Pedobacter sp. (DSM 102672, Leaf41)

Name: Pedobacter sp. (DSM 102672, Leaf41)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131865

Type strain

Strain Designation Leaf41

Culture col. no. DSM 102672 Leaf41

NCBI tax ID(s) 1411316

Special Collections DSMZ Arabidopsis

History DSMZ <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf41 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann

Links

Leaf41 is a bacterium that was isolated from leaf of Arabidopsis thaliana, wild-type genotype.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 397032

DSM 102672

@ref 20215

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

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Full scientific name Pedobacter Steyn et al. 1998

Synonyms (2)

Nubsella
Paradesertivirga

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.339
125439	negative	98.758

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23657	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)
23657	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.026

Spore formation

@ref	Spore formation	Confidence
125439		98.955

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
23657	leaf of Arabidopsis thaliana, wild-type genotype	Arabidopsis thaliana	Brugg (47.4816806N 8.217547222E)	Switzerland	CHE	Europe	47.4817	8.2176 47.4817/8.2176

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Leaf41 assembly for Pedobacter sp. Leaf41	contig	GCA_001422545	1736218.3	2643221768	1736218	75.35

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Leaf41 assembly for Pedobacter sp. Leaf41
BV-BRC: 1736218.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.03	no
125439	gram_stain	BacteriaNetⓘ	negative	98.76	no
125439	spore_formation	BacteriaNetⓘ	no	98.96	no
125439	motility	BacteriaNetⓘ	no	79.18	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter sp. Leaf41
PATRIC: 1736218.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.34	no
125438	anaerobic	anaerobicⓘ	no	97.96	no
125438	spore-forming	spore-formingⓘ	no	86.79	no
125438	aerobic	aerobicⓘ	yes	88.06	no
125438	thermophilic	thermophileⓘ	no	97.49	yes
125438	flagellated	motile2+ⓘ	no	85.50	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 )
#23657	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102672
#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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