Strain identifier
BacDive ID: 16713
Type strain: 
Species: Oceanithermus desulfurans
Strain Designation: St55B
Strain history: <- K. Mori, Natl. Inst. of Technol. and Evaluation (NITE), Japan; St55B
NCBI tax ID(s): 1227550 (strain), 227924 (species)
version 8.1 (current version)
General
@ref: 6101
BacDive-ID: 16713
DSM-Number: 15757
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Oceanithermus desulfurans St55B is a thermophilic, Gram-negative bacterium that was isolated from chimney in the Suiyo Seamount in the Izu-Bonin Arc .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1227550 | strain |
| 227924 | species |
strain history
- @ref: 6101
- history: <- K. Mori, Natl. Inst. of Technol. and Evaluation (NITE), Japan; St55B
doi: 10.13145/bacdive16713.20230509.8.1
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 desulfurans
- full scientific name: Oceanithermus desulfurans Mori et al. 2004
@ref: 6101
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Thermales
family: Thermaceae
genus: Oceanithermus
species: Oceanithermus desulfurans
full scientific name: Oceanithermus desulfurans Mori et al. 2004
strain designation: St55B
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.681
Culture and growth conditions
culture medium
- @ref: 6101
- name: OCEANITHERMUS MEDIUM (DSMZ Medium 1149)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1149
- composition: Name: OCEANITHERMUS MEDIUM (DSMZ Medium 1149) Composition: NaCl 20.0 g/l Yeast extract 2.0 g/l NaNO3 1.7 g/l K2HPO4 0.78 g/l KH2PO4 0.75 g/l NH4Cl 0.53 g/l MgCl2 x 6 H2O 0.36 g/l Na2SO4 0.14 g/l Nitrilotriacetic acid 0.128 g/l CaCl2 x 2 H2O 0.1 g/l FeCl3 x 6 H2O 0.0135 g/l NiCl2 x 6 H2O 0.0012 g/l MnCl2 x 4 H2O 0.001 g/l ZnCl2 0.001 g/l Na2SeO3 x 5 H2O 0.00026 g/l CuCl2 x 2 H2O 0.00025 g/l Na2MoO4 x 2 H2O 0.00024 g/l CoCl2 x 6 H2O 0.00024 g/l H3BO3 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l D-Calcium pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Riboflavin 5e-05 g/l Lipoic acid 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 6101 | positive | growth | 60 | thermophilic | |
| 69480 | thermophilic | 99.178 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 96 |
| 69480 | no | 99.858 |
Isolation, sampling and environmental information
isolation
- @ref: 6101
- sample type: chimney in the Suiyo Seamount (at a depth of 1390 m) in the Izu-Bonin Arc (28° 34' N 140° 39' E)
- geographic location: Western Pacific
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Hydrothermal vent
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: AB107956
- Sequence Identity:
- Total samples: 237
- soil counts: 55
- aquatic counts: 157
- animal counts: 25
Safety information
risk assessment
- @ref: 6101
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6101
- description: Oceanithermus desulfurans gene for 16S rRNA, partial sequence
- accession: AB107956
- length: 1383
- database: ena
- NCBI tax ID: 1227550
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Oceanithermus desulfurans NBRC 100063 | GCA_007991015 | contig | ncbi | 1227550 |
| 66792 | Oceanithermus desulfurans DSM 15757 | GCA_014201675 | contig | ncbi | 227924 |
| 66792 | Oceanithermus desulfurans NBRC 100063 | 1227550.3 | wgs | patric | 1227550 |
| 66792 | Oceanithermus desulfurans strain DSM 15757 | 227924.3 | wgs | patric | 227924 |
| 66792 | Oceanithermus desulfurans DSM 15757 | 2861248673 | draft | img | 227924 |
GC content
- @ref: 6101
- GC-content: 71.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 96 | no |
| motile | no | 84.242 | no |
| gram-positive | no | 93.104 | no |
| anaerobic | no | 84.124 | no |
| aerobic | no | 80.136 | no |
| halophile | no | 83.79 | no |
| spore-forming | no | 93.289 | no |
| thermophile | yes | 99.539 | no |
| glucose-util | yes | 80.718 | no |
| flagellated | no | 97.618 | no |
| glucose-ferment | no | 83.568 | no |
External links
@ref: 6101
culture collection no.: DSM 15757, NBRC 100063
straininfo link
- @ref: 85732
- straininfo: 134302
literature
- topic: Phylogeny
- Pubmed-ID: 15388711
- title: Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount.
- authors: Mori K, Kakegawa T, Higashi Y, Nakamura KI, Maruyama A, Hanada S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02962-0
- year: 2004
- mesh: Aerobiosis, Bacterial Typing Techniques, Base Composition, Culture Media/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gram-Negative Bacteria/*classification/cytology/*isolation & purification/metabolism, *Hot Temperature, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Nucleic Acid Hybridization, Oxidation-Reduction, Oxygen/metabolism, Pacific Ocean, Peptones/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfides, Sulfur/*metabolism, Temperature, Water Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6101 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15757) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15757 | |
| 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 | |
| 85732 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134302.1 | StrainInfo: A central database for resolving microbial strain identifiers |