Xanthomonas citri (3213, Gabriel 3213, ICPB 10518)

Name: Xanthomonas citri (3213, Gabriel 3213, ICPB 10518)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 170009

Type strain

Strain Designation Gabriel 3213, 3213

Culture col. no. 3213 Gabriel 3213 ICPB 10518 ICMP 15804 LMG 9322 1 more

NCBI tax ID(s) 346

Links

Xanthomonas citri Gabriel 3213 is a plant pathogen of the family Lysobacteraceae.

plant pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 5404

ICMP 17123,ATCC 49118,LMG 9322,ICMP 15804,CFBP 3369

@ref 20215

Last LPSN update 2026-02-09 11:41:09

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas citri

Full scientific name Xanthomonas citri (ex Hasse 1915) Gabriel et al. 1989

Synonyms (2)

Xanthomonas fuscans
"Xanthomonas smithii subsp. citri"

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.5
125439	negative	98.1

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.8

Spore formation

@ref	Spore formation	Confidence
125439		96.4

Isolation, sampling and environmental information

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	NCBI tax ID	Score	IMG accession
66792	ASM201857v1 assembly for Xanthomonas citri pv. citri LMG9322	contig	GCA_002018575	434928.61	611301	36.53
124043	ASM149085v2 assembly for Xanthomonas citri pv. citri	scaffold	GCA_001490855		611301	29.55	2671180461
66792	Xcc_LMG9322 assembly for Xanthomonas citri pv. citri LMG 9322	contig	GCA_001401655	611301.24	611301		2651869745

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20215	Xanthomonas citri subsp. citri 16S ribosomal RNA gene, partial sequence	JX986961	1499		611301

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xanthomonas citri pv. citri LMG 9322
NCBI: GCA_001401655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.40	no
125439	motility	BacteriaNetⓘ	yes	76.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xanthomonas citri subsp. citri strain LMG 9322
PATRIC: 611301.24

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	98.74	no
125438	spore-forming	spore-formingⓘ	no	86.69	no
125438	aerobic	aerobicⓘ	yes	84.68	no
125438	thermophilic	thermophileⓘ	no	97.98	no
125438	flagellated	motile2+ⓘ	yes	68.11	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Clustered Regularly Interspaced Short Palindromic Repeats in Xanthomonas citri-Witnesses to a Global Expansion of a Bacterial Pathogen over Time.	Bellanger N, Dereeper A, Koebnik R.	Microorganisms	10.3390/microorganisms10091715	2022
Phylogeny	Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity.	Bansal K, Midha S, Kumar S, Patil PB.	Appl Environ Microbiol	10.1128/aem.02993-16	2017
Genetics	Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses.	Patane JSL, Martins J, Rangel LT, Belasque J, Digiampietri LA, Facincani AP, Ferreira RM, Jaciani FJ, Zhang Y, Varani AM, Almeida NF, Wang N, Ferro JA, Moreira LM, Setubal JC.	BMC Genomics	10.1186/s12864-019-6007-4	2019
Phylogeny	CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri.	Jeong K, Munoz-Bodnar A, Arias Rojas N, Poulin L, Rodriguez-R LM, Gagnevin L, Verniere C, Pruvost O, Koebnik R.	BMC Genomics	10.1186/s12864-019-6267-z	2019
	Bacterial Secretome Analysis in Hunt for Novel Bacteriocins with Ability to Control Xanthomonas citri subsp. Citri.	Gholami D, Goodarzi T, Aminzadeh S, Alavi SM, Kazemipour N, Farrokhi N.	Iran J Biotechnol	10.15171/ijb.1123	2015
Phylogeny	Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges.	Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O.	BMC Genomics	10.1186/s12864-015-2310-x	2015
	Narrow host range phages associated with citrus canker lesions in Florida and Argentina	Balogh B, Dickstein ER, Jones JB, Canteros BI.	Eur J Plant Pathol	10.1007/s10658-012-0082-6	2013
	First Report of Xanthomonas citri pv. citri-A* Causing Citrus Canker on Lime in Cambodia.	Ngoc LBT, Verniere C, Pruvost O, So T, Johnson GI	Plant Dis	10.1094/PDIS-92-11-1588A	2008

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) .
#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

Xanthomonas citri (3213, Gabriel 3213, ICPB 10518)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002018575

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media