Pseudomonas sp. (DSM 102503, Root401)

Name: Pseudomonas sp. (DSM 102503, Root401)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131897

Type strain

Strain Designation Root401

Culture col. no. DSM 102503 Root401

NCBI tax ID(s) 306

Special Collections DSMZ Arabidopsis

History DSMZ <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root401 <- Y. Bai

Links

Root401 is a bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .

genome sequence Bacteria

Name and taxonomic classification

SI-ID 400275

DSM 102503

@ref 20215

Last LPSN update 2026-05-29 08:37:43

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Full scientific name Pseudomonas Migula 1894 (Approved Lists 1980)

Synonyms (9)

Metapseudomonas
Zestomonas
"Caenipseudomonas"
Phytopseudomonas
Ectopseudomonas
Aquipseudomonas
Geopseudomonas
Flavimonas
Chryseomonas

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	92.14
125438		92.726
125438	negative	99

Multimedia

@ref:	23689
multimedia content:	DSM_102503.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_102503.jpg
caption:	cells of DSM 102503 on medium 535 at 28 °C
intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23689	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
23689	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	93.349

Spore formation

@ref	Spore formation	Confidence
125439		99.796

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
23689	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	Root401 assembly for Pseudomonas sp. Root401	scaffold	GCA_001425105	1736526.3	2643221650	1736526	63.12

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Root401 assembly for Pseudomonas sp. Root401
BV-BRC: 1736526.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.75	no
125439	gram_stain	BacteriaNetⓘ	negative	92.14	no
125439	motility	BacteriaNetⓘ	yes	83.28	no
125439	spore_formation	BacteriaNetⓘ	no	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas sp. Root401 Root401
NCBI: GCA_001425105.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	97.35	no
125438	aerobic	aerobicⓘ	yes	93.35	no
125438	spore-forming	spore-formingⓘ	no	83.13	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	yes	92.73	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 )
#23689	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102503
#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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