Xanthomonas oryzae (ATCC 35933, Rao X08, NCCPPB 3002)

Name: Xanthomonas oryzae (ATCC 35933, Rao X08, NCCPPB 3002)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 168649

Type strain

Strain Designation Rao X08, NCCPPB 3002, PDDCC 3125, Dye YK9

Culture col. no. ATCC 35933 Rao X08 NCCPPB 3002 CFBP 2532 ICMP 3125 3 more

NCBI tax ID(s) 1313303 347

Links

Xanthomonas oryzae Rao X08 is a plant pathogen of the family Lysobacteraceae.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 6222

LMG 5047,ICMP 3125,LMG 5164,NCPPB 3002,PDDCC 3125,ATCC 35933,CIP 105507,KCTC 2676,CFBP 2532,NCAIM B.01410

@ref 20215

Last LPSN update 2026-02-09 11:40:51

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas oryzae

Full scientific name Xanthomonas oryzae (ex Ishiyama 1922) Swings et al. 1990

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	95.3
125438	negative	98.25

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97

Spore formation

@ref	Spore formation	Confidence
125438		90.38
125439		94.2

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence X95921 (>99% sequence identity) for Xanthomonas from Microbeatlas

Aquatic Samples	6826
Soil Samples	10026
Animal Samples	28252
Plant Samples	7048
Total Samples	52152

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
20215		1	Risk group

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM413637v1 assembly for Xanthomonas oryzae pv. oryzae ICMP3125	complete	GCA_004136375	64187.548	2922892330	64187	97.5
66792	ASM48244v1 assembly for Xanthomonas oryzae ATCC 35933	scaffold	GCA_000482445	1313303.3	2528768237	1313303	18.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20215	X.oryzae 16S rRNA gene	X95921	1502		347

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xanthomonas oryzae pv. oryzae strain ICMP3125
PATRIC: 64187.548

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.20	no
125439	motility	BacteriaNetⓘ	yes	77.70	no
125439	gram_stain	BacteriaNetⓘ	negative	95.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xanthomonas oryzae pv. oryzae ICMP3125
NCBI: GCA_004136375.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.25	no
125438	anaerobic	anaerobicⓘ	no	97.03	no
125438	aerobic	aerobicⓘ	yes	82.18	no
125438	spore-forming	spore-formingⓘ	no	90.38	no
125438	thermophilic	thermophileⓘ	no	97.47	no
125438	flagellated	motile2+ⓘ	yes	67.08	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Detection of Francisella tularensis within infected mouse tissues by using a hand-held PCR thermocycler.	Emanuel PA, Bell R, Dang JL, McClanahan R, David JC, Burgess RJ, Thompson J, Collins L, Hadfield T.	J Clin Microbiol	10.1128/jcm.41.2.689-693.2003	2003
	Novel Tetraplex Quantitative PCR Assays for Simultaneous Detection and Identification of Xylella fastidiosa Subspecies in Plant Tissues.	Dupas E, Briand M, Jacques MA, Cesbron S.	Front Plant Sci	10.3389/fpls.2019.01732	2019
	Evaluation of the Biolog Substrate Utilization System To Identify and Assess Metabolic Variation among Strains of Xanthomonas campestris pv. Citri.	Verniere C, Pruvost O, Civerolo EL, Gambin O, Jacquemoud-Collet JP, Luisetti J.	Appl Environ Microbiol	10.1128/aem.59.1.243-249.1993	1993
	Epigenetic features improve TALE target prediction.	Erkes A, Mucke S, Reschke M, Boch J, Grau J.	BMC Genomics	10.1186/s12864-021-08210-z	2021
Phylogeny	Identification of Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis.	Albuquerque P, Caridade CM, Marcal AR, Cruz J, Cruz L, Santos CL, Mendes MV, Tavares F.	Appl Environ Microbiol	10.1128/aem.05189-11	2011
	Transcriptional Reprogramming of Rice Cells by Xanthomonas oryzae TALEs.	Mucke S, Reschke M, Erkes A, Schwietzer CA, Becker S, Streubel J, Morgan RD, Wilson GG, Grau J, Boch J	Front Plant Sci	10.3389/fpls.2019.00162	2019
	Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material.	Liu X, Liu X, Deng Z, He X, Jiang Y.	Antonie Van Leeuwenhoek	10.1007/s10482-023-01904-2	2024

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 )
#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 .
#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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Xanthomonas oryzae (ATCC 35933, Rao X08, NCCPPB 3002)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004136375

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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