Strain identifier
BacDive ID: 132041
Type strain: 
Species: Variovorax sp.
Strain Designation: Root473
Strain history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root473 <- Y. Bai
NCBI tax ID(s): 1871043 (species)
version 9.3 (current version)
General
@ref: 23832
BacDive-ID: 132041
DSM-Number: 102558
keywords: genome sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Variovorax sp. Root473 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .
NCBI tax id
- NCBI tax id: 1871043
- Matching level: species
strain history
- @ref: 23832
- history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root473 <- Y. Bai
doi: 10.13145/bacdive132041.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Variovorax
- species: Variovorax sp.
- full scientific name: Variovorax Willems et al. 1991
@ref: 23832
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Variovorax
species: Variovorax sp.
full scientific name: Variovorax sp.
strain designation: Root473
type strain: no
Morphology
cell morphology
- @ref: 125438
- gram stain: negative
- confidence: 98.3
Culture and growth conditions
culture medium
- @ref: 23832
- name: TRYPTONE YEAST EXTRACT GLUCOSE MEDIUM (TYG) (DSMZ Medium 1618)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1618
- composition: Name: TRYPTONE YEAST EXTRACT GLUCOSE MEDIUM (TYG) (DSMZ Medium 1618) Composition: Agar 20.0 g/l KCl 6.34 g/l Na2SO4 2.4 g/l NaCl 1.2 g/l Tryptone 1.0 g/l Yeast extract 1.0 g/l NaHCO3 0.5 g/l D-Glucose 0.5 g/l MgSO4 x 7 H2O 0.25 g/l CaCl2 x 2 H2O 0.22 g/l K2SO4 0.17 g/l K2HPO4 0.13 g/l Na2CO3 0.09 g/l Fe(III)-EDTA 0.07 g/l Distilled water
culture temp
- @ref: 23832
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 125438 | aerobe | 91.578 |
| 125439 | obligate aerobe | 99.6 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 94.3
Isolation, sampling and environmental information
isolation
- @ref: 23832
- sample type: roots of Arabidopsis thaliana ecotype Shakdara (Sha)
- host species: Arabidopsis thaliana
- geographic location: Cologne (50.958N 6.856E)
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 50.958
- longitude: 6.856
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Variovorax sp. Root473 | GCA_001426505 | scaffold | ncbi | 1736541 |
| 66792 | Variovorax sp. Root473 | 1736541.3 | wgs | patric | 1736541 |
| 66792 | Variovorax sp. Root473 | 2643221683 | draft | img | 1736541 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.3 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.329 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 91.578 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.909 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.5 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 80.329 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 94.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 70.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 78.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.6 |
External links
@ref: 23832
culture collection no.: DSM 102558
straininfo link
- @ref: 90405
- straininfo: 407139
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 23832 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102558 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102558) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 90405 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID407139.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |