Strain identifier
BacDive ID: 131868
Type strain: 
Species: Pedobacter sp.
Strain Designation: Leaf176
Strain history: <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf176 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann
NCBI tax ID(s): 1411316 (species)
version 9.1 (current version)
General
@ref: 23660
BacDive-ID: 131868
DSM-Number: 102675
keywords: genome sequence, Bacteria, Gram-negative
description: Pedobacter sp. Leaf176 is a Gram-negative bacterium that was isolated from leaf of Arabidopsis thaliana, wild-type genotype.
NCBI tax id
- NCBI tax id: 1411316
- Matching level: species
strain history
- @ref: 23660
- history: <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf176 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann
doi: 10.13145/bacdive131868.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter sp.
- full scientific name: Pedobacter Steyn et al. 1998
@ref: 23660
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter sp.
full scientific name: Pedobacter sp.
strain designation: Leaf176
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 96
Culture and growth conditions
culture medium
- @ref: 23660
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: 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: 23660
- growth: positive
- type: growth
- temperature: 28
Isolation, sampling and environmental information
isolation
- @ref: 23660
- sample type: leaf of Arabidopsis thaliana, wild-type genotype
- host species: Arabidopsis thaliana
- geographic location: Brugg (47.4816806N 8.217547222E)
- country: Switzerland
- origin.country: CHE
- continent: Europe
- latitude: 47.4817
- longitude: 8.2176
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Leaf (Phyllosphere) |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pedobacter sp. Leaf176 | GCA_001424305 | scaffold | ncbi | 1736286 |
| 66792 | Pedobacter sp. Leaf176 | 1736286.3 | wgs | patric | 1736286 |
| 66792 | Pedobacter sp. Leaf176 | 2643221914 | draft | img | 1736286 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.432 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.018 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.936 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.49 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 84.007 | no |
External links
@ref: 23660
culture collection no.: DSM 102675
straininfo link
- @ref: 90256
- straininfo: 399100
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 | |
| 23660 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102675 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102675) | |
| 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 | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 90256 | 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-ID399100.1 |