickeya chrysanthemi in Minnesota	McNally RR, Curland RD, Webster BT, Robinson AP, Ishimaru CA.	Plant Dis	10.1094/pdis-07-17-0966-pdn	2018
	Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus.	Buttimer C, Lynch C, Hendrix H, Neve H, Noben JP, Lavigne R, Coffey A.	Antibiotics (Basel)	10.3390/antibiotics9060352	2020
Phylogeny	Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus 'Phimunavirus'.	Buttimer C, Lucid A, Neve H, Franz CMAP, O'Mahony J, Turner D, Lavigne R, Coffey A.	Viruses	10.3390/v10080394	2018
	First Report of Filamentous Phages Isolated from Tunisian Orchards to Control Erwinia amylovora.	Akremi I, Holtappels D, Brabra W, Jlidi M, Hadj Ibrahim A, Ben Ali M, Fortuna K, Ahmed M, Meerbeek BV, Rhouma A, Lavigne R, Ben Ali M, Wagemans J.	Microorganisms	10.3390/microorganisms8111762	2020
Phylogeny	Novel N4-Like Bacteriophages of Pectobacterium atrosepticum.	Buttimer C, Hendrix H, Lucid A, Neve H, Noben JP, Franz C, O'Mahony J, Lavigne R, Coffey A.	Pharmaceuticals (Basel)	10.3390/ph11020045	2018
Genetics	Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB.	Buttimer C, Hendrix H, Oliveira H, Casey A, Neve H, McAuliffe O, Ross RP, Hill C, Noben JP, O'Mahony J, Lavigne R, Coffey A.	Front Microbiol	10.3389/fmicb.2017.00044	2017
	Complete Genome Sequence of Dickeya chrysanthemi Bacteriophage DchS19.	Mutusamy P, Jaya Jothi S, Kumarasan Y, Loke S, Lee SY, Rajandas H, Parimannan S.	Microbiol Resour Announc	10.1128/mra.00800-22	2022
Enzymology	Characterization of two related Erwinia myoviruses that are distant relatives of the PhiKZ-like Jumbo phages.	Arens DK, Brady TS, Carter JL, Pape JA, Robinson DM, Russell KA, Staley LA, Stettler JM, Tateoka OB, Townsend MH, Whitley KV, Wienclaw TM, Williamson TL, Johnson SM, Grose JH.	PLoS One	10.1371/journal.pone.0200202	2018
Phylogeny	Phylogeny and virulence of naturally occurring type III secretion system-deficient Pectobacterium strains.	Kim HS, Ma B, Perna NT, Charkowski AO.	Appl Environ Microbiol	10.1128/aem.01336-08	2009
	Biological and Molecular Characterization of the Lytic Bacteriophage SoKa against Pseudomonas syringae pv. syringae, Causal Agent of Citrus Blast and Black Pit in Tunisia.	Oueslati M, Holtappels D, Fortuna K, Hajlaoui MR, Lavigne R, Sadfi-Zouaoui N, Wagemans J.	Viruses	10.3390/v14091949	2022
	Retrospective survey of Dickeya fangzhongdai using a novel validated real-time PCR assay.	Alic S, Bacnik K, Dreo T.	Front Microbiol	10.3389/fmicb.2023.1249955	2023
	L-Amino Acid Oxidases From Mushrooms Show Antibacterial Activity Against the Phytopathogen Ralstonia solanacearum.	Sabotic J, Brzin J, Erjavec J, Dreo T, Tusek Znidaric M, Ravnikar M, Kos J.	Front Microbiol	10.3389/fmicb.2020.00977	2020
Metabolism	Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq.	Matilla MA, Leeper FJ, Salmond GP.	Environ Microbiol	10.1111/1462-2920.12839	2015
	May the Phage be With You? Prophage-Like Elements in the Genomes of Soft Rot Pectobacteriaceae: Pectobacterium spp. and Dickeya spp.	Czajkowski R.	Front Microbiol	10.3389/fmicb.2019.00138	2019
	Simultaneous detection of major blackleg and soft rot bacterial pathogens in potato by multiplex polymerase chain reaction.	Potrykus M, Sledz W, Golanowska M, Slawiak M, Binek A, Motyka A, Zoledowska S, Czajkowski R, Lojkowska E.	Ann Appl Biol	10.1111/aab.12156	2014
Enzymology	Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes.	Nassar A, Darrasse A, Lemattre M, Kotoujansky A, Dervin C, Vedel R, Bertheau Y.	Appl Environ Microbiol	10.1128/aem.62.7.2228-2235.1996	1996
	Bacterial Stem Rot of Poinsettia Caused by a Dickeya sp. (Pectobacterium chrysanthemi) in China.	Rungnapha K, Yu SH, Xie GL	Plant Dis	10.1094/PDIS-92-7-1135B	2008

References

#1800	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4610
#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 )
#54451	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38766
#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) .
#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.: MicrobeAtlas 1.0 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Dickeya chrysanthemi (CCUG 38766, LMG 2804, DSM 4610)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000406105

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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