Strain identifier
BacDive ID: 17067
Type strain: 
Species: Pseudothermotoga hypogea
Strain history: <- M. L. Fardeau, Université de Provence, Marseille, France; SEBR 7054 <- M. L. Fardeau {1995}
NCBI tax ID(s): 1123384 (strain), 57487 (species)
version 8.1 (current version)
General
@ref: 4223
BacDive-ID: 17067
DSM-Number: 11164
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative
description: Pseudothermotoga hypogea DSM 11164 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from oil-producing well.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123384 | strain |
| 57487 | species |
strain history
- @ref: 4223
- history: <- M. L. Fardeau, Université de Provence, Marseille, France; SEBR 7054 <- M. L. Fardeau {1995}
doi: 10.13145/bacdive17067.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/thermotogota
- domain: Bacteria
- phylum: Thermotogota
- class: Thermotogae
- order: Thermotogales
- family: Thermotogaceae
- genus: Pseudothermotoga
- species: Pseudothermotoga hypogea
- full scientific name: Pseudothermotoga hypogea (Fardeau et al. 1997) Bhandari and Gupta 2017
synonyms
@ref synonym 20215 Pseudothermotoga hypogea 20215 Thermotoga hypogea
@ref: 4223
domain: Bacteria
phylum: Thermotogae
class: Thermotogae
order: Thermotogales
family: Thermotogaceae
genus: Pseudothermotoga
species: Pseudothermotoga hypogea
full scientific name: Pseudothermotoga hypogea (Fardeau et al. 1997) Bhandari and Gupta 2017
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.92
Culture and growth conditions
culture medium
- @ref: 4223
- name: THERMOTOGA HYPOGEA MEDIUM (DSMZ Medium 794)
- growth: yes
- link: https://mediadive.dsmz.de/medium/794
- composition: Name: PSEUDOTHERMOTOGA HYPOGEA MEDIUM (DSMZ Medium 794) Composition: Na2S2O3 x 5 H2O 4.9505 g/l D-Xylose 2.9703 g/l NaHCO3 1.9802 g/l Yeast extract 1.9802 g/l Trypticase peptone 1.9802 g/l NH4Cl 0.990099 g/l Na-acetate 0.49505 g/l Na2S x 9 H2O 0.49505 g/l L-Cysteine HCl x H2O 0.49505 g/l K2HPO4 0.29703 g/l KH2PO4 0.29703 g/l MgCl2 x 6 H2O 0.19802 g/l KCl 0.0990099 g/l MgSO4 x 7 H2O 0.029703 g/l Nitrilotriacetic acid 0.0148515 g/l NaCl 0.00990099 g/l MnSO4 x H2O 0.00495049 g/l CoSO4 x 7 H2O 0.00178218 g/l ZnSO4 x 7 H2O 0.00178218 g/l FeSO4 x 7 H2O 0.000990099 g/l CaCl2 x 2 H2O 0.000990099 g/l Sodium resazurin 0.00049505 g/l NiCl2 x 6 H2O 0.00029703 g/l AlK(SO4)2 x 12 H2O 0.00019802 g/l CuSO4 x 5 H2O 9.90099e-05 g/l H3BO3 9.90099e-05 g/l Na2MoO4 x 2 H2O 9.90099e-05 g/l Na2WO4 x 2 H2O 3.9604e-06 g/l Na2SeO3 x 5 H2O 2.9703e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 4223 | positive | growth | 70 | thermophilic | |
| 69480 | thermophilic | 99.615 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4223 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 98 |
| 69480 | no | 99.919 |
Isolation, sampling and environmental information
isolation
- @ref: 4223
- sample type: oil-producing well
- country: Cameroon
- origin.country: CMR
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Industrial | #Engineered product |
| #Engineered | #Industrial | #Oil reservoir |
taxonmaps
- @ref: 69479
- File name: preview.99_130222.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_177;96_585;97_684;98_87183;99_130222&stattab=map
- Last taxonomy: Pseudothermotoga
- 16S sequence: U89768
- Sequence Identity:
- Total samples: 5
- aquatic counts: 5
Safety information
risk assessment
- @ref: 4223
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4223
- description: Thermotoga hypogea 16S ribosomal RNA gene, partial sequence
- accession: U89768
- length: 1521
- database: ena
- NCBI tax ID: 57487
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudothermotoga hypogea DSM 11164 = NBRC 106472 | GCA_000504105 | complete | ncbi | 1123384 |
| 66792 | Pseudothermotoga hypogea DSM 11164 = NBRC 106472 | GCA_000816145 | complete | ncbi | 1123384 |
| 66792 | Pseudothermotoga hypogea DSM 11164 = NBRC 106472 | GCA_000711815 | scaffold | ncbi | 1123384 |
| 66792 | Pseudothermotoga hypogea DSM 11164 = NBRC 106472 | 1123384.7 | complete | patric | 1123384 |
| 66792 | Thermotoga hypogea DSM 11164 | 1123384.3 | wgs | patric | 1123384 |
| 66792 | Thermotoga hypogea NBRC 106472 | 1219084.8 | complete | patric | 1123384 |
| 66792 | Pseudothermotoga hypogea NBRC 106472 | 2558309119 | complete | img | 1123384 |
| 66792 | Pseudothermotoga hypogea DSM 11164 | 2565956526 | draft | img | 1123384 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| motile | yes | 82.44 | no |
| flagellated | no | 94.239 | no |
| gram-positive | no | 95.875 | no |
| anaerobic | yes | 99.342 | yes |
| halophile | no | 91.053 | no |
| spore-forming | no | 88.976 | no |
| thermophile | yes | 100 | yes |
| glucose-util | yes | 88.533 | no |
| aerobic | no | 97.616 | yes |
| glucose-ferment | no | 58.563 | no |
External links
@ref: 4223
culture collection no.: DSM 11164, NBRC 106472, SEBR 7054
straininfo link
- @ref: 86067
- straininfo: 49041
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 9336900 | Thermotoga hypogea sp. nov., a xylanolytic, thermophilic bacterium from an oil-producing well. | Fardeau ML, Ollivier B, Patel BK, Magot M, Thomas P, Rimbault A, Rocchiccioli F, Garcia JL | Int J Syst Bacteriol | 10.1099/00207713-47-4-1013 | 1997 | Base Composition, Culture Media, Conditioned, DNA, Bacterial/*analysis, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/*genetics/growth & development/physiology/ultrastructure, Microbial Sensitivity Tests, Microscopy, Electron, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis | Cultivation |
| Phylogeny | 24676729 | Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs. | Mori K, Yamazoe A, Hosoyama A, Ohji S, Fujita N, Ishibashi JI, Kimura H, Suzuki KI | Int J Syst Evol Microbiol | 10.1099/ijs.0.060137-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4223 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11164) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11164 | |||
| 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 | |||
| 86067 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49041.1 | StrainInfo: A central database for resolving microbial strain identifiers |