Strain identifier
BacDive ID: 11850
Type strain: 
Species: Tepidibacter thalassicus
Strain history: <- A. Slobodkin, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; SC562 <- A. Slobodkin {2000}
NCBI tax ID(s): 1123350 (strain), 214905 (species)
version 8.1 (current version)
General
@ref: 5826
BacDive-ID: 11850
DSM-Number: 15285
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-positive
description: Tepidibacter thalassicus DSM 15285 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from deep-sea hydrothermal vent chimney, depth 2650 m.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 214905 | species |
| 1123350 | strain |
strain history
- @ref: 5826
- history: <- A. Slobodkin, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; SC562 <- A. Slobodkin {2000}
doi: 10.13145/bacdive11850.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Peptostreptococcaceae
- genus: Tepidibacter
- species: Tepidibacter thalassicus
- full scientific name: Tepidibacter thalassicus Slobodkin et al. 2003
@ref: 5826
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptostreptococcaceae
genus: Tepidibacter
species: Tepidibacter thalassicus
full scientific name: Tepidibacter thalassicus Slobodkin et al. 2003
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 5826
- name: ANAEROBIC SEAWATER (SWM) MEDIUM (DSMZ Medium 504)
- growth: yes
- link: https://mediadive.dsmz.de/medium/504
- composition: Name: ANAEROBIC SEAWATER (SWM) MEDIUM (DSMZ Medium 504; with strain-specific modifications) Composition: NaCl 19.9402 g/l Proteose peptone 9.97009 g/l MgCl2 x 6 H2O 2.99102 g/l D-Glucose 1.99402 g/l Na2CO3 1.49551 g/l KCl 0.498505 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 MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l Calcium pantothenate 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 | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 5826 | positive | growth | 50 | thermophilic | |
| 69480 | thermophilic | 95.907 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5826 | anaerobe | |
| 69480 | anaerobe | 99.398 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 5826
- sample type: deep-sea hydrothermal vent chimney, depth 2650 m
- geographic location: East Pacific Rise
- latitude: 12.8333
- longitude: -103.933
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_25702.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2;96_12877;97_15626;98_19336;99_25702&stattab=map
- Last taxonomy: Tepidibacter thalassicus subclade
- 16S sequence: AY158079
- Sequence Identity:
- Total samples: 15
- aquatic counts: 15
Safety information
risk assessment
- @ref: 5826
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5826
- description: Tepidibacter thalassicus 16S ribosomal RNA gene, partial sequence
- accession: AY158079
- length: 1404
- database: ena
- NCBI tax ID: 214905
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Tepidibacter thalassicus DSM 15285 | GCA_900129915 | scaffold | ncbi | 1123350 |
| 66792 | Tepidibacter thalassicus DSM 15285 | 1123350.4 | wgs | patric | 1123350 |
| 66792 | Tepidibacter thalassicus DSM 15285 | 2585428065 | draft | img | 1123350 |
GC content
- @ref: 5826
- GC-content: 24
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 90.183 | no |
| flagellated | no | 81.564 | no |
| gram-positive | yes | 66.563 | no |
| anaerobic | yes | 99.506 | yes |
| aerobic | no | 98.093 | yes |
| halophile | no | 83.023 | no |
| spore-forming | yes | 89.345 | no |
| thermophile | yes | 97.29 | yes |
| glucose-util | yes | 85.316 | no |
| glucose-ferment | yes | 63.335 | no |
External links
@ref: 5826
culture collection no.: DSM 15285, UNIQEM 215, SC 562
straininfo link
- @ref: 81068
- straininfo: 113588
literature
- topic: Phylogeny
- Pubmed-ID: 12892139
- title: Tepidibacter thalassicus gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, fermentative bacterium from a deep-sea hydrothermal vent.
- authors: Slobodkin AI, Tourova TP, Kostrikina NA, Chernyh NA, Bonch-Osmolovskaya EA, Jeanthon C, Jones BE
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02600-0
- year: 2003
- mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fermentation, Gram-Positive Endospore-Forming Rods/*classification/genetics/*isolation & purification/metabolism, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Water Microbiology
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5826 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15285) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15285 | |||
| 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 | |||
| 81068 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID113588.1 | StrainInfo: A central database for resolving microbial strain identifiers |