Strain identifier

BacDive ID: 17606

Type strain: Yes

Species: Xanthomonas cassavae

Strain Designation: VdM 147, ZD1

Strain history: <- NCPPB <- ?

NCBI tax ID(s): 1219375 (strain), 56450 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7804

BacDive-ID: 17606

DSM-Number: 18958

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

description: Xanthomonas cassavae VdM 147 is a mesophilic, motile plant pathogen that was isolated from Manihot esculenta, leaf spots.

NCBI tax id

NCBI tax idMatching level
56450species
1219375strain

strain history

  • @ref: 7804
  • history: <- NCPPB <- ?

doi: 10.13145/bacdive17606.20230509.8.1

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 cassavae
  • full scientific name: Xanthomonas cassavae (ex Wiehe and Dowson 1953) Vauterin et al. 1995

@ref: 7804

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Xanthomonas

species: Xanthomonas cassavae

full scientific name: Xanthomonas cassavae (ex Wiehe and Dowson 1953) Vauterin et al. 1995

strain designation: VdM 147, ZD1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes96.827
6948099.996negative

Culture and growth conditions

culture medium

  • @ref: 7804
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: 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: 7804
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no92
69480no99.995

Isolation, sampling and environmental information

isolation

  • @ref: 7804
  • sample type: Manihot esculenta, leaf spots
  • host species: Manihot esculenta
  • country: Malawi
  • origin.country: MWI
  • continent: Africa

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#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: Y10762
  • Sequence Identity:
  • Total samples: 52152
  • soil counts: 10026
  • aquatic counts: 6826
  • animal counts: 28252
  • plant counts: 7048

Safety information

risk assessment

  • @ref: 7804
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Xanthomonas cassavae strain LMG673 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF209756513ena1219375
7804X.cassavae 16S rRNA geneY107621502ena1219375

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xanthomonas cassavae CFBP 4642 NCPPB 101GCA_020783895contigncbi1219375
66792Xanthomonas cassavae CFBP 46421219375.3completepatric1219375

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileyes80.87no
gram-positiveno97.78no
anaerobicno98.992no
aerobicyes95.157no
halophileno95.445no
spore-formingno95.025no
glucose-utilyes93.962no
flagellatedno83.608no
thermophileno99.418yes
glucose-fermentno88.876no

External links

@ref: 7804

culture collection no.: DSM 18958, ICMP 204, LMG 673, NCPPB 101

straininfo link

  • @ref: 86599
  • straininfo: 5374

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7804Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18958)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18958
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
86599Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5374.1StrainInfo: A central database for resolving microbial strain identifiers