Strain identifier
BacDive ID: 140262
Type strain: 
Species: Thermodesulfobium acidiphilum
Strain Designation: 3127-1
Strain history: <- E. Frolov, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; 3127-1
NCBI tax ID(s): 1794699 (species)
version 8.1 (current version)
General
@ref: 42869
BacDive-ID: 140262
DSM-Number: 102892
keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, chemolithoautotroph, thermophilic, motile, rod-shaped
description: Thermodesulfobium acidiphilum 3127-1 is an obligate anaerobe, chemolithoautotroph, thermophilic bacterium that was isolated from geothermally heated soil.
NCBI tax id
- NCBI tax id: 1794699
- Matching level: species
strain history
- @ref: 42869
- history: <- E. Frolov, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; 3127-1
doi: 10.13145/bacdive140262.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Thermoanaerobacterales
- family: Thermodesulfobiaceae
- genus: Thermodesulfobium
- species: Thermodesulfobium acidiphilum
- full scientific name: Thermodesulfobium acidiphilum Frolov et al. 2017
@ref: 42869
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Thermoanaerobacterales
family: Thermodesulfobiaceae
genus: Thermodesulfobium
species: Thermodesulfobium acidiphilum
full scientific name: Thermodesulfobium acidiphilum Frolov et al. 2017
strain designation: 3127-1
type strain: yes
Morphology
cell morphology
| @ref | cell length | cell width | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|---|---|
| 43216 | 1-5 µm | 0.5 µm | rod-shaped | yes | ||
| 43216 | no | |||||
| 69480 | negative | 99.807 |
Culture and growth conditions
culture medium
- @ref: 42869
- name: THERMODESULFOBIUM ACIDIPHILUM MEDIUM (DSMZ Medium 901a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/901a
- composition: Name: THERMODESULFOBIUM ACIDIPHILUM MEDIUM (DSMZ Medium 901a) Composition: Yeast extract 2.94985 g/l Na2SO4 2.7532 g/l Na2S x 9 H2O 0.442478 g/l KCl 0.324484 g/l KH2PO4 0.324484 g/l MgCl2 x 6 H2O 0.324484 g/l CaCl2 x 2 H2O 0.324484 g/l NH4Cl 0.324484 g/l HCl 0.00245821 g/l FeCl2 x 4 H2O 0.00147493 g/l Sodium resazurin 0.000491642 g/l CoCl2 x 6 H2O 0.000186824 g/l Pyridoxine hydrochloride 9.83284e-05 g/l MnCl2 x 4 H2O 9.83284e-05 g/l ZnCl2 6.88299e-05 g/l Nicotinic acid 4.91642e-05 g/l Calcium D-(+)-pantothenate 4.91642e-05 g/l Thiamine HCl 4.91642e-05 g/l p-Aminobenzoic acid 4.91642e-05 g/l (DL)-alpha-Lipoic acid 4.91642e-05 g/l Riboflavin 4.91642e-05 g/l Na2MoO4 x 2 H2O 3.53982e-05 g/l NiCl2 x 6 H2O 2.35988e-05 g/l Biotin 1.96657e-05 g/l Folic acid 1.96657e-05 g/l H3BO3 5.89971e-06 g/l CuCl2 x 2 H2O 1.96657e-06 g/l Vitamin B12 9.83284e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 43216 | positive | optimum | 54 | thermophilic | |
| 43216 | positive | growth | 37-65 | ||
| 69480 | thermophilic | 99.431 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 43216 | positive | growth | 3.7-6.5 | acidophile |
| 43216 | positive | optimum | 4.8-5.0 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 43216 | obligate anaerobe | |
| 69480 | anaerobe | 99.035 |
nutrition type
- @ref: 43216
- type: chemolithoautotroph
spore formation
| @ref | type of spore | spore formation | confidence |
|---|---|---|---|
| 43216 | spore | no | |
| 69481 | no | 100 | |
| 69480 | no | 99.964 |
halophily
- @ref: 43216
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 1 %(w/v)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43216 | 16189 | sulfate | + | electron acceptor |
| 43216 | 16094 | thiosulfate | + | electron acceptor |
| 43216 | 17359 | sulfite | - | electron acceptor |
| 43216 | 33403 | elemental sulfur | - | electron acceptor |
| 43216 | 29806 | fumarate | - | electron acceptor |
| 43216 | 17632 | nitrate | - | electron acceptor |
| 43216 | 16301 | nitrite | - | electron acceptor |
| 43216 | 15379 | dioxygen | - | electron acceptor |
| 43216 | yeast extract | - | growth | |
| 43216 | peptone | - | growth | |
| 43216 | 17234 | glucose | - | growth |
| 43216 | 17716 | lactose | - | growth |
| 43216 | 17306 | maltose | - | growth |
| 43216 | 17992 | sucrose | - | growth |
| 43216 | 30089 | acetate | - | growth |
| 43216 | 24996 | lactate | - | growth |
| 43216 | 15361 | pyruvate | - | growth |
| 43216 | 25115 | malate | - | growth |
| 43216 | 17272 | propionate | - | growth |
| 43216 | 17968 | butyrate | - | growth |
| 43216 | 29806 | fumarate | - | growth |
| 43216 | 143136 | succinamate | - | growth |
| 43216 | 16947 | citrate | - | growth |
| 43216 | 16236 | ethanol | - | growth |
| 43216 | 28831 | propanol | - | growth |
| 43216 | 17754 | glycerol | - | growth |
| 43216 | 17790 | methanol | - | growth |
| 43216 | 17245 | carbon monoxide | - | growth |
| 43216 | 15740 | formate | + | electron donor |
| 43216 | 18276 | dihydrogen | + | electron donor |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | sampling date |
|---|---|---|---|---|---|---|---|---|
| 42869 | geothermally heated soil | Kamchatka, Kronotsky Nature Reserve, Uzon Caldera, Oil Site (elevation 654 m) | Russia | RUS | Europe | 54.5004 | 160.001 | |
| 43216 | geothermally heated soil sampled at the Oil Site | Oil Site, Uzon Caldera, Kronotsky Nature Reserve, Kamchatka, Russia | Russia | RUS | Asia | 54 | 160 | 2014-08 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Thermophilic (>45°C) | |
| #Environmental | #Aquatic |
taxonmaps
- @ref: 69479
- File name: preview.99_152959.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_697;96_3767;97_4637;98_5953;99_152959&stattab=map
- Last taxonomy: Thermodesulfobium acidiphilum
- 16S sequence: KU664659
- Sequence Identity:
- Total samples: 109
- aquatic counts: 100
- animal counts: 8
- plant counts: 1
Safety information
risk assessment
- @ref: 42869
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 42869
- description: Thermodesulfobium acidiphilum strain 3127-1 16S ribosomal RNA gene, partial sequence
- accession: KU664659
- length: 1544
- database: ena
- NCBI tax ID: 1794699
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermodesulfobium acidiphilum 3127-1 | GCA_003057965 | complete | ncbi | 1794699 |
| 66792 | Thermodesulfobium acidiphilum strain 3127-1 | 1794699.3 | complete | patric | 1794699 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 43216 | 33.7 | |
| 42869 | 33.7 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 91.883 | no |
| gram-positive | no | 97.577 | no |
| anaerobic | yes | 99.231 | yes |
| halophile | no | 93.062 | yes |
| spore-forming | no | 94.561 | no |
| glucose-util | no | 67.2 | yes |
| aerobic | no | 98.6 | no |
| thermophile | yes | 99.642 | yes |
| motile | yes | 83.69 | no |
| glucose-ferment | no | 71.983 | no |
External links
@ref: 42869
culture collection no.: DSM 102892, VKM B-3043
straininfo link
- @ref: 96568
- straininfo: 398408
literature
- topic: Phylogeny
- Pubmed-ID: 27995866
- title: Thermodesulfobium acidiphilum sp. nov., a thermoacidophilic, sulfate-reducing, chemoautotrophic bacterium from a thermal site.
- authors: Frolov EN, Kublanov IV, Toshchakov SV, Samarov NI, Novikov AA, Lebedinsky AV, Bonch-Osmolovskaya EA, Chernyh NA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001745
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Firmicutes/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Nucleic Acid Hybridization, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, *Soil Microbiology
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 42869 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102892 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102892) | |||
| 43216 | Evgenii N. Frolov, Ilya V. Kublanov, Stepan V. Toshchakov, Nazar I. Samarov, Andrei A. Novikov, Alexander V. Lebedinsky, Elizaveta A. Bonch-Osmolovskaya and Nikolai A. Chernyh | Thermodesulfobium acidiphilum sp. nov., a thermoacidophilic, sulfate-reducing, chemoautotrophic bacterium from a thermal site | 10.1099/ijsem.0.001745 | IJSEM 67: 1482-1485 2017 | 27995866 | |
| 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 | |||
| 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/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 96568 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID398408.1 |