Dickeya fangzhongdai JS5 is a Gram-negative, motile, rod-shaped plant pathogen that was isolated from branches of a pear tree displaying symptoms of bleeding canker.
Gram-negative motile rod-shaped plant pathogen genome sequence 16S sequence Bacteria| @ref 20215 |
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Last LPSN update
2026-02-09 11:31:45 |
| Domain Bacteria |
| Phylum Pseudomonadota |
| Class Gammaproteobacteria |
| Order Enterobacterales |
| Family Pectobacteriaceae |
| Genus Dickeya |
| Species Dickeya fangzhongdai |
| Full scientific name Dickeya fangzhongdai Tian et al. 2016 |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 43585 | Yeast peptone dextrose adenine medium | ||||
| 24374 | NUTRIENT AGAR (DSMZ Medium 1) | Medium recipe at MediaDive  | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
| @ref | Oxygen tolerance | Confidence | |
|---|---|---|---|
| 125439 | aerobe | 93.9 |
| @ref | Chebi-ID | Metabolite | Utilization activity | Kind of utilization tested | |
|---|---|---|---|---|---|
| 43585 | 58143 ChEBI | 5-dehydro-D-gluconate | - | builds acid from | |
| 68368 | 27613 ChEBI | amygdalin | + | fermentation | from API 20E |
| 68368 | 29016 ChEBI | arginine | - | hydrolysis | from API 20E |
| 43585 | casein | - | hydrolysis | ||
| 68368 | 16947 ChEBI | citrate | + | assimilation | from API 20E |
| 43585 | 17108 ChEBI | D-arabinose | + | builds acid from | |
| 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 |
| 43585 | 28066 ChEBI | gentiobiose | - | builds acid from | |
| 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 |
| 43585 | 29864 ChEBI | mannitol | + | builds acid from | |
| 43585 | 28053 ChEBI | melibiose | + | builds acid from | |
| 68368 | 28053 ChEBI | melibiose | + | fermentation | from API 20E |
| 43585 | 17268 ChEBI | myo-inositol | + | builds acid from | |
| 68368 | 17268 ChEBI | myo-inositol | + | fermentation | from API 20E |
| 68368 | 18257 ChEBI | ornithine | - | degradation | from API 20E |
| 43585 | 16634 ChEBI | raffinose | + | builds acid from | |
| 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 |
| @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 |
| @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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 24374 | + | - | - | - | + | - | - | - | + | - | - | + | + | + | - | + | + | + | + | + | - | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | |
| 24374 | + | - | - | - | + | - | - | - | + | + | - | + | + | + | - | + | + | + | + | + | - | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. | not determinedn.d. |
| Cat1 | Cat2 | Cat3 | |
|---|---|---|---|
| #Host Body Product | #Plant | #Plant sap (Flux) | |
| #Host | #Plants | #Tree | |
| #Host Body-Site | #Plant | #Stem (Branch) |
| @ref | Sample type | Host species | Country | Country ISO 3 Code | Continent | Latitude | Longitude | Geographic location | |
|---|---|---|---|---|---|---|---|---|---|
| 24374 | branches of a pear tree (Pyrus pyrifolia cv. 'Cuiguan') displaying symptoms of bleeding canker | Pyrus pyrifolia | China | CHN | Asia | 30.43 | 120.3 | ||
| 43585 | Branches of the pear tree Pyrus pyrifolia cv. 'Cuiguan' with symptoms of bleeding canker | China | CHN | Asia | China |
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 |
| @ref | Description | Assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | Score | |
|---|---|---|---|---|---|---|---|---|
| 66792 | ASM281248v1 assembly for Dickeya fangzhongdai DSM 101947 | complete | GCA_002812485   | 1778540.117  | 2775506966  | 1778540 | 98.09 | |
| 66792 | ASM1464295v1 assembly for Dickeya fangzhongdai CGMCC 1.15464 | scaffold | GCA_014642955 | 1778540.45 | 8113172152 | 1778540 | 67.07 | |
| 24374 | GC-content (mol%)56.76 |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Method to Study Induced Systemic Resistance Against Bacterial Pathogens in Orchids Primed by Root Colonization of Mycorrhizal Fungi. | Pujasatria GC, Miura C, Kaminaka H. | Methods Mol Biol | 10.1007/978-1-0716-4981-7_15 | 2026 | | |
| Genetics | First detection of Dickeya fangzhongdai in Italy: double-edged role from virulent on vegetables to potent VOC-mediated anti-Xylella fastidiosa activity. | Sabri M, El Handi K, Mektoubi K, Trani A, Cara O, Elbeaino T. | Front Microbiol | 10.3389/fmicb.2025.1655235 | 2025 | |
| Identification and Comparative Analysis of Pathogenic Characteristics of Two Bacterial Diseases in Bananas Caused by Dickeya spp. | Yang D, Du CJ, Jiang S, Qi Y, Zhang J, Pan LF, Fu G. | Plant Dis | 10.1094/pdis-01-25-0190-re | 2025 | | |
| Genetics | First detection of Dickeya fangzhongdai in Italy: double-edged role from virulent on vegetables to potent VOC-mediated anti-Xylella fastidiosa activity | Sabri M, El Handi K, Mektoubi K, Trani A, Cara O, Elbeaino T. | Front Microbiol | 2025 | | |
| Soft rot disease of Belamcanda chinensis caused by Dickeya fangzhongdai in China | Yang Y, Chen Q, Zhou J, Xu J, Li J, Zhao T, Luo M, Huang B, Miao Y, Liu D. | Physiol Mol Plant Pathol | 2024 | | ||
| Colonization by orchid mycorrhizal fungi primes induced systemic resistance against necrotrophic pathogen. | Pujasatria GC, Miura C, Yamaguchi K, Shigenobu S, Kaminaka H. | Front Plant Sci | 10.3389/fpls.2024.1447050 | 2024 | | |
| Dickeya fangzhongdai was prevalent and caused taro soft rot when coexisting with the Pectobacterium complex, with a preference for Araceae plants. | Zhang J, Sun D, Shen H, Pu X, Liu P, Lin B, Yang Q. | Front Microbiol | 10.3389/fmicb.2024.1431047 | 2024 | | |
| First Report of Dickeya fangzhongdai Causing Soft Rot in Orchid in Canada | Zhou A, Nie J, Tian Y, Chuan J, Hu B, Zou J, Li X. | Plant Dis | 2022 | | ||
| First Report of Bacterial Soft Rot Disease on Taro Caused by Dickeya fangzhongdai in China | Huang S, Chen Z, Hu M, Xue Y, Liao L, Zhang L. | Plant Dis | 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 | | |
| 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 | 2021 | | ||
| Characterization of Dickeya fangzhongdai causing bacterial soft rot disease on Dendrobium nobile in India | Balamurugan A, Kumar A, Sakthivel K, Ashajyothi M, Sahu KP, Karthikeyan M. | Eur J Plant Pathol | 10.1007/s10658-020-02094-7 | 2020 | | |
| Enzymology | Polyamine signaling communications play a key role in regulating the pathogenicity of Dickeya fangzhongdai. | Xie C, Gu W, Chen Z, Liang Z, Huang S, Zhang L-H, Chen S. | Microbiol Spectr | 10.1128/spectrum.01965-23 | 2023 | |
| Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region. | DeLude A, Wells R, Boomla S, Chuang SC, Urena F, Shipman A, Rubas N, Kuehu DL, Bickerton B, Peterson T, Dobhal S, Arizala D, Klair D, Ochoa-Corona F, Ali ME, Odani J, Bingham JP, Jenkins DM, Fletcher J, Stack JP, Alvarez AM, Arif M. | Sci Rep | 10.1038/s41598-022-22023-4 | 2022 | | |
| A Herpetosiphon llansteffanensis Strain from Forest Soil Exhibits Biocontrol Activity Against Pear Fire Blight. | Lv W, Wang R, Ji W, Fu B, Luo M, Han J. | Plants (Basel) | 10.3390/plants14111564 | 2025 | | |
| First Report of Dickeya fangzhongdai Causing Soft Rot of Onion in New York State | Ma X, Bonasera JM, Asselin JAE, Beer SV, Swingle B. | Plant Dis | 10.1094/pdis-09-19-1940-pdn | 2020 | | |
| First Report of Dickeya fangzhongdai Causing Soft Rot of Phalaenopsis aphrodite in China | Shen Y, Lv WG, Du YH, Zhang YX, Li HP. | Plant Dis | 10.1094/pdis-01-19-0234-pdn | 2019 | | |
| Highly Targeted Detection of Priority Phytopathogen Pectobacterium brasiliense: From Obtaining Polyclonal Antibodies to Development and Approbation of Enzyme-Linked Immunoassay and Lateral Flow Immunoassay. | Safenkova IV, Galushka PA, Varitsev YA, Kamionskaya MV, Drenova NV, Vasilyeva AA, Zherdev AV, Uskov AI, Dzantiev BB. | Microorganisms | 10.3390/microorganisms12122436 | 2024 | | |
| Diversity within the novel Dickeya fangzhongdai sp., isolated from infected orchids, water and pears | Alic S, Van Gijsegem F, Pedron J, Ravnikar M, Dreo T. | Plant Pathol | 10.1111/ppa.12866 | 2018 | | |
| Dickeya Manipulates Multiple Quorum Sensing Systems to Control Virulence and Collective Behaviors. | Liu F, Hu M, Zhang Z, Xue Y, Chen S, Hu A, Zhang LH, Zhou J. | Front Plant Sci | 10.3389/fpls.2022.838125 | 2022 | | |
| The C3H gene PtZFP2-like in Pinellia ternata acts as a positive regulator of the resistance to soft rot caused by Pectobacterium carotovorum. | Luo M, Li X, Zhang J, Miao Y, Liu D. | Physiol Plant | 10.1111/ppl.70121 | 2025 | | |
| A combined pseudouridine biomanufacturing platform enabled by a streamlined designer pathway. | Yu L, Chen R, Zhang C, Wang Z, Wang Z, Zeng X, Liang H, He Y, She Y, Wang Y, Gong R, Song X, Deng Z, Fei Q, Chen W. | Nat Commun | 10.1038/s41467-025-63906-0 | 2025 | | |
| Phylogeny | Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates. | Alic S, Pedron J, Dreo T, Van Gijsegem F. | BMC Genomics | 10.1186/s12864-018-5332-3 | 2019 | |
| Comparative transcriptome analysis reveals defense responses against soft rot induced by Pectobacterium aroidearum and Pectobacterium carotovorum in Pinellia ternata. | Luo M, Wang M, Xu J, Qu K, Miao Y, Liu D. | BMC Genomics | 10.1186/s12864-024-10746-9 | 2024 | | |
| From predator to protector: Myxococcus fulvus WCH05 emerges as a potent biocontrol agent for fire blight. | Han J, Dong Z, Ji W, Lv W, Luo M, Fu B. | Front Microbiol | 10.3389/fmicb.2024.1378288 | 2024 | | |
| Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. | Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Cardenas Rodriguez J, Mondi R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin EV, Patel DJ, Nobrega FL. | Cell | 10.1016/j.cell.2025.07.002 | 2025 | | |
| yggS Encoding Pyridoxal 5'-Phosphate Binding Protein Is Required for Acidovorax citrulli Virulence. | Wang Y, Zhao Y, Xia L, Chen L, Liao Y, Chen B, Liu Y, Gong W, Tian Y, Hu B. | Front Microbiol | 10.3389/fmicb.2021.783862 | 2021 | | |
| Genetics | Genomic analysis of the Phalaenopsis pathogen Dickeya sp. PA1, representing the emerging species Dickeya fangzhongdai. | Zhang J, Hu J, Shen H, Zhang Y, Sun D, Pu X, Yang Q, Fan Q, Lin B. | BMC Genomics | 10.1186/s12864-018-5154-3 | 2018 | |
| Natural Infections of Potato Plants Grown from Minitubers with Blackleg-Causing Soft Rot Pectobacteriaceae. | van der Wolf J, Krijger M, Mendes O, Kurm V, Gros J. | Microorganisms | 10.3390/microorganisms10122504 | 2022 | | |
| Conventional tobacco products harbor unique and heterogenous microbiomes. | Chattopadhyay S, Ramachandran P, Malayil L, Mongodin EF, Sapkota AR. | Environ Res | 10.1016/j.envres.2022.115205 | 2023 | | |
| Metabolism | Genomic diversity and organization of complex polysaccharide biosynthesis clusters in the genus Dickeya. | Ranjan M, Khokhani D, Nayaka S, Srivastava S, Keyser ZP, Ranjan A. | PLoS One | 10.1371/journal.pone.0245727 | 2021 | |
| Metabolism | Genetic and Biochemical Diversity for N-acylhomoserine Lactone Biosynthesis in the Plant Pathogen Pectobacterium carotovorum subsp. carotovorum. | Morohoshi T, Ogasawara Y, Xie X, Hamamoto H, Someya N. | Microbes Environ | 10.1264/jsme2.me19105 | 2019 | |
| Pathogenicity | Defence Warriors: Exploring the crosstalk between polyamines and oxidative stress during microbial pathogenesis. | Nair AV, Singh A, Chakravortty D. | Redox Biol | 10.1016/j.redox.2025.103648 | 2025 | |
| 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 | | |
| Genetics | Genomic Characterization, Formulation and Efficacy in Planta of a Siphoviridae and Podoviridae Protection Cocktail against the Bacterial Plant Pathogens Pectobacterium spp. | Zaczek-Moczydlowska MA, Young GK, Trudgett J, Fleming CC, Campbell K, O'Hanlon R. | Viruses | 10.3390/v12020150 | 2020 | |
| Insight into biodiversity of the recently rearranged genus Dickeya. | Hugouvieux-Cotte-Pattat N, Pedron J, Van Gijsegem F. | Front Plant Sci | 10.3389/fpls.2023.1168480 | 2023 | | |
| Genetics | Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani. | Motyka-Pomagruk A, Zoledowska S, Misztak AE, Sledz W, Mengoni A, Lojkowska E. | BMC Genomics | 10.1186/s12864-020-06863-w | 2020 | |
| Metabolism | Lon Protease Is Important for Growth Under Stressful Conditions and Pathogenicity of the Phytopathogen, Bacterium Dickeya solani. | Figaj D, Czaplewska P, Przepiora T, Ambroziak P, Potrykus M, Skorko-Glonek J. | Int J Mol Sci | 10.3390/ijms21103687 | 2020 | |
| 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 | |
| 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 | | |
| 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 | |
| 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 | |
How to citeIf you want to cite this particular strain cite the following doi:
https://doi.org/10.13145/bacdive132585.20251217.10
When using BacDive for research please cite the following paper
BacDive in 2025: the core database for prokaryotic strain data
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