Strain identifier

BacDive ID: 17609

Type strain: Yes

Species: Xanthomonas pisi

Strain Designation: VdM 111, Xa1

Strain history: <- NCPPB <- D. Dye; XA1 <- N. Okabe

NCBI tax ID(s): 1440766 (strain), 56457 (species)

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General

@ref: 7802

BacDive-ID: 17609

DSM-Number: 18956

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile, plant pathogen

description: Xanthomonas pisi VdM 111 is a mesophilic, motile plant pathogen that was isolated from Pisum sativum, leaf spot.

NCBI tax id

NCBI tax idMatching level
56457species
1440766strain

strain history

  • @ref: 7802
  • history: <- NCPPB <- D. Dye; XA1 <- N. Okabe

doi: 10.13145/bacdive17609.20230509.8.1

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 pisi
  • full scientific name: Xanthomonas pisi (ex Goto and Okabe 1958) Vauterin et al. 1995

@ref: 7802

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Xanthomonas

species: Xanthomonas pisi

full scientific name: Xanthomonas pisi (ex Goto and Okabe 1958) Vauterin et al. 1995

strain designation: VdM 111, Xa1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes96.006
6948099.988negative

Culture and growth conditions

culture medium

  • @ref: 7802
  • name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1a
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

  • @ref: 7802
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no92
69480no99.999

Isolation, sampling and environmental information

isolation

  • @ref: 7802
  • sample type: Pisum sativum, leaf spot
  • host species: Pisum sativum
  • country: Japan
  • origin.country: JPN
  • continent: Asia

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: Y10758
  • Sequence Identity:
  • Total samples: 52152
  • soil counts: 10026
  • aquatic counts: 6826
  • animal counts: 28252
  • plant counts: 7048

Safety information

risk assessment

  • @ref: 7802
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Xanthomonas pisi clone K0876 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceHM181889557ena56457
7802X.pisi 16S rRNA geneY107581502ena56457

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xanthomonas pisi DSM 18956GCA_001010415contigncbi1440766
66792Xanthomonas pisi DSM 189561440766.4wgspatric1440766
66792Xanthomonas pisi DSM 189562636415828draftimg1440766

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileyes77.144no
gram-positiveno97.554no
anaerobicno98.837no
halophileno96.074no
spore-formingno96.505no
thermophileno98.714yes
glucose-utilyes94.668no
aerobicyes94.93no
flagellatedno88.25no
glucose-fermentno87.731no

External links

@ref: 7802

culture collection no.: DSM 18956, ICMP 570, NCPPB 762

straininfo link

  • @ref: 86602
  • straininfo: 5910

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7802Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18956)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18956
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
86602Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5910.1StrainInfo: A central database for resolving microbial strain identifiers