Strain identifier
BacDive ID: 132038
Type strain: 
Species: Variovorax sp.
Strain Designation: Root318D1
Strain history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root318D1 <- Y. Bai
NCBI tax ID(s): 1871043 (species)
version 9.3 (current version)
General
@ref: 23829
BacDive-ID: 132038
DSM-Number: 102555
keywords: genome sequence, Bacteria, mesophilic, Gram-negative
description: Variovorax sp. Root318D1 is a mesophilic, Gram-negative bacterium that was isolated from roots of wild-type Arabidopsis thaliana plants.
NCBI tax id
- NCBI tax id: 1871043
- Matching level: species
strain history
- @ref: 23829
- history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root318D1 <- Y. Bai
doi: 10.13145/bacdive132038.20250331.9.3
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: 23829
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Variovorax
species: Variovorax sp.
full scientific name: Variovorax sp.
strain designation: Root318D1
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 97.2 |
| 125438 | negative | 97.8 |
Culture and growth conditions
culture medium
- @ref: 23829
- name: FLOUR MEDIUM (DSMZ Medium 1613)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1613
- composition: Name: FLOUR MEDIUM (DSMZ Medium 1613) Composition: Agar 16.0 g/l Plain flour 4.0 g/l CaCO3 0.4 g/l Distilled water
culture temp
- @ref: 23829
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 98.3
spore formation
- @ref: 125439
- spore formation: no
- confidence: 94.1
Isolation, sampling and environmental information
isolation
- @ref: 23829
- sample type: roots of wild-type Arabidopsis thaliana plants
- host species: Arabidopsis thaliana
- geographic location: Cologne, Widdersdorf district (50.982N 6.827E)
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 50.982
- longitude: 6.827
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. Root318D1 | GCA_001424835 | scaffold | ncbi | 1736513 |
| 66792 | Variovorax sp. Root318D1 | 1736513.3 | wgs | patric | 1736513 |
| 66792 | Variovorax sp. Root318D1 | 2643221628 | draft | img | 1736513 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.8 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.592 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.905 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.306 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 99.393 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 56.205 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 94.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 76.1 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.2 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 98.3 |
External links
@ref: 23829
culture collection no.: DSM 102555
straininfo link
- @ref: 90402
- straininfo: 407845
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 | |
| 23829 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102555 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102555) | |
| 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 | |
| 90402 | 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-ID407845.1 | |
| 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 |