Strain identifier
BacDive ID: 10541
Type strain: 
Species: Thermodesulfovibrio thiophilus
Strain Designation: TDV
Strain history: Y. Sekiguchi TDV.
NCBI tax ID(s): 1123376 (strain), 340095 (species)
version 8.1 (current version)
General
@ref: 6819
BacDive-ID: 10541
DSM-Number: 17215
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, rod-shaped
description: Thermodesulfovibrio thiophilus TDV is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from thermophilic sewage sludge decomposing organic solid wastes.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123376 | strain |
| 340095 | species |
strain history
| @ref | history |
|---|---|
| 6819 | <- Y. Sekiguchi; TDV |
| 67770 | Y. Sekiguchi TDV. |
doi: 10.13145/bacdive10541.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/nitrospirota
- domain: Bacteria
- phylum: Nitrospirota
- class: Thermodesulfovibrionia
- order: Thermodesulfovibrionales
- family: Thermodesulfovibrionaceae
- genus: Thermodesulfovibrio
- species: Thermodesulfovibrio thiophilus
- full scientific name: Thermodesulfovibrio thiophilus Sekiguchi et al. 2008
@ref: 6819
domain: Bacteria
phylum: Nitrospirae
class: Nitrospira
order: Nitrospirales, not validated
family: Nitrospiraceae
genus: Thermodesulfovibrio
species: Thermodesulfovibrio thiophilus
full scientific name: Thermodesulfovibrio thiophilus Sekiguchi et al. 2008
strain designation: TDV
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31197 | negative | 02-03 µm | 0.3-0.4 µm | rod-shaped | no | |
| 69480 | negative | 99.997 |
pigmentation
- @ref: 31197
- production: yes
Culture and growth conditions
culture medium
- @ref: 6819
- name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)
- growth: yes
- link: https://mediadive.dsmz.de/medium/641
- composition: Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) Composition: Na-DL-lactate 2.49252 g/l Na2SO4 1.99402 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l Na2S2O3 x 5 H2O 0.997009 g/l KH2PO4 0.498504 g/l Na2S x 9 H2O 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 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 Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 6819 | positive | growth | 55 | thermophilic | |
| 31197 | positive | growth | 45-60 | thermophilic | |
| 31197 | positive | optimum | 55 | thermophilic | |
| 67770 | positive | growth | 55 | thermophilic | |
| 69480 | thermophilic | 99.6 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31197 | positive | growth | 6-8.5 | alkaliphile |
| 31197 | positive | optimum | 7-7.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6819 | anaerobe | |
| 31197 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31197 | no | |
| 69480 | no | 99.17 |
observation
- @ref: 31197
- observation: aggregates in chains
metabolite utilization
- @ref: 31197
- Chebi-ID: 30089
- metabolite: acetate
- utilization activity: +
- kind of utilization tested: carbon source
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 6819 | thermophilic sewage sludge decomposing organic solid wastes | Japan | JPN | Asia |
| 67770 | Thermophilic sewage sludge decomposing organic solid wastes |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Sewage sludge |
| #Engineered | #Waste | #Solid waste |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_3489.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_392;96_1815;97_2178;98_2672;99_3489&stattab=map
- Last taxonomy: Thermodesulfovibrio thiophilus subclade
- 16S sequence: AB231857
- Sequence Identity:
- Total samples: 995
- soil counts: 285
- aquatic counts: 481
- animal counts: 202
- plant counts: 27
Safety information
risk assessment
- @ref: 6819
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6819
- description: Thermodesulfovibrio thiophilus gene for 16S rRNA, partial sequence
- accession: AB231857
- length: 1490
- database: ena
- NCBI tax ID: 340095
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermodesulfovibrio thiophilus DSM 17215 | 1123376.3 | wgs | patric | 1123376 |
| 66792 | Thermodesulfovibrio thiophilus DSM 17215 | 2523533630 | draft | img | 1123376 |
| 67770 | Thermodesulfovibrio thiophilus DSM 17215 | GCA_000423865 | scaffold | ncbi | 1123376 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6819 | 34.0 | high performance liquid chromatography (HPLC) |
| 31197 | 34 | |
| 67770 | 34 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 87 | no |
| motile | yes | 80.95 | yes |
| flagellated | no | 91.767 | yes |
| gram-positive | no | 99.401 | no |
| anaerobic | yes | 99.005 | yes |
| aerobic | no | 98.248 | no |
| halophile | no | 88.106 | no |
| spore-forming | no | 91.373 | yes |
| thermophile | yes | 100 | yes |
| glucose-util | no | 57.49 | no |
| glucose-ferment | no | 86.684 | no |
External links
@ref: 6819
culture collection no.: DSM 17215, JCM 13216
straininfo link
- @ref: 79817
- straininfo: 397855
literature
- topic: Phylogeny
- Pubmed-ID: 18984690
- title: Thermodesulfovibrio aggregans sp. nov. and Thermodesulfovibrio thiophilus sp. nov., anaerobic, thermophilic, sulfate-reducing bacteria isolated from thermophilic methanogenic sludge, and emended description of the genus Thermodesulfovibrio.
- authors: Sekiguchi Y, Muramatsu M, Imachi H, Narihiro T, Ohashi A, Harada H, Hanada S, Kamagata Y
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.2008/000893-0
- year: 2008
- mesh: Anaerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, *Hot Temperature, In Situ Hybridization, Fluorescence, Methane/*metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sulfur-Reducing Bacteria/*classification/genetics/isolation & purification/physiology, Waste Disposal, Fluid/methods
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6819 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17215) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17215 | |||
| 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 | |||
| 31197 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27524 | 28776041 | |
| 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) | |||
| 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. | 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) | |||
| 79817 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397855.1 | StrainInfo: A central database for resolving microbial strain identifiers |