Strain identifier
BacDive ID: 132325
Type strain: 
Species: Phycicoccus sp.
Strain Designation: Root563
Strain history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root563 <- Y. Bai
NCBI tax ID(s): 1902410 (species)
version 9.1 (current version)
General
@ref: 24114
BacDive-ID: 132325
DSM-Number: 102499
keywords: genome sequence, Bacteria, Gram-positive
description: Phycicoccus sp. Root563 is a Gram-positive bacterium that was isolated from roots of Arabidopsis thaliana ecotype Columbia-0 .
NCBI tax id
- NCBI tax id: 1902410
- Matching level: species
strain history
- @ref: 24114
- history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root563 <- Y. Bai
doi: 10.13145/bacdive132325.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Intrasporangiaceae
- genus: Phycicoccus
- species: Phycicoccus sp.
- full scientific name: Phycicoccus Lee 2006
@ref: 24114
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Intrasporangiaceae
genus: Phycicoccus
species: Phycicoccus sp.
full scientific name: Phycicoccus sp.
strain designation: Root563
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 92.573
Culture and growth conditions
culture medium
- @ref: 24114
- 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: 24114
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: aerobe
- confidence: 92.257
Isolation, sampling and environmental information
isolation
- @ref: 24114
- sample type: roots of Arabidopsis thaliana ecotype Columbia-0 (Col-0)
- 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 | Phycicoccus sp. Root563 | GCA_001427915 | scaffold | ncbi | 1736562 |
| 66792 | Phycicoccus sp. Root563 | 1736562.3 | wgs | patric | 1736562 |
| 66792 | Phycicoccus sp. Root563 | 2643221567 | draft | img | 1736562 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 92.573 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.719 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 92.257 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 60.176 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.5 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 76.5 | no |
External links
@ref: 24114
culture collection no.: DSM 102499
straininfo link
- @ref: 90672
- straininfo: 396618
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 | |
| 24114 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102499 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102499) | |
| 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 | |
| 90672 | 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-ID396618.1 |