Strain identifier
BacDive ID: 16727
Type strain: 
Species: Thermus igniterrae
Strain Designation: RF-4
Strain history: DSM 12459 <-- M. S. da Costa RF-4.
NCBI tax ID(s): 1123388 (strain), 88189 (species)
version 8.1 (current version)
General
@ref: 4727
BacDive-ID: 16727
DSM-Number: 12459
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Thermus igniterrae RF-4 is a thermophilic, Gram-negative bacterium that was isolated from hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 88189 | species |
| 1123388 | strain |
strain history
| @ref | history |
|---|---|
| 4727 | <- M.S. da Costa, Univ. Coimbra; RF-4 |
| 67770 | DSM 12459 <-- M. S. da Costa RF-4. |
doi: 10.13145/bacdive16727.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deinococcota
- domain: Bacteria
- phylum: Deinococcota
- class: Deinococci
- order: Thermales
- family: Thermaceae
- genus: Thermus
- species: Thermus igniterrae
- full scientific name: Thermus igniterrae Chung et al. 2000
@ref: 4727
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Thermales
family: Thermaceae
genus: Thermus
species: Thermus igniterrae
full scientific name: Thermus igniterrae Chung et al. 2000
strain designation: RF-4
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.988
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4727 | MODIFIED THERMUS 162 MEDIUM (DSMZ Medium 630) | yes | https://mediadive.dsmz.de/medium/630 | Name: MODIFIED THERMUS 162 MEDIUM (DSMZ Medium 630) Composition: Agar 28.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 2.5 g/l Tryptone 2.5 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l CaSO4 x 2 H2O 0.04 g/l Nitrilotriacetic acid 0.0064 g/l Fe(III) citrate 0.00122472 g/l FeCl2 x 4 H2O 0.0005 g/l MnCl2 x 4 H2O 0.00025 g/l CoCl2 x 4 H2O 0.00015 g/l CuCl2 x 2 H2O 2.5e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l H3BO3 1e-05 g/l NiCl2 x 6 H2O 1e-05 g/l Distilled water |
| 4727 | THERMUS 162 MEDIUM (DSMZ Medium 878) | yes | https://mediadive.dsmz.de/medium/878 | Name: THERMUS 162 MEDIUM (DSMZ Medium 878) Composition: Agar 28.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.04 g/l Fe(III) citrate 0.00122472 g/l MnSO4 x H2O 0.00114 g/l ZnSO4 x 7 H2O 0.00025 g/l H3BO3 0.00025 g/l CoCl2 x 6 H2O 2.25e-05 g/l CuSO4 x 5 H2O 1.25e-05 g/l Na2MoO4 x 2 H2O 1.25e-05 g/l H2SO4 Distilled water |
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 4727 | positive | growth | 70 | thermophilic | |
| 67770 | positive | growth | 70 | thermophilic | |
| 69480 | thermophilic | 100 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.845 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 4727 | hot spring | Rykyaflot | Iceland | ISL | Europe |
| 67770 | Hot springs at Reykyaflot in Iceland |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_104988.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_87;96_2025;97_25470;98_32294;99_104988&stattab=map
- Last taxonomy: Thermus igniterrae subclade
- 16S sequence: Y18406
- Sequence Identity:
- Total samples: 2017
- soil counts: 141
- aquatic counts: 678
- animal counts: 1084
- plant counts: 114
Safety information
risk assessment
- @ref: 4727
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4727
- description: Thermus igniterrae 16S rRNA gene, strain RF-4T
- accession: Y18406
- length: 1472
- database: ena
- NCBI tax ID: 1123388
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermus igniterrae ATCC 700962 | 1123388.3 | wgs | patric | 1123388 |
| 66792 | Thermus igniterrae ATCC 700962 | 2515154172 | draft | img | 1123388 |
| 67770 | Thermus igniterrae ATCC 700962 | GCA_000376265 | contig | ncbi | 1123388 |
GC content
- @ref: 67770
- GC-content: 70.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 87.486 | no |
| flagellated | no | 97.32 | no |
| gram-positive | no | 96.314 | no |
| anaerobic | no | 93.27 | no |
| aerobic | yes | 65.688 | no |
| halophile | no | 83.99 | no |
| spore-forming | no | 93.083 | no |
| glucose-util | yes | 87.01 | no |
| thermophile | yes | 100 | yes |
| glucose-ferment | no | 87.597 | no |
External links
@ref: 4727
culture collection no.: DSM 12459, JCM 19899, ATCC 700962, BCRC 17264
straininfo link
- @ref: 85746
- straininfo: 44231
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 10826806 | Thermus igniterrae sp. nov. and Thermus antranikianii sp. nov., two new species from Iceland. | Chung AP, Rainey FA, Valente M, Nobre MF, da Costa MS | Int J Syst Evol Microbiol | 10.1099/00207713-50-1-209 | 2000 | Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Iceland, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Thermus/chemistry/*classification/genetics/growth & development/isolation & purification, *Water Microbiology | Genetics |
| Phylogeny | 19628590 | Thermus islandicus sp. nov., a mixotrophic sulfur-oxidizing bacterium isolated from the Torfajokull geothermal area. | Bjornsdottir SH, Petursdottir SK, Hreggvidsson GO, Skirnisdottir S, Hjorleifsdottir S, Arnfinnsson J, Kristjansson JK | Int J Syst Evol Microbiol | 10.1099/ijs.0.007013-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Iceland, Molecular Sequence Data, Oxidation-Reduction, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfur/*metabolism, Thermus/*classification/genetics/*isolation & purification/metabolism | Metabolism |
| Phylogeny | 31967954 | Thermus thermamylovorans sp. nov., isolated from a hot spring. | Ming H, Zhao ZL, Ji WL, Ding CL, Cheng LJ, Niu MM, Li M, Yi BF, Xia TT, Nie GX | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003965 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hot Springs/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thermus/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4727 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12459) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12459 | |
| 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/ | ||
| 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 | |
| 85746 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44231.1 | StrainInfo: A central database for resolving microbial strain identifiers |