Strain identifier
BacDive ID: 131793
Type strain: 
Species: Microbacterium sp.
Strain Designation: Root1433D1
Strain history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root1433D1 <- Y. Bai
NCBI tax ID(s): 51671 (species)
version 9.3 (current version)
General
@ref: 23588
BacDive-ID: 131793
DSM-Number: 102458
keywords: genome sequence, Bacteria, mesophilic
description: Microbacterium sp. Root1433D1 is a mesophilic bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .
NCBI tax id
- NCBI tax id: 51671
- Matching level: species
strain history
- @ref: 23588
- history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root1433D1 <- Y. Bai
doi: 10.13145/bacdive131793.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Microbacterium
- species: Microbacterium sp.
- full scientific name: Microbacterium Orla-Jensen 1919 (Approved Lists 1980)
synonyms
@ref synonym 20215 Aureobacterium 20215 Paramicrobacterium
@ref: 23588
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium sp.
full scientific name: Microbacterium sp.
strain designation: Root1433D1
type strain: no
Morphology
cell morphology
- @ref: 125439
- gram stain: positive
- confidence: 96.1
Culture and growth conditions
culture medium
- @ref: 23588
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
- @ref: 23588
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 99.2
Isolation, sampling and environmental information
isolation
- @ref: 23588
- 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 | Microbacterium sp. Root1433D1 | GCA_001426835 | scaffold | ncbi | 1736463 |
| 66792 | Microbacterium sp. Root1433D1 | 1736463.3 | wgs | patric | 1736463 |
| 66792 | Microbacterium sp. Root1433D1 | 2643221542 | draft | img | 1736463 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.744 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.653 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.157 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 76.444 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.967 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 77 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 82.4 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 63.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 96.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.2 |
External links
@ref: 23588
culture collection no.: DSM 102458
straininfo link
- @ref: 90184
- straininfo: 398732
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 | |
| 23588 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102458 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102458) | |
| 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 | |
| 90184 | 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-ID398732.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 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 | https://github.com/GenomeNet/deepG |