Strain identifier
BacDive ID: 17610
Type strain:
Species: Xanthomonas sacchari
Strain history: <- LMG <- F. Leoville, INRA Guadeloupe <- M. Beramis
NCBI tax ID(s): 56458 (species)
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
- @ref: 16366
- history: <- LMG <- F. Leoville, INRA Guadeloupe <- M. Beramis
doi: 10.13145/bacdive17610.20230509.8.1
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 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
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
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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Xanthomonas sacchari strain LMG471 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF209762 | 492 | ena | 56458 |
16366 | X.sacchari 16S rRNA gene | Y10766 | 1500 | ena | 56458 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Xanthomonas sacchari CFBP4641 | GCA_002940085 | contig | ncbi | 56458 |
66792 | Xanthomonas sacchari strain CFBP4641 | 56458.17 | wgs | patric | 56458 |
66792 | Xanthomonas sacchari CFBP4641 | 2878102749 | draft | img | 56458 |
GC content
- @ref: 16366
- GC-content: 68.5
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 98.025 | no |
anaerobic | no | 99.248 | no |
halophile | no | 94.161 | no |
spore-forming | no | 95.99 | no |
glucose-util | yes | 95.257 | no |
thermophile | no | 99.246 | no |
flagellated | no | 82.407 | no |
motile | yes | 85.714 | no |
aerobic | yes | 94.781 | no |
glucose-ferment | no | 89.511 | no |
External links
@ref: 16366
culture collection no.: DSM 22617, CFBP 4641, ICMP 16916, LMG 471
straininfo link
- @ref: 86603
- straininfo: 5158
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16366 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22617) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22617 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69479 | João 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 | |||
86603 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID5158.1 | StrainInfo: A central database for resolving microbial strain identifiers |