Strain identifier
BacDive ID: 3840
Type strain: 
Species: Geovibrio thiophilus
Strain Designation: AAFu3
Strain history: <- P. H. Janssen, University of Melbourne, Parkville, Australia; AAFu3 <- H. Platen {1989}
NCBI tax ID(s): 139438 (species)
version 8.1 (current version)
General
@ref: 4270
BacDive-ID: 3840
DSM-Number: 11263
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Geovibrio thiophilus AAFu3 is an anaerobe, mesophilic, motile bacterium that was isolated from methanogenic mixed culture growing with acetone.
NCBI tax id
- NCBI tax id: 139438
- Matching level: species
strain history
- @ref: 4270
- history: <- P. H. Janssen, University of Melbourne, Parkville, Australia; AAFu3 <- H. Platen {1989}
doi: 10.13145/bacdive3840.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deferribacterota
- domain: Bacteria
- phylum: Deferribacterota
- class: Deferribacteres
- order: Deferribacterales
- family: Geovibrionaceae
- genus: Geovibrio
- species: Geovibrio thiophilus
- full scientific name: Geovibrio thiophilus Janssen et al. 2002
@ref: 4270
domain: Bacteria
phylum: Deferribacteres
class: Deferribacteres
order: Deferribacterales
family: Deferribacteraceae
genus: Geovibrio
species: Geovibrio thiophilus
full scientific name: Geovibrio thiophilus Janssen et al. 2002
strain designation: AAFu3
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.602 | |
| 69480 | 99.999 | negative |
Culture and growth conditions
culture medium
- @ref: 4270
- name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)
- growth: yes
- link: https://mediadive.dsmz.de/medium/503
- composition: Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Sodium fumarate 3.19043 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l Na acetate 0.817547 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
culture temp
- @ref: 4270
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4270 | anaerobe | |
| 69480 | anaerobe | 99.998 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.973 |
Isolation, sampling and environmental information
isolation
- @ref: 4270
- sample type: methanogenic mixed culture growing with acetone
- geographic location: Konstanz, drainage ditch
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Laboratory | #Lab enrichment |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_153005.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_609;96_22160;97_27681;98_100974;99_153005&stattab=map
- Last taxonomy: Geovibrio thiophilus subclade
- 16S sequence: AJ299402
- Sequence Identity:
- Total samples: 22
- soil counts: 6
- aquatic counts: 14
- animal counts: 2
Safety information
risk assessment
- @ref: 4270
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4270
- description: Geovibrio thiophilus 16S rRNA gene
- accession: AJ299402
- length: 1474
- database: ena
- NCBI tax ID: 139438
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geovibrio thiophilus DSM 11263 | GCA_004087915 | complete | ncbi | 139438 |
| 66792 | Geovibrio thiophilus strain DSM 11263 | 139438.5 | complete | patric | 139438 |
| 66792 | Geovibrio thiophilus DSM 11263 | 2836696539 | complete | img | 139438 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 4270 | 50.2 | high performance liquid chromatography (HPLC) |
| 4270 | 48.2 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 92.884 | no |
| flagellated | no | 59.773 | no |
| gram-positive | no | 99.471 | no |
| anaerobic | yes | 99.163 | yes |
| aerobic | no | 97.988 | no |
| halophile | no | 91.657 | no |
| spore-forming | no | 94.348 | no |
| glucose-util | no | 68.021 | no |
| thermophile | no | 93.237 | yes |
| glucose-ferment | no | 85.727 | no |
External links
@ref: 4270
culture collection no.: DSM 11263, ATCC BAA 311
straininfo link
- @ref: 73350
- straininfo: 87758
literature
- topic: Phylogeny
- Pubmed-ID: 12148649
- title: Geovibrio thiophilus sp. nov., a novel sulfur-reducing bacterium belonging to the phylum Deferribacteres.
- authors: Janssen PH, Liesack W, Schink B
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-52-4-1341
- year: 2002
- mesh: Acetone/metabolism, Anaerobiosis, Bacterial Typing Techniques, DNA, Ribosomal, Gram-Negative Bacteria/*classification/growth & development/isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Sulfur-Reducing Bacteria/*classification/growth & development/isolation & purification/metabolism
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4270 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11263) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11263 | |||
| 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) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 73350 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87758.1 | StrainInfo: A central database for resolving microbial strain identifiers |