Strain identifier
BacDive ID: 132040
Type strain: 
Species: Variovorax sp.
Strain Designation: Root434
Strain history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root434 <- Y. Bai
NCBI tax ID(s): 1871043 (species)
version 9.3 (current version)
General
@ref: 23831
BacDive-ID: 132040
DSM-Number: 102557
keywords: genome sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Variovorax sp. Root434 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: 23831
- history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root434 <- Y. Bai
doi: 10.13145/bacdive132040.20250331.9.3
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: 23831
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Variovorax
species: Variovorax sp.
full scientific name: Variovorax sp.
strain designation: Root434
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 98.4 |
| 125438 | negative | 97 |
Culture and growth conditions
culture medium
- @ref: 23831
- name: YEAST EXTRACT MANITOL MEDIUM (YEM) (DSMZ Medium 1626)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1626
- composition: Name: YEAST EXTRACT MANITOL MEDIUM (YEM) (DSMZ Medium 1626) Composition: Agar 20.0 g/l Mannitol 5.0 g/l K2HPO4 0.5 g/l Yeast extract 0.5 g/l MgSO4 x 7 H2O 0.2 g/l NaCl 0.1 g/l Distilled water
culture temp
- @ref: 23831
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 125438 | aerobe | 91.798 |
| 125439 | obligate aerobe | 98.2 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98.1
Isolation, sampling and environmental information
isolation
- @ref: 23831
- sample type: roots of Arabidopsis thaliana ecotype Shakdara (Sha)
- host species: Arabidopsis thaliana
- geographic location: Potsdam, Golm district (52.416N 12.968E)
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 52.416
- longitude: 12.968
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. Root434 | GCA_001426595 | scaffold | ncbi | 1736536 |
| 66792 | Variovorax sp. Root434 | 1736536.3 | wgs | patric | 1736536 |
| 66792 | Variovorax sp. Root434 | 2643221672 | draft | img | 1736536 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.273 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 91.798 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.142 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.393 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 54.479 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 85.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 98.2 |
External links
@ref: 23831
culture collection no.: DSM 102557
straininfo link
- @ref: 90404
- straininfo: 407264
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 | |
| 23831 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102557 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102557) | |
| 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 | |
| 90404 | 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-ID407264.1 | |
| 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 |