Strain identifier

BacDive ID: 17600

Type strain: Yes

Species: Xanthomonas vasicola

Strain Designation: F465, ICMP, VdM 71

Strain history: <- LMG <- NCPPB <- D. Dye; YW5 <- D. Watson; F465

NCBI tax ID(s): 56459 (species)

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General

@ref: 6647

BacDive-ID: 17600

DSM-Number: 16926

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, plant pathogen

description: Xanthomonas vasicola F465 is a mesophilic, Gram-negative plant pathogen that was isolated from red-brown leaf-stripe in Sorghum bicolor.

NCBI tax id

  • NCBI tax id: 56459
  • Matching level: species

strain history

  • @ref: 6647
  • history: <- LMG <- NCPPB <- D. Dye; YW5 <- D. Watson; F465

doi: 10.13145/bacdive17600.20230509.8.1

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 vasicola
  • full scientific name: Xanthomonas vasicola Vauterin et al. 1995

@ref: 6647

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Xanthomonas

species: Xanthomonas vasicola

full scientific name: Xanthomonas vasicola Vauterin et al. 1995

strain designation: F465, ICMP, VdM 71

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.94

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6647COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
6647TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

  • @ref: 6647
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.848

Isolation, sampling and environmental information

isolation

  • @ref: 6647
  • sample type: red-brown leaf-stripe in Sorghum bicolor
  • host species: Sorghum bicolor
  • country: New Zealand
  • origin.country: NZL
  • continent: Australia and Oceania

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

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: Y10755
  • Sequence Identity:
  • Total samples: 52152
  • soil counts: 10026
  • aquatic counts: 6826
  • animal counts: 28252
  • plant counts: 7048

Safety information

risk assessment

  • @ref: 6647
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Xanthomonas vasicola strain LMG736 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF209765510ena56459
6647X.vasicola 16S rRNA geneY107551502ena56459

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xanthomonas vasicola CFBP2543GCA_002939925contigncbi56459
66792Xanthomonas vasicola NCPPB 2417GCA_000772705contigncbi56459
66792Raoultella ornithinolytica DSM 16926GCA_013425975completencbi54291
66792Raoultella ornithinolytica strain DSM 1692654291.283completepatric54291
66792Xanthomonas vasicola NCPPB 241756459.22wgspatric56459
66792Xanthomonas vasicola strain CFBP254356459.70wgspatric56459
66792Xanthomonas vasicola NCPPB 24172630968353draftimg56459
66792Xanthomonas vasicola CFBP25432880466697draftimg56459

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno76.621no
flagellatedno94.007no
gram-positiveno97.5no
anaerobicno97.533no
aerobicyes88.63no
halophileno88.495no
spore-formingno94.391no
glucose-utilyes94.019no
glucose-fermentyes89.807no
thermophileno99.588no

External links

@ref: 6647

culture collection no.: DSM 16926, CFBP 2543, LMG 736, LMG 8707, NCPPB 2417

straininfo link

  • @ref: 86593
  • straininfo: 5602

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6647Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16926)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16926
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86593Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5602.1StrainInfo: A central database for resolving microbial strain identifiers