Strain identifier
BacDive ID: 5793
Type strain: 
Species: Geobacter sp.
Strain Designation: RE1
Strain history: <- E. Samain and H.C. Dubourguier, RE1
NCBI tax ID(s): 2135459 (species)
version 8.1 (current version)
General
@ref: 1242
BacDive-ID: 5793
DSM-Number: 2909
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Geobacter sp. RE1 is an anaerobe, mesophilic, motile bacterium that was isolated from mesophilic digester fed with waste water from starch industry.
NCBI tax id
- NCBI tax id: 2135459
- Matching level: species
strain history
- @ref: 1242
- history: <- E. Samain and H.C. Dubourguier, RE1
doi: 10.13145/bacdive5793.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfuromonadales
- family: Geobacteraceae
- genus: Geobacter
- species: Geobacter sp.
- full scientific name: Geobacter Lovley et al. 1995
synonyms
@ref synonym 20215 Geomobilibacter 20215 Trichlorobacter
@ref: 1242
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfuromonadales
family: Geobacteraceae
genus: Geobacter
species: Geobacter sp.
full scientific name: Geobacter sp.
strain designation: RE1
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 91.282 | |
| 69480 | 99.997 | negative |
Culture and growth conditions
culture medium
- @ref: 1242
- name: SYNTHROPHOMONAS MEDIUM (SULFATE FREE) (DSMZ Medium 213)
- growth: yes
- link: https://mediadive.dsmz.de/medium/213
- composition: Name: SYNTHROPHOMONAS MEDIUM (SULFATE FREE) (DSMZ Medium 213; with strain-specific modifications) Composition: None 1.48075 g/l Na2CO3 1.48075 g/l Trypticase peptone 0.987167 g/l KH2PO4 0.493583 g/l NaCl 0.394867 g/l NH4Cl 0.394867 g/l MgCl2 x 6 H2O 0.325765 g/l Na2S x 9 H2O 0.29615 g/l L-Cysteine HCl x H2O 0.29615 g/l CaCl2 x 2 H2O 0.0493583 g/l HCl 0.00246792 g/l FeCl2 x 4 H2O 0.00148075 g/l Sodium resazurin 0.000493583 g/l Pyridoxine hydrochloride 0.00029615 g/l Nicotinic acid 0.000197433 g/l Thiamine-HCl x 2 H2O 0.000197433 g/l CoCl2 x 6 H2O 0.000187562 g/l Calcium pantothenate 9.87167e-05 g/l MnCl2 x 4 H2O 9.87167e-05 g/l Vitamin B12 9.87167e-05 g/l p-Aminobenzoic acid 7.89733e-05 g/l ZnCl2 6.91017e-05 g/l Na2MoO4 x 2 H2O 3.5538e-05 g/l NiCl2 x 6 H2O 2.3692e-05 g/l D-(+)-biotin 1.97433e-05 g/l H3BO3 5.923e-06 g/l CuCl2 x 2 H2O 1.97433e-06 g/l Distilled water
culture temp
- @ref: 1242
- growth: positive
- type: growth
- temperature: 35
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1242 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.749
Isolation, sampling and environmental information
isolation
- @ref: 1242
- sample type: mesophilic digester fed with waste water from starch industry
- country: France
- origin.country: FRA
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Biodegradation | |
| #Engineered | #Waste | #Industrial wastewater |
taxonmaps
- @ref: 69479
- File name: preview.99_12667.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15357;96_6475;97_7764;98_9547;99_12667&stattab=map
- Last taxonomy: Geobacter sp.
- 16S sequence: LT626261
- Sequence Identity:
- Total samples: 850
- soil counts: 120
- aquatic counts: 685
- animal counts: 20
- plant counts: 25
Sequence information
16S sequences
- @ref: 1242
- description: Geobacter sp. partial 16S rRNA gene, strain DSM 2909
- accession: LT626261
- length: 1528
- database: ena
- NCBI tax ID: 46610
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geobacter sp. DSM 2909 | 2135459.3 | wgs | patric | 2135459 |
| 66792 | Geobacter sp. DSM 2909 | 2754412939 | draft | img | 2135459 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 81 | no |
| motile | yes | 77.747 | no |
| gram-positive | no | 98.5 | no |
| anaerobic | yes | 99.391 | no |
| aerobic | no | 97.007 | no |
| halophile | no | 92.494 | no |
| spore-forming | no | 91.466 | no |
| glucose-util | no | 50 | no |
| flagellated | no | 83.098 | no |
| thermophile | no | 97.061 | yes |
| glucose-ferment | no | 80.351 | no |
External links
@ref: 1242
culture collection no.: DSM 2909
straininfo link
- @ref: 75272
- straininfo: 47670
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1242 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2909) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2909 | |||
| 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 | |||
| 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 | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 75272 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47670.1 | StrainInfo: A central database for resolving microbial strain identifiers |