Strain identifier
BacDive ID: 132414
Type strain: 
Species: Inmirania thermothiophila
Strain Designation: S2479
Strain history: <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; S2479 <- G. Slobodkina {2014}
NCBI tax ID(s): 1750597 (species)
version 8.1 (current version)
General
@ref: 24203
BacDive-ID: 132414
DSM-Number: 100275
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, chemolithoautotroph, Gram-negative, motile, rod-shaped
description: Inmirania thermothiophila S2479 is a facultative anaerobe, chemolithoautotroph, Gram-negative bacterium that was isolated from water and sediment from a shallow marine hydrothermal vent.
NCBI tax id
- NCBI tax id: 1750597
- Matching level: species
strain history
- @ref: 24203
- history: <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; S2479 <- G. Slobodkina {2014}
doi: 10.13145/bacdive132414.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Ectothiorhodospiraceae
- genus: Inmirania
- species: Inmirania thermothiophila
- full scientific name: Inmirania thermothiophila Slobodkina et al. 2016
@ref: 24203
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Ectothiorhodospiraceae
genus: Inmirania
species: Inmirania thermothiophila
full scientific name: Inmirania thermothiophila Slobodkina et al. 2016
strain designation: S2479
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
|---|---|---|---|---|---|---|---|
| 43793 | negative | 1-2 µm | 0.6-0.7 µm | rod-shaped | yes | monotrichous, polar | |
| 69480 | negative | 99.999 | |||||
| 69480 | yes | 92.817 |
Culture and growth conditions
culture medium
- @ref: 24203
- name: THERMOSULFURIMONAS MEDIUM (DSMZ Medium 1210a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1210a
- composition: Name: THERMOSULFURIMONAS MEDIUM (DSMZ Medium 1210a; with strain-specific modifications) Composition: NaCl 17.9462 g/l Sulfur powder 4.98504 g/l MgCl2 x 6 H2O 3.98804 g/l Na2S2O3 x 5 H2O 3.48953 g/l Na-acetate 1.49551 g/l KNO3 0.997009 g/l Na2CO3 0.997009 g/l (NH4)2SO4 0.498504 g/l CaCl2 x 2 H2O 0.329013 g/l KH2PO4 0.329013 g/l KCl 0.329013 g/l Yeast extract 0.199402 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 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 Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 43793 | positive | growth | 35-68 | |
| 43793 | positive | optimum | 65 | thermophilic |
| 24203 | positive | growth | 65 | thermophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 43793 | positive | growth | 5.5-8.8 | alkaliphile |
| 43793 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 43793
- oxygen tolerance: facultative anaerobe
nutrition type
- @ref: 43793
- type: chemolithoautotroph
spore formation
| @ref | type of spore | spore formation | confidence |
|---|---|---|---|
| 43793 | endospore | no | |
| 69481 | no | 99 | |
| 69480 | no | 99.975 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 43793 | NaCl | positive | growth | 0.5-3.5 %(w/v) |
| 43793 | NaCl | positive | optimum | 1.5-2 %(w/v) |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43793 | 33403 | elemental sulfur | - | electron acceptor |
| 43793 | ferrihydrite | - | electron acceptor | |
| 43793 | 16301 | nitrite | - | electron acceptor |
| 43793 | 16189 | sulfate | - | electron acceptor |
| 43793 | 17359 | sulfite | - | electron acceptor |
| 43793 | 16094 | thiosulfate | - | electron acceptor |
| 43793 | yeast extract | + | growth | |
| 43793 | 33403 | elemental sulfur | + | oxidation |
| 43793 | 16094 | thiosulfate | + | oxidation |
| 43793 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 24203 | water and sediment from a shallow marine hydrothermal vent | Kurils, Kunashir Island (43° 59.742' N 145° 48.166' E) | Russia | RUS | Asia | 43.9957 | 145.803 |
| 43793 | A sample of sand and water from a thermal spring located in a tidal zone of a hydrothermally heated beach | Kunashir Island, Kurils | Russia | RUS | Asia | 44.189 | 145.846 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Aquatic | #Thermal spring |
| #Environmental | #Terrestrial | #Tidal flat |
| #Environmental | #Terrestrial | #Sandy |
taxonmaps
- @ref: 69479
- File name: preview.99_171093.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_56;96_63789;97_82735;98_112106;99_171093&stattab=map
- Last taxonomy: Inmirania thermothiophila subclade
- 16S sequence: KT159732
- Sequence Identity:
- Total samples: 240
- soil counts: 34
- aquatic counts: 177
- animal counts: 26
- plant counts: 3
Safety information
risk assessment
- @ref: 24203
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24203
- description: Inmirania thermothiophila strain S2479 16S ribosomal RNA gene, partial sequence
- accession: KT159732
- length: 1513
- database: ena
- NCBI tax ID: 1750597
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Inmirania thermothiophila DSM 100275 | GCA_003751635 | contig | ncbi | 1750597 |
| 66792 | Inmirania thermothiophila strain DSM 100275 | 1750597.3 | wgs | patric | 1750597 |
| 66792 | Inmirania thermothiophila DSM 100275 | 2788499858 | draft | img | 1750597 |
GC content
- @ref: 24203
- GC-content: 71.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | yes | 93.28 | yes |
| gram-positive | no | 99.556 | yes |
| anaerobic | no | 69.874 | no |
| aerobic | no | 94.926 | yes |
| halophile | no | 77.16 | no |
| spore-forming | no | 95.393 | no |
| thermophile | yes | 96.726 | no |
| glucose-util | no | 62.985 | no |
| flagellated | yes | 77.399 | yes |
| glucose-ferment | no | 88.655 | no |
External links
@ref: 24203
culture collection no.: DSM 100275, VKM B-2962
straininfo link
- @ref: 90754
- straininfo: 397016
literature
- topic: Phylogeny
- Pubmed-ID: 26582356
- title: Inmirania thermothiophila gen. nov., sp. nov., a thermophilic, facultatively autotrophic, sulfur-oxidizing gammaproteobacterium isolated from a shallow-sea hydrothermal vent.
- authors: Slobodkina GB, Baslerov RV, Novikov AA, Viryasov MB, Bonch-Osmolovskaya EA, Slobodkin AI
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000773
- year: 2015
- mesh: Autotrophic Processes, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Hydrothermal Vents/*microbiology, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sulfur Compounds/metabolism, Sulfur-Reducing Bacteria/classification/genetics/isolation & purification
- topic2: Enzymology
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 24203 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100275 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100275) | |||
| 43793 | Galina B. Slobodkina, Roman V. Baslerov, Andrei A. Novikov, Mikhail B. Viryasov, Elizaveta A. Bonch-Osmolovskaya, Alexander I. Slobodkin | Inmirania thermothiophila gen. nov., sp. nov., a thermophilic, facultatively autotrophic, sulfur-oxidizing gammaproteobacterium isolated from a shallow-sea hydrothermal vent | 10.1099/ijsem.0.000773 | IJSEM 66: 701-706 2016 | 26582356 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 90754 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID397016.1 |