Name: Dickeya fangzhongdai JS5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132585

Type strain:

Species: Dickeya fangzhongdai

Strain Designation: JS5

Culture col. no.: DSM 101947, CGMCC 1.15464

Strain history: <- Y. Tian, Nanjing Agricultural University, China; JS5

NCBI tax ID(s): 1778540 (species)

SI-ID 398073

DSM 101947

Section

Dickeya fangzhongdai JS5 is a mesophilic, Gram-negative, motile plant pathogen that was isolated from branches of a pear tree displaying symptoms of bleeding canker.

Gram-negative
motile
rod-shaped
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 fangzhongdai**
	Full Scientific Name (LPSN)	Dickeya fangzhongdai Tian et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43585]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.977

[Ref.: #43585]	Cell shape	rod-shaped

[Ref.: #43585]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.259

[Ref.: #43585]	Colony size	2 mm
[Ref.: #43585]	Incubation period	2 days
[Ref.: #43585]	Cultivation medium used	Yeast peptone dextrose adenine medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43585]

Culture medium

Yeast peptone dextrose adenine medium

[Ref.: #43585]

Culture medium growth

[Ref.: #24374]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #24374]

Culture medium growth

[Ref.: #24374]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24374]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #24374]			growth	28 °C
[Ref.: #43585]			growth	39 °C

[Ref.: #24374]	Temperature range	mesophilic
[Ref.: #43585]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %97
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.796

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43585]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #43585]	casein	-	hydrolysis
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #43585]	D-arabinose ChEBI	+	builds acid from
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #43585]	gentiobiose ChEBI	-	builds acid from
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #43585]	mannitol ChEBI	+	builds acid from
[Ref.: #43585]	melibiose ChEBI	+	builds acid from
[Ref.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #43585]	myo-inositol ChEBI	+	builds acid from
[Ref.: #68368]	myo-inositol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #43585]	raffinose ChEBI	+	builds acid from
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	+	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68368]		hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]		indole ChEBI	yes	* from API 20E

	Physiological tests	Metabolite	Indole test
[Ref.: #68368]		indole ChEBI	+	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #24374]	17815	+	-	-	-	+	-	-	-	+	-	-	+	+	+	-	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #24374]	16838	+	-	-	-	+	-	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #24374]	Sample type/isolated from	branches of a pear tree (Pyrus pyrifolia cv. 'Cuiguan') displaying symptoms of bleeding canker
[Ref.: #24374]	Host species	Pyrus pyrifolia
[Ref.: #24374]	Country	China
[Ref.: #24374]	Country ISO 3 Code	CHN
[Ref.: #24374]	Continent	Asia
[Ref.: #24374]	Geographic location	30.4300°/120.3000°

[Ref.: #43585]	Sample type/isolated from	Branches of the pear tree Pyrus pyrifolia cv. 'Cuiguan' with symptoms of bleeding canker
[Ref.: #43585]	Geographic location (country and/or sea, region)	China
[Ref.: #43585]	Country	China
[Ref.: #43585]	Country ISO 3 Code	CHN
[Ref.: #43585]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host Body Product	#Plant	#Plant sap (Flux)
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Stem (Branch)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT992690 (>99% sequence identity) for Dickeya from Microbeatlas

Aquatic Samples	160
Soil Samples	36
Animal Samples	416
Plant Samples	68
Total Samples	680

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

[Ref.: #24374]	Pathogenicity (plant)	yes
[Ref.: #24374]	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.: #24374]	Dickeya fangzhongdai strain JS5 16S ribosomal RNA gene, partial sequence	KT992690	1426	ENA	1778540 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dickeya fangzhongdai DSM 101947	GCA_002812485	complete	GenBank	1778540 tax ID	*
[Ref.: #66792]	Dickeya fangzhongdai CGMCC 1.15464	GCA_014642955	scaffold	GenBank	1778540 tax ID	*
[Ref.: #66792]	Dickeya fangzhongdai strain CGMCC 1.15464	1778540.45	wgs	PATRIC	1778540 tax ID	*
[Ref.: #66792]	Dickeya fangzhongdai strain DSM 101947	1778540.3	plasmid	PATRIC	1778540 tax ID	*
[Ref.: #66792]	Dickeya fangzhongdai DSM 101947	2775506966	complete	JGI IMG/M	1778540 tax ID	*

[Ref.: #24374]

GC-content

56.76 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 fangzhongdai DSM 101947 NCBI: GCA_002812485.1
[Ref.: #69481]	spore-forming	no	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Dickeya fangzhongdai DSM 101947 NCBI: GCA_002812485.1
[Ref.: #69480]	flagellated	yes	53.362	no
[Ref.: #69480]	gram-positive	no	98.543	yes
[Ref.: #69480]	anaerobic	no	97.258	no
[Ref.: #69480]	halophile	no	94.063	no
[Ref.: #69480]	spore-forming	no	93.234	no
[Ref.: #69480]	glucose-util	yes	95.044	no
[Ref.: #69480]	aerobic	no	68.098	no
[Ref.: #69480]	thermophile	no	99.302	no
[Ref.: #69480]	motile	yes	91.165	yes
[Ref.: #69480]	glucose-ferment	yes	89.735	yes

Availability in culture collections External links

[Ref.: #24374]

Culture collection no.

DSM 101947, CGMCC 1.15464

[Ref.: #90902]

SI-ID 398073

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dickeyafangzhongdai sp. nov., a plant-pathogenic bacterium isolated from pear trees (Pyrus pyrifolia).	Tian Y, Zhao Y, Yuan X, Yi J, Fan J, Xu Z, Hu B, De Boer SH, Li X	Int J Syst Evol Microbiol	10.1099/ijsem.0.001060	2016	*
Phylogeny	Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia.	Oulghazi S, Pedron J, Cigna J, Lau YY, Moumni M, Van Gijsegem F, Chan KG, Faure D	Int J Syst Evol Microbiol	10.1099/ijsem.0.003497	2019	*
Genetics	Complete Genome Sequence of a Dickeya fangzhongdai Type Strain Causing Bleeding Canker of Pear Tree Trunks.	Zhao Y, Tian Y, Li X, Hu B	Genome Announc	10.1128/genomeA.00177-18	2018	*
	Occurrence of Dickeya fangzhongdai Causing Soft Rot of Banxia (Pinellia ternata) in China.	Wang F, Tang T, Mao T, Guo J, Guo X, Duan Y, You J	Plant Dis	10.1094/PDIS-01-21-0030-PDN	2021	*

References

#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 )

#24374

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101947

#43585

Yanli Tian, Yuqiang Zhao, Xiaoli Yuan, Jianping Yi, Jiaqin Fan, Zhigang Xu, Baishi Hu, Solke H. De Boer, Xiang Li: Dickeya fangzhongdai sp. nov., a plant-pathogenic bacterium isolated from pear trees (Pyrus pyrifolia). IJSEM 66: 2831 - 2835 2016 ( DOI 10.1099/ijsem.0.001060 , PubMed 27045848 )

#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 .

#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 )

#90902

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-ID398073.1 )

* These data were automatically processed and therefore are not curated

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Dickeya fangzhongdai DSM 101947

Dickeya fangzhongdai DSM 101947

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