Dickeya oryzae (ACCC 61554, JCM 33020)

Name: Dickeya oryzae (ACCC 61554, JCM 33020)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164439

Type strain

Culture col. no. ACCC 61554 JCM 33020

NCBI tax ID(s) 1240404

Special Collections JCM

Links

Dickeya oryzae JCM 33020 is a mesophilic prokaryote that was isolated from Rice roots at Red Soil Eco-environment of the Ministry of Agriculture in Qiyang County.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 133405

JCM 33020

@ref 20215

Last LPSN update 2025-12-16 10:09:27

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Pectobacteriaceae

Genus Dickeya

Species Dickeya oryzae

Full scientific name Dickeya oryzae Wang et al. 2020

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	93.5
125438	negative	99

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	91.6

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
67770	Rice roots at Red Soil Eco-environment of the Ministry of Agriculture in Qiyang County	Hunan Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence MK791744 (>99% sequence identity) for Dickeya from Microbeatlas

Aquatic Samples	90
Soil Samples	12
Animal Samples	292
Plant Samples	251
Total Samples	645

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM937223v1 assembly for Dickeya oryzae ZYY5	scaffold	GCA_009372235	1240404.3	2898845556	1240404	68.62
124043	ASM5178378v1 assembly for Dickeya oryzae JCM 33020	contig	GCA_051783785			1240404	67.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Dickeya oryzae strain ZYY5 16S ribosomal RNA gene, partial sequence	MK791744	1538		1240404

GC content

@ref	GC-content (mol%)	Method
67770	53.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dickeya oryzae ZYY5
NCBI: GCA_009372235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	74.50	no
125439	motility	BacteriaNetⓘ	yes	85.70	no
125439	gram_stain	BacteriaNetⓘ	negative	93.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dickeya oryzae ZYY5
NCBI: GCA_009372235.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	95.83	no
125438	aerobic	aerobicⓘ	no	72.00	no
125438	spore-forming	spore-formingⓘ	no	88.49	no
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	80.38	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dickeya oryzae sp. nov., isolated from the roots of rice.	Wang X, He SW, Guo HB, Han JG, Thin KK, Gao JS, Wang Y, Zhang XX	Int J Syst Evol Microbiol	10.1099/ijsem.0.004265	2020

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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

Rate our new design

Content

About us

Dickeya oryzae (ACCC 61554, JCM 33020)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_009372235

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media