Xanthomonas prunicola (CECT 9404, IVIA 3287.1, CFBP 8353)

Name: Xanthomonas prunicola (CECT 9404, IVIA 3287.1, CFBP 8353)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158738

Type strain

Culture col. no. CECT 9404 IVIA 3287.1 CFBP 8353

NCBI tax ID(s) 2053930

Special Collections Literature strains

Links

Xanthomonas prunicola CECT 9404 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and has a yellow pigmentation.

Gram-negative rod-shaped colony-forming pigmented aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 415095

CECT 9404,CFBP 8353

@ref 20215

Last LPSN update 2026-02-09 11:38:24

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas prunicola

Full scientific name Xanthomonas prunicola López et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
65489	negative	rod-shaped
125438	negative		98.25
125439	negative		97

Colony morphology

@ref	Colony size	Colony shape	Incubation period	Medium used
65489	2-3 mm	circular	2 days	yeast peptone glucose agar

Pigmentation

@ref	Production	Color	Name
65489		yellow	xanthomonadin

Culture and growth conditions

Culture medium

@ref	Name	Growth
65489	yeast peptone glucose agar

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65489	aerobe
125439	obligate aerobe	98.8

Spore formation

65489

Spore formationno

Observation

65489

ObservationStrains are pathogenic to P. persica, producing necrotic spots after inoculation on detached leaves and whole plants. Additionally, they elicit a hypersensitivity reaction when inoculated in tobacco and tomato leaves.

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65489	62064 ChEBI	2,3-butanediol	-	assimilation
65489	30916 ChEBI	2-oxoglutarate	+	carbon source
65489	28644 ChEBI	2-oxopentanoate	-	assimilation
65489	16724 ChEBI	4-hydroxybutyrate	-	assimilation
65489	18101 ChEBI	4-hydroxyphenylacetic acid	-	assimilation
65489	30089 ChEBI	acetate	-	assimilation
65489	17128 ChEBI	adipate	-	assimilation
65489	40585 ChEBI	alpha-cyclodextrin	-	assimilation
65489	17925 ChEBI	alpha-D-glucose	-	assimilation
65489	17925 ChEBI	alpha-D-glucose	+	carbon source
65489	27613 ChEBI	amygdalin	-	builds acid from
65489	18305 ChEBI	arbutin	-	builds acid from
65489	73706 ChEBI	bromosuccinate	+	carbon source
65489	17057 ChEBI	cellobiose	-	builds acid from
65489	17057 ChEBI	cellobiose	+	carbon source
65489	16383 ChEBI	cis-aconitate	+	carbon source
65489	16947 ChEBI	citrate	-	assimilation
65489	17108 ChEBI	D-arabinose	+	builds acid from
65489	18333 ChEBI	D-arabitol	-	builds acid from
65489	15824 ChEBI	D-fructose	-	builds acid from
65489	15824 ChEBI	D-fructose	+	carbon source
65489	28847 ChEBI	D-fucose	+	builds acid from
65489	15895 ChEBI	D-galactonic acid lactone	-	assimilation
65489	12936 ChEBI	D-galactose	-	builds acid from
65489	18024 ChEBI	D-galacturonic acid	-	assimilation
65489	8391 ChEBI	D-gluconate	-	assimilation
65489	17784 ChEBI	D-glucosaminic acid	-	assimilation
65489	17634 ChEBI	D-glucose	-	builds acid from
65489	14314 ChEBI	D-glucose 6-phosphate	-	assimilation
65489	62318 ChEBI	D-lyxose	-	builds acid from
65489	16899 ChEBI	D-mannitol	-	assimilation
65489	16899 ChEBI	D-mannitol	-	builds acid from
65489	16024 ChEBI	D-mannose	-	builds acid from
65489	16024 ChEBI	D-mannose	+	carbon source
65489	27605 ChEBI	D-psicose	+	carbon source
65489	16988 ChEBI	D-ribose	-	builds acid from
65489	16523 ChEBI	D-serine	-	assimilation
65489	17924 ChEBI	D-sorbitol	-	assimilation
65489	17924 ChEBI	D-sorbitol	-	builds acid from
65489	16443 ChEBI	D-tagatose	-	builds acid from
65489	65327 ChEBI	D-xylose	-	builds acid from
65489	27689 ChEBI	decanoate	-	assimilation
65489	17113 ChEBI	erythritol	-	assimilation
65489	17113 ChEBI	erythritol	-	builds acid from
65489		esculin ferric citrate	+	builds acid from
65489	16000 ChEBI	ethanolamine	-	assimilation
65489	15740 ChEBI	formate	-	assimilation
65489	16813 ChEBI	galactitol	-	builds acid from
65489	16865 ChEBI	gamma-aminobutyric acid	-	assimilation
65489	28066 ChEBI	gentiobiose	-	builds acid from
65489	28066 ChEBI	gentiobiose	+	carbon source
65489	17234 ChEBI	glucose	+	assimilation
65489	32323 ChEBI	glucuronamide	-	assimilation
65489	17754 ChEBI	glycerol	-	builds acid from
65489	15978 ChEBI	glycerol 3-phosphate	-	assimilation
65489	28087 ChEBI	glycogen	-	builds acid from
65489	73804 ChEBI	glycyl L-aspartic acid	+	carbon source
65489	17596 ChEBI	inosine	-	assimilation
65489	15443 ChEBI	inulin	-	builds acid from
65489	17240 ChEBI	itaconate	-	assimilation
65489	21217 ChEBI	L-alaninamide	+	carbon source
65489	30849 ChEBI	L-arabinose	-	assimilation
65489	30849 ChEBI	L-arabinose	-	builds acid from
65489	18403 ChEBI	L-arabitol	-	builds acid from
65489	17196 ChEBI	L-asparagine	-	assimilation
65489	18287 ChEBI	L-fucose	+	builds acid from
65489	29985 ChEBI	L-glutamate	+	carbon source
65489	15971 ChEBI	L-histidine	-	assimilation
65489	15603 ChEBI	L-leucine	-	assimilation
65489	17295 ChEBI	L-phenylalanine	-	assimilation
65489	18183 ChEBI	L-pyroglutamic acid	-	assimilation
65489	62345 ChEBI	L-rhamnose	-	assimilation
65489	62345 ChEBI	L-rhamnose	-	builds acid from
65489	17266 ChEBI	L-sorbose	-	builds acid from
65489	65328 ChEBI	L-xylose	-	builds acid from
65489	17716 ChEBI	lactose	-	builds acid from
65489	25115 ChEBI	malate	+	assimilation
65489	17306 ChEBI	maltose	-	builds acid from
65489	17306 ChEBI	maltose	+	assimilation
65489	29864 ChEBI	mannitol	+	assimilation
65489	37684 ChEBI	mannose	+	assimilation
65489	6731 ChEBI	melezitose	-	builds acid from
65489	28053 ChEBI	melibiose	-	assimilation
65489	28053 ChEBI	melibiose	-	builds acid from
65489	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
65489	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
65489	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
65489	17268 ChEBI	myo-inositol	-	builds acid from
65489	17268 ChEBI	myo-inositol	-	assimilation
65489	28037 ChEBI	N-acetylgalactosamine	-	assimilation
65489	506227 ChEBI	N-acetylglucosamine	-	builds acid from
65489	506227 ChEBI	N-acetylglucosamine	+	assimilation
65489	17632 ChEBI	nitrate	-	reduction
65489	18401 ChEBI	phenylacetate	-	assimilation
65489		potassium 2-dehydro-D-gluconate	-	builds acid from
65489		potassium 5-dehydro-D-gluconate	-	builds acid from
65489	32032 ChEBI	potassium gluconate	-	assimilation
65489	32032 ChEBI	potassium gluconate	-	builds acid from
65489	17148 ChEBI	putrescine	-	assimilation
65489	16634 ChEBI	raffinose	-	assimilation
65489	16634 ChEBI	raffinose	-	builds acid from
65489	15963 ChEBI	ribitol	-	assimilation
65489	15963 ChEBI	ribitol	-	builds acid from
65489	17814 ChEBI	salicin	-	builds acid from
65489	41865 ChEBI	sebacic acid	-	assimilation
65489	53258 ChEBI	sodium citrate	+	assimilation
65489	28017 ChEBI	starch	-	builds acid from
65489	30031 ChEBI	succinate	+	carbon source
65489	17992 ChEBI	sucrose	-	builds acid from
65489	17992 ChEBI	sucrose	+	carbon source
65489	17748 ChEBI	thymidine	-	assimilation
65489	27082 ChEBI	trehalose	-	builds acid from
65489	27082 ChEBI	trehalose	+	carbon source
65489	32528 ChEBI	turanose	-	builds acid from
65489	16704 ChEBI	uridine	-	assimilation
65489	17151 ChEBI	xylitol	-	builds acid from

Enzymes

@ref	Value	Activity	Ec
65489	beta-galactosidase	+	3.2.1.23
65489	beta-glucosidase	+	3.2.1.21
65489	catalase	+	1.11.1.6
65489	cytochrome oxidase	-	1.9.3.1
65489	urease	-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Plant infections	-
#Host	#Plants	#Tree
#Infection	#Plant infections	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture duration	Enrichment culture temperature	Isolation date	Isolation procedure
65489	symptomatic nectarine trees (Prunus persica var. nectarina)	Murcia	Spain	ESP	Europe	3 days	25	2007	Isolate was recovered from trunk canker exudates of the trees after three days incubation at 25°C on yeast peptone glucose agar (YPGA) medium. The colonies were purified three times in YPGA.

Taxonmaps

69479

Global distribution of 16S sequence MG523312 (>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

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM284620v1 assembly for Xanthomonas prunicola CFBP 8353	contig	GCA_002846205	2053928.3	2878129378	2053930	60.66

16S sequences

@ref	Description	Accession	Database
65489	Xanthomonas prunicola 16S ribosomal RNA gene, partial sequence	MG523312

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xanthomonas prunicola CFBP 8353
NCBI: GCA_002846205

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.90	no
125439	motility	BacteriaNetⓘ	yes	73.80	no
125439	gram_stain	BacteriaNetⓘ	negative	97.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xanthomonas sp. CFBP8353
PATRIC: 2053928.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.25	yes
125438	anaerobic	anaerobicⓘ	no	98.33	yes
125438	spore-forming	spore-formingⓘ	no	87.42	yes
125438	aerobic	aerobicⓘ	yes	83.00	yes
125438	thermophilic	thermophileⓘ	no	98.98	no
125438	flagellated	motile2+ⓘ	yes	75.02	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
Phylogeny	Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees.	Lopez MM, Lopez-Soriano P, Garita-Cambronero J, Beltran C, Taghouti G, Portier P, Cubero J, Fischer-Le Saux M, Marco-Noales E	Int J Syst Evol Microbiol	10.1099/ijsem.0.002743	2018

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 )
#65489	María M. López, Pablo Lopez-Soriano, Jerson Garita-Cambronero, Carmen Beltrán, Geraldine Taghouti, Perrine Portier, Jaime Cubero, Marion Fischer-Le Saux, Ester Marco-Noales: Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees. IJSEM 68: 1857 - 1866 2018 ( DOI 10.1099/ijsem.0.002743 , PubMed 29741474 )
#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 prunicola (CECT 9404, IVIA 3287.1, CFBP 8353)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002846205

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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