Strain identifier
BacDive ID: 162231
Type strain: 
Species: Erythrobacter colymbi
Strain history: K. Furuhata TPW-24.
NCBI tax ID(s): 1161202 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162231
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Erythrobacter colymbi JCM 18338 is a mesophilic, Gram-negative bacterium that was isolated from Swimming pool water in Tokyo.
NCBI tax id
- NCBI tax id: 1161202
- Matching level: species
strain history
- @ref: 67770
- history: K. Furuhata TPW-24.
doi: 10.13145/bacdive162231.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Erythrobacter
- species: Erythrobacter colymbi
- full scientific name: Erythrobacter colymbi (Furuhata et al. 2013) Xu et al. 2020
synonyms
- @ref: 20215
- synonym: Porphyrobacter colymbi
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Erythrobacter
species: Erythrobacter colymbi
full scientific name: Erythrobacter colymbi (Furuhata et al. 2013) Xu et al. 2020
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 97 |
| 125439 | negative | 97.3 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 93.2
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 90.819 |
| 125439 | no | 95.8 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Swimming pool water (free residual chlorine: 0.4 mg/L) in Tokyo
- country: Japan
- origin.country: JPN
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_2165.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_1392;98_1691;99_2165&stattab=map
- Last taxonomy: Erythrobacter
- 16S sequence: AB702992
- Sequence Identity:
- Total samples: 4806
- soil counts: 1335
- aquatic counts: 2635
- animal counts: 540
- plant counts: 296
Sequence information
16S sequences
- @ref: 67770
- description: Porphyrobacter colymbi gene for 16S rRNA, partial sequence
- accession: AB702992
- length: 1445
- database: nuccore
- NCBI tax ID: 1161202
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Porphyrobacter colymbi strain JCM 18338 | 1161202.8 | wgs | patric | 1161202 |
| 66792 | Erythrobacter colymbi JCM 18338 | 2845798653 | draft | img | 1161202 |
| 67770 | Erythrobacter colymbi JCM 18338 | GCA_002155685 | scaffold | ncbi | 1161202 |
GC content
- @ref: 67770
- GC-content: 66.5
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 93.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 54 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 95.8 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 92.184 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.819 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.744 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 93.629 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 63.578 | no |
External links
@ref: 67770
culture collection no.: JCM 18338, KCTC 32078
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |
| 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 |