Strain identifier
BacDive ID: 16712
Type strain: 
Species: Oceanithermus profundus
Strain Designation: 506
Strain history: <- M. L. Miroshnichenko; 506
NCBI tax ID(s): 670487 (strain), 187137 (species)
version 8.1 (current version)
General
@ref: 5648
BacDive-ID: 16712
DSM-Number: 14977
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, thermophilic, Gram-negative
description: Oceanithermus profundus 506 is a microaerophile, thermophilic, Gram-negative bacterium that was isolated from deep-sea hot vent.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 670487 | strain |
| 187137 | species |
strain history
- @ref: 5648
- history: <- M. L. Miroshnichenko; 506
doi: 10.13145/bacdive16712.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deinococcota
- domain: Bacteria
- phylum: Deinococcota
- class: Deinococci
- order: Thermales
- family: Thermaceae
- genus: Oceanithermus
- species: Oceanithermus profundus
- full scientific name: Oceanithermus profundus Miroshnichenko et al. 2003
@ref: 5648
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Thermales
family: Thermaceae
genus: Oceanithermus
species: Oceanithermus profundus
full scientific name: Oceanithermus profundus Miroshnichenko et al. 2003
strain designation: 506
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.806
multimedia
- @ref: 66793
- multimedia content: EM_DSM_14977_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 5648
- name: OCEANITHERMUS PROFUNDUS MEDIUM (DSMZ Medium 975)
- growth: yes
- link: https://mediadive.dsmz.de/medium/975
- composition: Name: OCEANITHERMUS PROFUNDUS MEDIUM (DSMZ Medium 975) Composition: HEPES 2.38 g/l Sucrose 2.0 g/l KNO3 1.0 g/l Tryptone 1.0 g/l NH4Cl 0.33 g/l KCl 0.33 g/l MgCl2 x 6 H2O 0.33 g/l Yeast extract 0.2 g/l MgSO4 x 7 H2O 0.003 g/l Nitrilotriacetic acid 0.0015 g/l NaCl 0.001 g/l MnSO4 x H2O 0.0005 g/l ZnSO4 x 7 H2O 0.00018 g/l CoSO4 x 7 H2O 0.00018 g/l CaCl2 x 2 H2O 0.0001 g/l FeSO4 x 7 H2O 0.0001 g/l NiCl2 x 6 H2O 3e-05 g/l AlK(SO4)2 x 12 H2O 2e-05 g/l CuSO4 x 5 H2O 1e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l Pyridoxine hydrochloride 1e-05 g/l H3BO3 1e-05 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine HCl 5e-06 g/l (DL)-alpha-Lipoic acid 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l Calcium D-(+)-pantothenate 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l Na2WO4 x 2 H2O 4e-07 g/l Na2SeO3 x 5 H2O 3e-07 g/l Vitamin B12 1e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 5648 | positive | growth | 60 | thermophilic | |
| 69480 | thermophilic | 99.137 |
Physiology and metabolism
oxygen tolerance
- @ref: 5648
- oxygen tolerance: microaerophile
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 99.92 |
Isolation, sampling and environmental information
isolation
- @ref: 5648
- sample type: deep-sea hot vent
- geographic location: 13°N, East Pacific Rise
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_5526.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16852;96_2671;97_3278;98_4125;99_5526&stattab=map
- Last taxonomy: Oceanithermus
- 16S sequence: AJ430586
- Sequence Identity:
- Total samples: 237
- soil counts: 55
- aquatic counts: 157
- animal counts: 25
Safety information
risk assessment
- @ref: 5648
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5648
- description: Oceanothermus profundus 16S rRNA gene, type strain DSM 14977T
- accession: AJ430586
- length: 1498
- database: ena
- NCBI tax ID: 670487
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Oceanithermus profundus DSM 14977 | GCA_000183745 | complete | ncbi | 670487 |
| 66792 | Oceanithermus profundus DSM 14977 | 670487.13 | plasmid | patric | 670487 |
| 66792 | Oceanithermus profundus DSM 14977 | 670487.3 | complete | patric | 670487 |
| 66792 | Oceanithermus profundus 506, DSM 14977 | 649633077 | complete | img | 670487 |
GC content
- @ref: 5648
- GC-content: 45.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 86.06 | no |
| flagellated | no | 97.667 | no |
| gram-positive | no | 92.152 | no |
| anaerobic | no | 88.59 | no |
| aerobic | no | 80.11 | yes |
| halophile | no | 85.477 | no |
| spore-forming | no | 94.305 | no |
| thermophile | yes | 99.492 | no |
| glucose-util | yes | 81.65 | no |
| glucose-ferment | no | 85.381 | no |
External links
@ref: 5648
culture collection no.: DSM 14977
straininfo link
- @ref: 85731
- straininfo: 100113
literature
- topic: Phylogeny
- Pubmed-ID: 12807196
- title: Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent.
- authors: Miroshnichenko ML, L'Haridon S, Jeanthon C, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02367-0
- year: 2003
- mesh: Bacterial Typing Techniques, Base Composition, Culture Media, DNA, Ribosomal, Gram-Negative Bacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNA, Temperature
- topic2: Cultivation
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5648 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14977) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14977 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |||
| 85731 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100113.1 | StrainInfo: A central database for resolving microbial strain identifiers |