Strain identifier
BacDive ID: 17593
Type strain: 
Species: Xanthomonas axonopodis
Strain history: <- ATCC <- NCPPB <- ICPB
NCBI tax ID(s): 53413 (species)
version 8.1 (current version)
General
@ref: 1410
BacDive-ID: 17593
DSM-Number: 3585
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, plant pathogen
description: Xanthomonas axonopodis DSM 3585 is a mesophilic plant pathogen that was isolated from Axonoperis scoparius.
NCBI tax id
- NCBI tax id: 53413
- Matching level: species
strain history
- @ref: 1410
- history: <- ATCC <- NCPPB <- ICPB
doi: 10.13145/bacdive17593.20230509.8.1
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 axonopodis
- full scientific name: Xanthomonas axonopodis Starr and Garces 1950 (Approved Lists 1980)
@ref: 1410
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Xanthomonas
species: Xanthomonas axonopodis
full scientific name: Xanthomonas axonopodis Starr and Garcés 1950 emend. Constantin et al. 2016
type strain: yes
Culture and growth conditions
culture medium
- @ref: 1410
- 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: 1410
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 1410
- sample type: Axonoperis scoparius
- host species: Axonoperis scoparius
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
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: X95919
- Sequence Identity:
- Total samples: 52152
- soil counts: 10026
- aquatic counts: 6826
- animal counts: 28252
- plant counts: 7048
Safety information
risk assessment
- @ref: 1410
- 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 axonopodis pv. axonopodis clone K0891 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence | HM181898 | 558 | ena | 316581 |
| 20218 | Xanthomonas axonopodis strain LMG538 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF209753 | 519 | ena | 53413 |
| 20218 | X.axonopodis 16S rRNA gene | X95919 | 1502 | ena | 53413 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Xanthomonas axonopodis DSM 3585 | GCA_001304695 | contig | ncbi | 53413 |
| 66792 | Xanthomonas axonopodis pv. axonopodis LMG 982 | GCA_001401595 | contig | ncbi | 316581 |
| 66792 | Xanthomonas axonopodis pv. axonopodis strain LMG 982 | 316581.4 | wgs | patric | 316581 |
| 66792 | Xanthomonas axonopodis strain DSM 3585 | 53413.25 | wgs | patric | 53413 |
| 66792 | Xanthomonas axonopodis pv. axonopodis LMG 982 | 2651869742 | draft | img | 316581 |
| 66792 | Xanthomonas axonopodis DSM 3585 | 2639762869 | draft | img | 53413 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 98.045 | no |
| anaerobic | no | 99.003 | no |
| halophile | no | 96.051 | no |
| spore-forming | no | 95.692 | no |
| glucose-util | yes | 93.409 | no |
| motile | yes | 78.101 | no |
| flagellated | no | 90.177 | no |
| aerobic | yes | 94.899 | no |
| thermophile | no | 98.487 | no |
| glucose-ferment | no | 89.392 | no |
External links
@ref: 1410
culture collection no.: DSM 3585, ATCC 19312, ICPB XA 103, LMG 982, NCPPB 457, CFBP 4924
straininfo link
- @ref: 86588
- straininfo: 14039
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1410 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3585) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3585 | |||
| 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 | |||
| 86588 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID14039.1 | StrainInfo: A central database for resolving microbial strain identifiers |