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Strain identifier

BacDive ID: 158738

Type strain: Yes

Species: Xanthomonas prunicola

NCBI tax ID(s): 2053930 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 65489

BacDive-ID: 158738

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming, pigmented

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

NCBI tax id

  • NCBI tax id: 2053930
  • Matching level: species

doi: 10.13145/bacdive158738.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Xanthomonas
  • species: Xanthomonas prunicola
  • full scientific name: Xanthomonas prunicola López et al. 2018

@ref: 65489

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Xanthomonadaceae

genus: Xanthomonas

species: Xanthomonas prunicola

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
65489negativerod-shaped
69480yes50
69480negative99.54

colony morphology

  • @ref: 65489
  • colony size: 2-3 mm
  • colony shape: circular
  • incubation period: 2 days
  • medium used: yeast peptone glucose agar

pigmentation

  • @ref: 65489
  • production: yes
  • color: yellow
  • name: xanthomonadin

Culture and growth conditions

culture medium

  • @ref: 65489
  • name: yeast peptone glucose agar
  • growth: yes

Physiology and metabolism

oxygen tolerance

  • @ref: 65489
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
65489no
69480no97.853

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 99.281

observation

  • @ref: 65489
  • observation: Strains 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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65489309162-oxoglutarate+carbon source
65489286442-oxopentanoate-assimilation
65489620642,3-butanediol-assimilation
6548916865gamma-aminobutyric acid-assimilation
65489181014-hydroxyphenylacetic acid-assimilation
6548930089acetate-assimilation
6548917128adipate-assimilation
6548915963ribitol-assimilation
6548940585alpha-cyclodextrin-assimilation
6548917925alpha-D-glucose-assimilation
6548917925alpha-D-glucose+carbon source
6548927613amygdalin-builds acid from
6548918305arbutin-builds acid from
6548973706bromosuccinate+carbon source
6548927689decanoate-assimilation
6548917057cellobiose-builds acid from
6548917057cellobiose+carbon source
6548916383cis-aconitate+carbon source
6548916947citrate-assimilation
6548915963ribitol-builds acid from
6548917108D-arabinose+builds acid from
6548918333D-arabitol-builds acid from
6548915824D-fructose-builds acid from
6548915824D-fructose+carbon source
6548928847D-fucose+builds acid from
6548915895D-galactonic acid lactone-assimilation
6548912936D-galactose-builds acid from
6548918024D-galacturonic acid-assimilation
654898391D-gluconate-assimilation
6548917784D-glucosaminic acid-assimilation
6548917634D-glucose-builds acid from
6548914314D-glucose 6-phosphate-assimilation
6548962318D-lyxose-builds acid from
6548916899D-mannitol-assimilation
6548916899D-mannitol-builds acid from
6548916024D-mannose-builds acid from
6548916024D-mannose+carbon source
6548928053melibiose-assimilation
6548927605D-psicose+carbon source
6548916988D-ribose-builds acid from
6548916523D-serine-assimilation
6548917924D-sorbitol-assimilation
6548917924D-sorbitol-builds acid from
6548916443D-tagatose-builds acid from
6548965327D-xylose-builds acid from
6548916813galactitol-builds acid from
6548917113erythritol-assimilation
6548917113erythritol-builds acid from
65489esculin ferric citrate+builds acid from
6548916000ethanolamine-assimilation
6548915740formate-assimilation
65489167244-hydroxybutyrate-assimilation
6548928066gentiobiose-builds acid from
6548928066gentiobiose+carbon source
6548917234glucose+assimilation
6548932323glucuronamide-assimilation
6548917754glycerol-builds acid from
6548915978glycerol 3-phosphate-assimilation
6548928087glycogen-builds acid from
6548973804glycyl L-aspartic acid+carbon source
6548917596inosine-assimilation
6548917268myo-inositol-builds acid from
6548915443inulin-builds acid from
6548917240itaconate-assimilation
6548921217L-alaninamide+carbon source
6548930849L-arabinose-assimilation
6548930849L-arabinose-builds acid from
6548918403L-arabitol-builds acid from
6548917196L-asparagine-assimilation
6548918287L-fucose+builds acid from
6548929985L-glutamate+carbon source
6548915971L-histidine-assimilation
6548915603L-leucine-assimilation
6548917295L-phenylalanine-assimilation
6548918183L-pyroglutamic acid-assimilation
6548962345L-rhamnose-assimilation
6548962345L-rhamnose-builds acid from
6548917266L-sorbose-builds acid from
6548965328L-xylose-builds acid from
6548917716lactose-builds acid from
6548925115malate+assimilation
6548917306maltose-builds acid from
6548917306maltose+assimilation
6548929864mannitol+assimilation
6548937684mannose+assimilation
654896731melezitose-builds acid from
6548928053melibiose-builds acid from
65489320061methyl alpha-D-glucopyranoside-builds acid from
6548943943methyl alpha-D-mannoside-builds acid from
6548974863methyl beta-D-xylopyranoside-builds acid from
6548917268myo-inositol-assimilation
6548928037N-acetylgalactosamine-assimilation
65489506227N-acetylglucosamine-builds acid from
65489506227N-acetylglucosamine+assimilation
6548917632nitrate-reduction
6548918401phenylacetate-assimilation
65489potassium 2-dehydro-D-gluconate-builds acid from
65489potassium 5-dehydro-D-gluconate-builds acid from
6548932032potassium gluconate-assimilation
6548932032potassium gluconate-builds acid from
6548917148putrescine-assimilation
6548916634raffinose-assimilation
6548916634raffinose-builds acid from
6548917814salicin-builds acid from
6548941865sebacic acid-assimilation
6548953258sodium citrate+assimilation
6548928017starch-builds acid from
6548930031succinate+carbon source
6548917992sucrose-builds acid from
6548917992sucrose+carbon source
6548917748thymidine-assimilation
6548927082trehalose-builds acid from
6548927082trehalose+carbon source
6548932528turanose-builds acid from
6548916704uridine-assimilation
6548917151xylitol-builds acid from

enzymes

@refvalueactivityec
65489catalase+1.11.1.6
65489cytochrome oxidase-1.9.3.1
65489urease-3.5.1.5
65489beta-glucosidase+3.2.1.21
65489beta-galactosidase+3.2.1.23

Isolation, sampling and environmental information

isolation

  • @ref: 65489
  • sample type: symptomatic nectarine trees (Prunus persica var. nectarina)
  • geographic location: Murcia
  • country: Spain
  • origin.country: ESP
  • continent: Europe
  • enrichment culture duration: 3 days
  • enrichment culture temperature: 25
  • isolation date: 2007
  • isolation procedure: 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.

isolation source categories

Cat1Cat2Cat3
#Infection#Plant infections
#Host#Plants#Tree
#Infection#Plant infections

taxonmaps

  • @ref: 69479
  • File name: preview.99_92.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_73;97_76;98_83;99_92&stattab=map
  • Last taxonomy: Xanthomonas
  • 16S sequence: MG523312
  • Sequence Identity:
  • Total samples: 52152
  • soil counts: 10026
  • aquatic counts: 6826
  • animal counts: 28252
  • plant counts: 7048

Sequence information

16S sequences

  • @ref: 65489
  • description: 16S rRNA gene sequence
  • accession: MG523312
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xanthomonas prunicola CFBP 8353GCA_002846205contigncbi2053930
66792Xanthomonas sp. CFBP83532053928.3wgspatric2053930
66792Xanthomonas prunicola CFBP 83532878129378draftimg2053930

External links

@ref: 65489

culture collection no.: CECT 9404, IVIA 3287.1, CFBP 8353

literature

  • topic: Phylogeny
  • Pubmed-ID: 29741474
  • title: Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees.
  • authors: Lopez MM, Lopez-Soriano P, Garita-Cambronero J, Beltran C, Taghouti G, Portier P, Cubero J, Fischer-Le Saux M, Marco-Noales E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002743
  • year: 2018
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fruit/microbiology, Multilocus Sequence Typing, *Phylogeny, Pigmentation, Plant Diseases/*microbiology, Plant Leaves/microbiology, Prunus persica/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Trees, Xanthomonas/*classification/isolation & purification/pathogenicity
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
65489María M. López, Pablo Lopez-Soriano, Jerson Garita-Cambronero, Carmen Beltrán, Geraldine Taghouti, Perrine Portier, Jaime Cubero, Marion Fischer-Le Saux, Ester Marco-NoalesXanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees10.1099/ijsem.0.002743IJSEM 68: 1857-1866 201829741474
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes