Xanthomonas axonopodis (DSM 3585, ATCC 19312, ICPB XA 103)

Name: Xanthomonas axonopodis (DSM 3585, ATCC 19312, ICPB XA 103)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17593

Type strain

Culture col. no. DSM 3585 ATCC 19312 ICPB XA 103 LMG 982 NCPPB 457 1 more

NCBI tax ID(s) 53413

Special Collections DSMZ

History <- ATCC <- NCPPB <- ICPB

Links

Xanthomonas axonopodis DSM 3585 is a plant pathogen that was isolated from Axonoperis scoparius.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 14039

LMG 982,ATCC 19312,CECT 548,DSM 3585,ICMP 50,LMG 538,NCPPB 457,PDDCC 50,CBMAI 201,KACC 10935,CFBP 4924

@ref 20215

Last LPSN update 2026-02-09 11:22:16

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas axonopodis

Full scientific name Xanthomonas axonopodis Starr and Garces 1950 (Approved Lists 1980)

BacDive ID	Other strains from **Xanthomonas axonopodis** (1)	Type strain
17594	X. axonopodis DSM 50850, DSM 60127, LMG 7178

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.75
125439	negative	97.9

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1410	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

Culture temp

@ref	Growth	Type	Temperature (°C)
1410	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.8

Spore formation

@ref	Spore formation	Confidence
125439		96.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Host species
1410	Axonoperis scoparius	Axonoperis scoparius

Taxonmaps

69479

Global distribution of 16S sequence X95919 (>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
1410		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	XAXN-20feb14 assembly for Xanthomonas axonopodis DSM 3585	contig	GCA_001304695	53413.25	2639762869	53413	8.55
66792	Xaa_LMG982 assembly for Xanthomonas axonopodis pv. axonopodis LMG 982	contig	GCA_001401595	316581.4	2651869742	316581

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Xanthomonas axonopodis strain LMG538 16S-23S ribosomal RNA intergenic spacer, complete sequence	AF209753	519		53413
20218	X.axonopodis 16S rRNA gene	X95919	1502		53413

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xanthomonas axonopodis DSM 3585
NCBI: GCA_001304695

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.30	no
125439	motility	BacteriaNetⓘ	yes	77.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.90	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 axonopodis pv. axonopodis strain LMG 982
PATRIC: 316581.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.75	no
125438	anaerobic	anaerobicⓘ	no	97.61	no
125438	spore-forming	spore-formingⓘ	no	89.49	no
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	aerobic	aerobicⓘ	yes	84.61	no
125438	flagellated	motile2+ⓘ	yes	67.33	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	High-Quality Draft Genome Sequences of Two Xanthomonas Pathotype Strains Infecting Aroid Plants.	Robene I, Bolot S, Pruvost O, Arlat M, Noel LD, Carrere S, Jacques MA, Koebnik R, Gagnevin L.	Genome Announc	10.1128/genomea.00902-16	2016
	Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas.	Liyanapathiranage P, Wagner N, Avram O, Pupko T, Potnis N.	Front Microbiol	10.3389/fmicb.2022.840308	2022
Pathogenicity	A "repertoire for repertoire" hypothesis: repertoires of type three effectors are candidate determinants of host specificity in Xanthomonas.	Hajri A, Brin C, Hunault G, Lardeux F, Lemaire C, Manceau C, Boureau T, Poussier S.	PLoS One	10.1371/journal.pone.0006632	2009
	Characterization of Xanthomonas campestris Pathovars by rRNA Gene Restriction Patterns.	Berthier Y, Verdier V, Guesdon JL, Chevrier D, Denis JB, Decoux G, Lemattre M.	Appl Environ Microbiol	10.1128/aem.59.3.851-859.1993	1993
	Isolation of an insertion sequence (IS1051) from Xanthomonas campestris pv. dieffenbachiae with potential use for strain identification and characterization.	Berthier Y, Thierry D, Lemattre M, Guesdon JL.	Appl Environ Microbiol	10.1128/aem.60.1.377-384.1994	1994
	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

References

#1410	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3585
#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 axonopodis (DSM 3585, ATCC 19312, ICPB XA 103)

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_001304695

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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