Variovorax sp. (DSM 102558, Root473)

Name: Variovorax sp. (DSM 102558, Root473)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132041

Type strain

Strain Designation Root473

Culture col. no. DSM 102558 Root473

NCBI tax ID(s) 1871043

Special Collections DSMZ Arabidopsis

History <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root473 <- Y. Bai

Links

Root473 is a bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .

genome sequence Bacteria

Name and taxonomic classification

SI-ID 407139

DSM 102558

@ref 20215

Last LPSN update 2026-02-09 11:31:37

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Variovorax

Full scientific name Variovorax Willems et al. 1991

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.3

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23832	TRYPTONE YEAST EXTRACT GLUCOSE MEDIUM (TYG) (DSMZ Medium 1618)		Medium recipe at MediaDive	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	Growth	Type	Temperature (°C)
23832	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	91.578
125439	obligate aerobe	99.6

Spore formation

@ref	Spore formation	Confidence
125439		94.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
23832	roots of Arabidopsis thaliana ecotype Shakdara (Sha)	Arabidopsis thaliana	Cologne (50.958N 6.856E)	Germany	DEU	Europe	50.958	6.856 50.958/6.856

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Root473 assembly for Variovorax sp. Root473	scaffold	GCA_001426505	1736541.3	2643221683	1736541	59.07

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Variovorax sp. Root473
NCBI: GCA_001426505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.30	no
125439	motility	BacteriaNetⓘ	yes	70.50	no
125439	gram_stain	BacteriaNetⓘ	negative	78.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Variovorax sp. Root473 Root473
NCBI: GCA_001426505.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.30	no
125438	anaerobic	anaerobicⓘ	no	98.33	no
125438	aerobic	aerobicⓘ	yes	91.58	no
125438	spore-forming	spore-formingⓘ	no	89.91	no
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	80.33	no

Literature

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#23832	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; 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) .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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