Strain identifier
BacDive ID: 132319
Type strain: 
Species: Methylibium sp.
Strain Designation: Root1272
Strain history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root1272 <- Y. Bai
NCBI tax ID(s): 2067992 (species)
version 9.1 (current version)
General
@ref: 24108
BacDive-ID: 132319
DSM-Number: 102455
keywords: genome sequence, Bacteria, Gram-negative
description: Methylibium sp. Root1272 is a Gram-negative bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .
NCBI tax id
- NCBI tax id: 2067992
- Matching level: species
strain history
- @ref: 24108
- history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root1272 <- Y. Bai
doi: 10.13145/bacdive132319.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiales, not assigned to family
- genus: Methylibium
- species: Methylibium sp.
- full scientific name: Methylibium Nakatsu et al. 2006
synonyms
- @ref: 20215
- synonym: Pseudorivibacter
@ref: 24108
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Betaproteobacteria, not assigned to order
family: Burkholderiales, not assigned to family
genus: Methylibium
species: Methylibium sp.
full scientific name: Methylibium sp.
strain designation: Root1272
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 94.894
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 24108 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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 |
| 24108 | TRYPTONE YEAST EXTRACT GLUCOSE MEDIUM (TYG) (DSMZ Medium 1618) | yes | https://mediadive.dsmz.de/medium/1618 | 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: 24108
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 93.835
Isolation, sampling and environmental information
isolation
- @ref: 24108
- sample type: roots of Arabidopsis thaliana ecotype Shakdara (Sha)
- host species: Arabidopsis thaliana
- geographic location: Cologne (50.958N 6.856E)
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 50.958
- longitude: 6.856
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methylibium sp. Root1272 | GCA_001425905 | contig | ncbi | 1736441 |
| 66792 | Methylibium sp. Root1272 | 1736441.3 | wgs | patric | 1736441 |
| 66792 | Methylibium sp. Root1272 | 2643221660 | draft | img | 1736441 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 94.894 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.887 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.835 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 79.863 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.857 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 81.115 | no |
External links
@ref: 24108
culture collection no.: DSM 102455
straininfo link
- @ref: 90666
- straininfo: 406674
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 | |
| 24108 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102455 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102455) | |
| 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 | |
| 90666 | 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-ID406674.1 |