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Strain identifier

BacDive ID: 17610

Type strain: Yes

Species: Xanthomonas sacchari

Strain history: <- LMG <- F. Leoville, INRA Guadeloupe <- M. Beramis

NCBI tax ID(s): 56458 (species)

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

@ref: 16366

BacDive-ID: 17610

DSM-Number: 22617

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

description: Xanthomonas sacchari DSM 22617 is a mesophilic plant pathogen that was isolated from diseased sugarcane Saccharum officinarum.

NCBI tax id

  • NCBI tax id: 56458
  • Matching level: species

strain history: <- LMG <- F. Leoville, INRA Guadeloupe <- M. Beramis

doi: 10.13145/bacdive17610.20221219.7.1

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

@ref: 16366

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Xanthomonas

species: Xanthomonas sacchari

full scientific name: Xanthomonas sacchari Vauterin et al. 1995

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 98.928

Culture and growth conditions

culture medium

  • @ref: 16366
  • 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: 16366
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.09

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 96.663

Isolation, sampling and environmental information

isolation

  • @ref: 16366
  • sample type: diseased sugarcane Saccharum officinarum
  • host species: Saccharum officinarum
  • country: Guadeloupe
  • origin.country: FRA
  • continent: Middle and South America

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_399.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_73;97_76;98_333;99_399&stattab=map
  • Last taxonomy: Xanthomonas
  • 16S sequence: Y10766
  • Sequence Identity:
  • Total samples: 20017
  • soil counts: 5101
  • aquatic counts: 3769
  • animal counts: 5827
  • plant counts: 5320

Safety information

risk assessment

  • @ref: 16366
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Xanthomonas sacchari strain LMG471 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF209762492ena56458
16366X.sacchari 16S rRNA geneY107661500ena56458

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xanthomonas sacchari CFBP4641GCA_002940085contigncbi56458
66792Xanthomonas sacchari strain CFBP464156458.17wgspatric56458
66792Xanthomonas sacchari CFBP46412878102749draftimg56458

GC content

  • @ref: 16366
  • GC-content: 68.5

External links

@ref: 16366

culture collection no.: DSM 22617, CFBP 4641, ICMP 16916, LMG 471

straininfo link

@refpassport
20218http://www.straininfo.net/strains/622192
20218http://www.straininfo.net/strains/721643
20218http://www.straininfo.net/strains/22902

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16366Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22617)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22617
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)