Strain identifier
BacDive ID: 17050
Type strain: 
Species: Petrotoga sibirica
Strain Designation: SL25
Strain history: S. L'Haridon SL25.
NCBI tax ID(s): 1122956 (strain), 156202 (species)
version 8.1 (current version)
General
@ref: 5091
BacDive-ID: 17050
DSM-Number: 13575
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative
description: Petrotoga sibirica SL25 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from oil/water mixtures from production well-heads of a deep, continental petroleum reservoir.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1122956 | strain |
| 156202 | species |
strain history
| @ref | history |
|---|---|
| 5091 | <- S. L'Haridon, Centre National de la Recherche Scientifique, and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Plouzané, France; SL25 <- S. L'Haridon {1998} |
| 67770 | S. L'Haridon SL25. |
doi: 10.13145/bacdive17050.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/thermotogota
- domain: Bacteria
- phylum: Thermotogota
- class: Thermotogae
- order: Petrotogales
- family: Petrotogaceae
- genus: Petrotoga
- species: Petrotoga sibirica
- full scientific name: Petrotoga sibirica L'Haridon et al. 2002
@ref: 5091
domain: Bacteria
phylum: Thermotogae
class: Thermotogae
order: Thermotogales
family: Petrotogaceae
genus: Petrotoga
species: Petrotoga sibirica
full scientific name: Petrotoga sibirica L'Haridon et al. 2002
strain designation: SL25
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.819
Culture and growth conditions
culture medium
- @ref: 5091
- name: PETROTOGA OLEARIA MEDIUM (DSMZ Medium 959)
- growth: yes
- link: https://mediadive.dsmz.de/medium/959
- composition: Name: PETROTOGA OLEARIA MEDIUM (DSMZ Medium 959) Composition: NaCl 15.0 g/l Maltose 3.5 g/l PIPES 3.4 g/l Na-acetate x 3 H2O 2.72 g/l Trypticase peptone 2.0 g/l Yeast extract 2.0 g/l NH4Cl 1.0 g/l Na2S x 9 H2O 0.5 g/l MgCl2 x 6 H2O 0.5 g/l K2HPO4 0.35 g/l KH2PO4 0.35 g/l KCl 0.2 g/l CaCl2 x 2 H2O 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 5091 | positive | growth | 55 | thermophilic | |
| 67770 | positive | growth | 55 | thermophilic | |
| 69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5091 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 99.982 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 5091 | oil/water mixtures from production well-heads of a deep, continental petroleum reservoir | Western Siberia | Russia | RUS | Asia |
| 67770 | Deep, continental oil reservoir | Western Siberia | Russia | RUS |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Industrial | #Oil reservoir |
| #Environmental | #Aquatic |
Safety information
risk assessment
- @ref: 5091
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 67770
- description: Petrotoga siberica 16S rRNA gene, strain SL25T
- accession: AJ311702
- length: 1482
- database: ena
- NCBI tax ID: 156202
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Petrotoga sibirica DSM 13575 | 1122956.3 | wgs | patric | 1122956 |
| 66792 | Petrotoga sibirica strain DSM 13575 | 156202.3 | wgs | patric | 156202 |
| 66792 | Petrotoga sibirica DSM 13575 | 2756170166 | draft | img | 156202 |
| 67770 | Petrotoga sibirica DSM 13575 | GCA_002924625 | contig | ncbi | 1122956 |
| 67770 | Petrotoga sibirica DSM 13575 | GCA_004366085 | scaffold | ncbi | 156202 |
GC content
- @ref: 5091
- GC-content: 33
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | yes | 74.959 | no |
| flagellated | no | 92.109 | no |
| gram-positive | no | 92.292 | no |
| anaerobic | yes | 99.238 | yes |
| aerobic | no | 98.199 | no |
| halophile | no | 88.783 | no |
| spore-forming | no | 88.209 | no |
| glucose-util | yes | 88.137 | no |
| thermophile | yes | 100 | yes |
| glucose-ferment | yes | 55.546 | no |
External links
@ref: 5091
culture collection no.: DSM 13575, JCM 11235
straininfo link
- @ref: 86050
- straininfo: 100862
literature
- topic: Phylogeny
- Pubmed-ID: 12361278
- title: Petrotoga olearia sp. nov. and Petrotoga sibirica sp. nov., two thermophilic bacteria isolated from a continental petroleum reservoir in Western Siberia.
- authors: L'Haridon S, Miroshnichenko ML, Hippe H, Fardeau ML, Bonch-Osmolovskaya EA, Stackebrandt E, Jeanthon C
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-52-5-1715
- year: 2002
- mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/*isolation & purification/metabolism, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, Petroleum/microbiology, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Siberia
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5091 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13575) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13575 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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 | |
| 86050 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100862.1 | StrainInfo: A central database for resolving microbial strain identifiers |