Strain identifier
BacDive ID: 3793
Type strain: 
Species: Thermoflexibacter ruber
Strain Designation: GEY
Strain history: <- ATCC <- R. A. Lewin, GEY
NCBI tax ID(s): 1003 (species)
version 9.3 (current version)
General
@ref: 3637
BacDive-ID: 3793
DSM-Number: 9560
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Thermoflexibacter ruber GEY is a mesophilic, Gram-negative bacterium that was isolated from hot spring.
NCBI tax id
- NCBI tax id: 1003
- Matching level: species
strain history
- @ref: 3637
- history: <- ATCC <- R. A. Lewin, GEY
doi: 10.13145/bacdive3793.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Thermoflexibacteraceae
- genus: Thermoflexibacter
- species: Thermoflexibacter ruber
- full scientific name: Thermoflexibacter ruber (Lewin 1969) Hahnke et al. 2017
synonyms
- @ref: 20215
- synonym: Flexibacter ruber
@ref: 3637
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Thermoflexibacteraceae
genus: Thermoflexibacter
species: Thermoflexibacter ruber
full scientific name: Thermoflexibacter ruber (Lewin 1969) Hahnke et al. 2017
strain designation: GEY
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 99.8 |
| 125438 | negative | 92.603 |
Culture and growth conditions
culture medium
- @ref: 3637
- name: FLEXIBACTER CANADENSIS MEDIUM (DSMZ Medium 357)
- growth: yes
- link: https://mediadive.dsmz.de/medium/357
- composition: Name: FLEXIBACTER CANADENSIS MEDIUM (DSMZ Medium 357) Composition: Agar 10.0 g/l Tris 1.0 g/l Glucose 1.0 g/l Casamino acids 1.0 g/l Sodium glycerophosphate 0.1 g/l CaCl2 x 2 H2O 0.1 g/l KNO3 0.1 g/l MgSO4 x 7 H2O 0.1 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Thiamine-HCl x 2 H2O 0.001 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-06 g/l Distilled water
culture temp
- @ref: 3637
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 98
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.2
Isolation, sampling and environmental information
isolation
- @ref: 3637
- sample type: hot spring
- geographic location: Geysir
- country: Iceland
- origin.country: ISL
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 3637
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Flexibacter ruber 16S ribosomal RNA | M58788 | 1462 | nuccore | 1003 |
| 20218 | Flexibacter ruber gene for 16S rRNA, strain:IFO 16675 | AB078064 | 1461 | nuccore | 1003 |
| 20218 | Flexibacter ruber gene for 16S rRNA, partial sequence, strain: NBRC 16677 | AB681104 | 1437 | nuccore | 1003 |
| 3637 | Flexibacter ruber gene for 16S rRNA, strain:IFO 16677 | AB078065 | 1467 | nuccore | 1003 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermoflexibacter ruber GEY, DSM 9560 | GCA_900113045 | scaffold | ncbi | 1003 |
| 66792 | Thermoflexibacter ruber strain GEY, DSM 9560 | 1003.8 | wgs | patric | 1003 |
| 66792 | Thermoflexibacter ruber DSM 9560 | 2636415974 | draft | img | 1003 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 98 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.8 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 82.1 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.2 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 92.603 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.42 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 80.81 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.072 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 91.567 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 82 | no |
External links
@ref: 3637
culture collection no.: DSM 9560, ATCC 23103
straininfo link
- @ref: 73305
- straininfo: 2843
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3637 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9560) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9560 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 73305 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID2843.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |