Strain identifier
BacDive ID: 131921
Type strain: 
Species: Rhodococcus sp.
Strain Designation: Leaf7
Strain history: <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf7 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann
NCBI tax ID(s): 194249 (species)
version 9.3 (current version)
General
@ref: 23713
BacDive-ID: 131921
DSM-Number: 102717
keywords: genome sequence, Bacteria, mesophilic
description: Rhodococcus sp. Leaf7 is a mesophilic bacterium that was isolated from leaf of Arabidopsis thaliana, wild-type genotype.
NCBI tax id
- NCBI tax id: 194249
- Matching level: species
strain history
- @ref: 23713
- history: <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf7 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann
doi: 10.13145/bacdive131921.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Nocardiaceae
- genus: Rhodococcus
- species: Rhodococcus sp.
- full scientific name: Rhodococcus Zopf 1891 (Approved Lists 1980)
synonyms
@ref synonym 20215 Rhodococcoides 20215 Prescottella 20215 Prescottia
@ref: 23713
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiaceae
genus: Rhodococcus
species: Rhodococcus sp.
full scientific name: Rhodococcus sp.
strain designation: Leaf7
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | no | 91.5 | |
| 125438 | 90.768 | positive | |
| 125439 | 95.1 | positive |
multimedia
- @ref: 23713
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_102717.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 23713
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
- @ref: 23713
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97.8
Isolation, sampling and environmental information
isolation
- @ref: 23713
- sample type: leaf of Arabidopsis thaliana, wild-type genotype
- host species: Arabidopsis thaliana
- geographic location: Seebach (47,4227222N 8,548666667E)
- country: Switzerland
- origin.country: CHE
- continent: Europe
- latitude: 47.4227
- longitude: 8.5487
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 | Rhodococcus sp. Leaf7 | GCA_001425985 | scaffold | ncbi | 1736210 |
| 66792 | Rhodococcus sp. Leaf7 | 1736210.3 | wgs | patric | 1736210 |
| 66792 | Rhodococcus sp. Leaf7 | 2643221948 | draft | img | 1736210 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 90.768 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.868 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.165 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 58.36 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.5 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 91.5 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 71.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 57.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 95.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97.8 |
External links
@ref: 23713
culture collection no.: DSM 102717
straininfo link
- @ref: 90308
- straininfo: 402761
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 | |
| 23713 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102717 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102717) | |
| 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 | |
| 90308 | 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-ID402761.1 | |
| 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 |