Strain identifier
BacDive ID: 17607
Type strain: 
Species: Xanthomonas codiaei
Strain history: <- CFBP <- ICMP
NCBI tax ID(s): 56463 (species)
version 9.3 (current version)
General
@ref: 7712
BacDive-ID: 17607
DSM-Number: 18812
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, plant pathogen
description: Xanthomonas codiaei DSM 18812 is a mesophilic, Gram-negative plant pathogen that was isolated from Codiacum variegatum.
NCBI tax id
- NCBI tax id: 56463
- Matching level: species
strain history
- @ref: 7712
- history: <- CFBP <- ICMP
doi: 10.13145/bacdive17607.20250331.9.3
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 codiaei
- full scientific name: Xanthomonas codiaei Vauterin et al. 1995
@ref: 7712
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Xanthomonas
species: Xanthomonas codiaei
full scientific name: Xanthomonas codiaei Vauterin et al. 1995
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 98.75 |
| 125439 | negative | 98.8 |
Culture and growth conditions
culture medium
- @ref: 7712
- 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: 7712
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 99.4
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 90.423 |
| 125439 | no | 97.9 |
Isolation, sampling and environmental information
isolation
- @ref: 7712
- sample type: Codiacum variegatum
- host species: Codiacum variegatum
- geographic location: Florida
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Shrub (Scrub)
Safety information
risk assessment
- @ref: 7712
- 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 codiaei 16S ribosomal RNA gene, partial sequence and 16S-23S ribosomal RNA intergenic spacer, complete sequence | AF260971 | 578 | nuccore | 56463 |
| 20218 | Xanthomonas codiaei clone K0906 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence | HM181910 | 615 | nuccore | 56463 |
| 7712 | X.codiaei 16S rRNA gene | Y10765 | 1502 | nuccore | 56463 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Xanthomonas codiaei CFBP4690 | GCA_002939785 | contig | ncbi | 56463 |
| 66792 | Xanthomonas codiaei strain CFBP4690 | 56463.3 | wgs | patric | 56463 |
| 66792 | Xanthomonas codiaei CFBP4690 | 2880484841 | draft | img | 56463 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.75 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.234 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.423 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.078 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 99.981 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 74.799 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 97.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 87.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.4 |
External links
@ref: 7712
culture collection no.: DSM 18812, CFBP 4690, ICMP 9513, LMG 8678
straininfo link
- @ref: 86600
- straininfo: 5924
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 7712 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18812) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18812 | |||
| 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) | |||
| 86600 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID5924.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |