Phenylobacterium sp. (DSM 102495, Root1290)

Name: Phenylobacterium sp. (DSM 102495, Root1290)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132089

Type strain

Strain Designation Root1290

Culture col. no. DSM 102495 Root1290

NCBI tax ID(s) 1871053

Special Collections DSMZ Arabidopsis

Links

Root1290 is a mesophilic prokaryote that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .

mesophilic genome sequence

Name and taxonomic classification

SI-ID 405144

DSM 102495

@ref 20215

Last LPSN update 2025-12-16 10:01:25

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Caulobacterales

Family Caulobacteraceae

Genus Phenylobacterium

Full scientific name Phenylobacterium Lingens et al. 1985

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.802
125439	negative	90.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23879	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
23879	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	96.7

Spore formation

@ref	Spore formation	Confidence
125439		95.4

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
23879	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	Root1290 assembly for Phenylobacterium sp. Root1290	scaffold	GCA_001425305	1736445.3	2643221666	1736445	77.24

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phenylobacterium sp. Root1290
NCBI: GCA_001425305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.40	no
125439	motility	BacteriaNetⓘ	yes	70.40	no
125439	gram_stain	BacteriaNetⓘ	negative	90.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phenylobacterium sp. Root1290 Root1290
NCBI: GCA_001425305.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.80	no
125438	anaerobic	anaerobicⓘ	no	96.12	no
125438	aerobic	aerobicⓘ	yes	86.73	no
125438	spore-forming	spore-formingⓘ	no	88.76	no
125438	thermophilic	thermophileⓘ	no	97.83	no
125438	flagellated	motile2+ⓘ	yes	65.68	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 )
#23879	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102495
#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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