Xanthomonas arboricola (DSM 18808, ATCC 49083, CFBP 2528)

Name: Xanthomonas arboricola (DSM 18808, ATCC 49083, CFBP 2528)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17602

Type strain

Strain Designation S3

Culture col. no. DSM 18808 ATCC 49083 CFBP 2528 ICMP 35 LMG 747 2 more

NCBI tax ID(s) 56448

Special Collections DSMZ

History DSMZ <- CFBP<- ? <- D. W. Dye

Links

Xanthomonas arboricola S3 is a plant pathogen that was isolated from Juglandis regia.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 5635

LMG 747,ICMP 35,NCPPB 411,PDDCC 35,ATCC 49083,CFBP 2528,NCAIM B.01395,DSM 18808

@ref 20215

Last LPSN update 2026-05-29 08:29:03

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas arboricola

Full scientific name Xanthomonas arboricola Vauterin et al. 1995

BacDive ID	Other strains from **Xanthomonas arboricola** (3)	Type strain
17601	X. arboricola MPS 1, DSM 1049, ATCC 29078, ICPB XJ 103
17603	X. arboricola ZZ26, DSM 50853, ATCC 19046, ICPB XC 144
17604	X. arboricola 5262, DSM 50854, ATCC 19313, ICPB XC 12, ...

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.494
125439	negative	96.334

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7710	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7710	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.586

Spore formation

@ref	Spore formation	Confidence
125439		99.17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
7710	Juglandis regia	Juglans regia	New Zealand	NZL	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence Y10757 (>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
7710		1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM101347v1 assembly for Xanthomonas arboricola pv. juglandis CFBP 2528	scaffold	GCA_001013475	195709.15	2627854245	195709	75.14

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Xanthomonas arboricola pv. juglandis gene for 16S rRNA, partial sequence, strain: NCPPB 411	AB558555	1450	195709
20218	Xanthomonas arboricola strain ICMP35 16S-23S ribosomal RNA intergenic spacer, complete sequence	AF209752	507	195709
7710	X.arboricola 16S rRNA gene	Y10757	1502	195709

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM101347v1 assembly for Xanthomonas arboricola pv. juglandis CFBP 2528
NCBI: GCA_001013475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.59	no
125439	motility	BacteriaNetⓘ	yes	78.85	no
125439	gram_stain	BacteriaNetⓘ	negative	96.33	no
125439	spore_formation	BacteriaNetⓘ	no	99.17	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xanthomonas arboricola pv. juglandis CFBP 2528
NCBI: GCA_001013475.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	no
125438	anaerobic	anaerobicⓘ	no	97.24	no
125438	aerobic	aerobicⓘ	yes	85.02	no
125438	spore-forming	spore-formingⓘ	no	87.92	no
125438	thermophilic	thermophileⓘ	no	99.48	yes
125438	flagellated	motile2+ⓘ	yes	70.15	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System.	Essakhi S, Cesbron S, Fischer-Le Saux M, Bonneau S, Jacques MA, Manceau C.	Appl Environ Microbiol	10.1128/aem.00835-15	2015
	Type three effector gene distribution and sequence analysis provide new insights into the pathogenicity of plant-pathogenic Xanthomonas arboricola.	Hajri A, Pothier JF, Fischer-Le Saux M, Bonneau S, Poussier S, Boureau T, Duffy B, Manceau C.	Appl Environ Microbiol	10.1128/aem.06119-11	2012
	High-Quality Draft Genome Sequence of Xanthomonas arboricola pv. juglandis CPBF 1521, Isolated from Leaves of a Symptomatic Walnut Tree in Portugal without a Past of Phytosanitary Treatment.	Fernandes C, Blom J, Pothier JF, Tavares F.	Microbiol Resour Announc	10.1128/mra.00887-18	2018
	High-Quality Draft Genome Sequence of Xanthomonas sp. Strain CPBF 424, a Walnut-Pathogenic Strain with Atypical Features.	Fernandes C, Blom J, Pothier JF, Tavares F.	Microbiol Resour Announc	10.1128/mra.00921-18	2018
Phylogeny	Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas.	Pena MM, Bhandari R, Bowers RM, Weis K, Newberry E, Wagner N, Pupko T, Jones JB, Woyke T, Vinatzer BA, Jacques MA, Potnis N.	Genome Biol Evol	10.1093/gbe/evae074	2024
	Comparative Analysis of Novel Lytic Phages for Biological Control of Phytopathogenic Xanthomonas spp.	Domingo-Calap ML, Bernabeu-Gimeno M, M Aure C, Marco-Noales E, Domingo-Calap P.	Microbiol Spectr	10.1128/spectrum.02960-22	2022
	Xanthomonas arboricola pv. pruni, causal agent of bacterial spot of stone fruits and almond: its genomic and phenotypic characteristics in the X. arboricola species context.	Garita-Cambronero J, Palacio-Bielsa A, Cubero J.	Mol Plant Pathol	10.1111/mpp.12679	2018
Genetics	Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens.	Merda D, Briand M, Bosis E, Rousseau C, Portier P, Barret M, Jacques MA, Fischer-Le Saux M.	Mol Ecol	10.1111/mec.14343	2017
Genetics	Pan-Genomic Analysis Permits Differentiation of Virulent and Non-virulent Strains of Xanthomonas arboricola That Cohabit Prunus spp. and Elucidate Bacterial Virulence Factors.	Garita-Cambronero J, Palacio-Bielsa A, Lopez MM, Cubero J.	Front Microbiol	10.3389/fmicb.2017.00573	2017
Enzymology	Aggressive Emerging Pathovars of Xanthomonas arboricola Represent Widespread Epidemic Clones Distinct from Poorly Pathogenic Strains, as Revealed by Multilocus Sequence Typing.	Fischer-Le Saux M, Bonneau S, Essakhi S, Manceau C, Jacques MA.	Appl Environ Microbiol	10.1128/aem.00050-15	2015
	Comparative Genomic and Phenotypic Characterization of Pathogenic and Non-Pathogenic Strains of Xanthomonas arboricola Reveals Insights into the Infection Process of Bacterial Spot Disease of Stone Fruits.	Garita-Cambronero J, Palacio-Bielsa A, Lopez MM, Cubero J.	PLoS One	10.1371/journal.pone.0161977	2016
	Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans.	Clavijo-Coppens F, Ginet N, Cesbron S, Briand M, Jacques MA, Ansaldi M.	Viruses	10.3390/v13050725	2021
	Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas.	An SQ, Potnis N, Dow M, Vorholter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL.	FEMS Microbiol Rev	10.1093/femsre/fuz024	2020
	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
	Stenotrophomonas rhizophila Ep2.2 inhibits growth of Botrytis cinerea through the emission of volatile organic compounds, restricts leaf infection and primes defense genes.	Raio A, Brilli F, Neri L, Baraldi R, Orlando F, Pugliesi C, Chen X, Baccelli I.	Front Plant Sci	10.3389/fpls.2023.1235669	2023
	Draft Genome Sequence of Xanthomonas arboricola pv. pruni Strain Xap33, Causal Agent of Bacterial Spot Disease on Almond.	Garita-Cambronero J, Sena-Velez M, Palacio-Bielsa A, Cubero J.	Genome Announc	10.1128/genomea.00440-14	2014
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
	Characterization of Xanthomonas arboricola pv. juglandis Bacteriophages against Bacterial Walnut Blight and Field Evaluation.	Retamales J, Nunez P, Alvarado R, Campan EDM, Otto T, Segovia C, Vasquez I, Santander J.	Viruses	10.3390/v14071380	2022
Enzymology	Combination of chromogenic differential medium and estA-specific PCR for isolation and detection of phytopathogenic Xanthomonas spp.	Lee YA, Sung AN, Liu TF, Lee YS.	Appl Environ Microbiol	10.1128/aem.01653-09	2009
Genetics	Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation.	Cesbron S, Briand M, Essakhi S, Gironde S, Boureau T, Manceau C, Fischer-Le Saux M, Jacques MA	Front Plant Sci	10.3389/fpls.2015.01126	2015

References

#7710	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18808
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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 arboricola (DSM 18808, ATCC 49083, CFBP 2528)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001013475

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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