Strain identifier
BacDive ID: 16894
Type strain:
Species: Thermodesulfobacterium hydrogeniphilum
Strain Designation: SL6
Strain history: <- C. Jeanthon, Centre National de la Recherche Scientifique, and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Plouzané, France; SL6 <- S. L'Haridon {1998}
NCBI tax ID(s): 161156 (species)
General
@ref: 5301
BacDive-ID: 16894
DSM-Number: 14290
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile
description: Thermodesulfobacterium hydrogeniphilum SL6 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from deep-sea hydrothermal vent sulfides, 2000 m depth.
NCBI tax id
- NCBI tax id: 161156
- Matching level: species
strain history
- @ref: 5301
- history: <- C. Jeanthon, Centre National de la Recherche Scientifique, and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Plouzané, France; SL6 <- S. L'Haridon {1998}
doi: 10.13145/bacdive16894.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/thermodesulfobacteriota
- domain: Bacteria
- phylum: Thermodesulfobacteriota
- class: Thermodesulfobacteria
- order: Thermodesulfobacteriales
- family: Thermodesulfobacteriaceae
- genus: Thermodesulfobacterium
- species: Thermodesulfobacterium hydrogeniphilum
- full scientific name: Thermodesulfobacterium hydrogeniphilum Jeanthon et al. 2002
@ref: 5301
domain: Bacteria
phylum: Thermodesulfobacteria
class: Thermodesulfobacteria
order: Thermodesulfobacteriales
family: Thermodesulfobacteriaceae
genus: Thermodesulfobacterium
species: Thermodesulfobacterium hydrogeniphilum
full scientific name: Thermodesulfobacterium hydrogeniphilum Jeanthon et al. 2002
strain designation: SL6
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 92.641 | |
69480 | 99.979 | negative |
Culture and growth conditions
culture medium
- @ref: 5301
- name: THERMODESULFOBACTERIUM HYDROGENIPHILUM MEDIUM (DSMZ Medium 829b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/829b
- composition: Name: THERMODESULFOBACTERIUM HYDROGENIPHILUM MEDIUM (DSMZ Medium 829b) Composition: Sea Salt 29.8507 g/l MES [2-(N-morpholino) ethane sulfonic acid] 1.9403 g/l NH4Cl 0.995025 g/l Na2CO3 0.497512 g/l Yeast extract 0.497512 g/l KH2PO4 0.348259 g/l Na2S2O4 0.0497512 g/l NaHCO3 0.0497512 g/l Succinic acid 0.00597015 g/l 3-Methylbutyric acid 0.00497512 g/l Valeric acid 0.00497512 g/l Isobutyric acid 0.00497512 g/l 2-Methylbutyric acid 0.00497512 g/l HCl 0.00248756 g/l Caproic acid 0.00199005 g/l FeCl2 x 4 H2O 0.00149254 g/l NaOH 0.000497512 g/l Sodium resazurin 0.000497512 g/l Pyridoxine hydrochloride 0.000298507 g/l Nicotinic acid 0.000199005 g/l Thiamine-HCl x 2 H2O 0.000199005 g/l CoCl2 x 6 H2O 0.000189055 g/l MnCl2 x 4 H2O 9.95025e-05 g/l Calcium pantothenate 9.95025e-05 g/l Vitamin B12 9.95025e-05 g/l p-Aminobenzoic acid 7.9602e-05 g/l ZnCl2 6.96517e-05 g/l Na2MoO4 x 2 H2O 3.58209e-05 g/l NiCl2 x 6 H2O 2.38806e-05 g/l D-(+)-biotin 1.99005e-05 g/l H3BO3 5.97015e-06 g/l Na2WO4 x 2 H2O 3.9801e-06 g/l Na2SeO3 x 5 H2O 2.98507e-06 g/l CuCl2 x 2 H2O 1.99005e-06 g/l Distilled water
culture temp
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
5301 | positive | growth | 70 | thermophilic | |
69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
5301 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | no | 99.922 |
Isolation, sampling and environmental information
isolation
- @ref: 5301
- sample type: deep-sea hydrothermal vent sulfides, 2000 m depth
- geographic location: Guaymas Basin hydrothermal vent field
- country: Mexico
- origin.country: MEX
- continent: North America
- latitude: 27.0167
- longitude: -111.4
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Hydrothermal vent |
#Environmental | #Aquatic | #Marine |
#Condition | #Sulfuric | |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_6135.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_515;96_2920;97_3595;98_4550;99_6135&stattab=map
- Last taxonomy: Thermodesulfobacterium hydrogeniphilum subclade
- 16S sequence: AF332514
- Sequence Identity:
- Total samples: 60
- soil counts: 1
- aquatic counts: 58
- animal counts: 1
Safety information
risk assessment
- @ref: 5301
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5301
- description: Thermodesulfobacterium hydrogeniphilum 16S ribosomal RNA gene, partial sequence
- accession: AF332514
- length: 1497
- database: ena
- NCBI tax ID: 161156
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thermodesulfobacterium hydrogeniphilum DSM 14290 | GCA_000746255 | scaffold | ncbi | 161156 |
66792 | Thermodesulfobacterium hydrogeniphilum strain DSM 14290 | 161156.3 | wgs | patric | 161156 |
66792 | Thermodesulfobacterium hydrogeniphilum DSM 14290 | 2579779159 | draft | img | 161156 |
GC content
- @ref: 5301
- GC-content: 28
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 87.095 | no |
flagellated | no | 93.922 | no |
gram-positive | no | 99.585 | no |
anaerobic | yes | 99.999 | yes |
aerobic | no | 99.481 | yes |
halophile | no | 87.753 | no |
spore-forming | no | 96.111 | no |
glucose-util | no | 65.801 | no |
thermophile | yes | 100 | no |
glucose-ferment | no | 85.661 | no |
External links
@ref: 5301
culture collection no.: DSM 14290, JCM 11239
straininfo link
- @ref: 85900
- straininfo: 101010
literature
- topic: Phylogeny
- Pubmed-ID: 12054236
- title: Thermodesulfobacterium hydrogeniphilum sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a deep-sea hydrothermal vent at Guaymas Basin, and emendation of the genus Thermodesulfobacterium.
- authors: Jeanthon C, L'Haridon S, Cueff V, Banta A, Reysenbach AL, Prieur D
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-52-3-765
- year: 2002
- mesh: Bacterial Typing Techniques, Base Composition, Culture Media, DNA, Ribosomal/analysis, *Hot Temperature, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/*genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfates/metabolism, Sulfur-Reducing Bacteria/*classification/genetics/*growth & development/isolation & purification
- topic2: Cultivation
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5301 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14290) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14290 | |
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) | |
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 | |
85900 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID101010.1 | StrainInfo: A central database for resolving microbial strain identifiers |