Strain identifier
BacDive ID: 16707
Type strain: 
Species: Calidithermus timidus
Strain Designation: SPS-243
Strain history: <- M. da Costa, Univ. Coimbra, Dept. Bioquímica; SPS-243 <- A. Pires
NCBI tax ID(s): 1122223 (strain), 307124 (species)
version 8.1 (current version)
General
@ref: 6688
BacDive-ID: 16707
DSM-Number: 17022
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Calidithermus timidus SPS-243 is a thermophilic, Gram-negative bacterium that was isolated from Biofilm sample from a hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1122223 | strain |
| 307124 | species |
strain history
- @ref: 6688
- history: <- M. da Costa, Univ. Coimbra, Dept. Bioquímica; SPS-243 <- A. Pires
doi: 10.13145/bacdive16707.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deinococcota
- domain: Bacteria
- phylum: Deinococcota
- class: Deinococci
- order: Thermales
- family: Thermaceae
- genus: Calidithermus
- species: Calidithermus timidus
- full scientific name: Calidithermus timidus (Pires et al. 2005) Raposo et al. 2019
synonyms
- @ref: 20215
- synonym: Meiothermus timidus
@ref: 6688
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Thermales
family: Thermaceae
genus: Calidithermus
species: Calidithermus timidus
full scientific name: Calidithermus timidus (Pires et al. 2005) Raposo et al. 2019
strain designation: SPS-243
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.807
Culture and growth conditions
culture medium
- @ref: 6688
- name: THERMUS 162 MEDIUM (DSMZ Medium 878)
- growth: yes
- link: https://mediadive.dsmz.de/medium/878
- composition: 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 |
|---|---|---|---|---|---|
| 6688 | positive | growth | 50 | thermophilic | |
| 69480 | thermophilic | 98.944 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 98 |
| 69480 | no | 99.896 |
Isolation, sampling and environmental information
isolation
- @ref: 6688
- sample type: Biofilm sample from a hot spring
- geographic location: São Pedro do Sul
- country: Portugal
- origin.country: PRT
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Environmental | #Biofilm | |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_7264.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16211;96_3394;97_4166;98_5327;99_7264&stattab=map
- Last taxonomy: Calidithermus timidus
- 16S sequence: AJ871168
- Sequence Identity:
- Total samples: 381
- soil counts: 15
- aquatic counts: 174
- animal counts: 188
- plant counts: 4
Safety information
risk assessment
- @ref: 6688
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6688
- description: Meiothermus timidus partial 16S rRNA gene, type strain SPS-243
- accession: AJ871168
- length: 1483
- database: ena
- NCBI tax ID: 307124
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Calidithermus timidus DSM 17022 | GCA_000373205 | scaffold | ncbi | 1122223 |
| 66792 | Meiothermus timidus DSM 17022 | 1122223.3 | wgs | patric | 1122223 |
| 66792 | Meiothermus timidus DSM 17022 | 2515154081 | draft | img | 1122223 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| motile | no | 92.376 | no |
| flagellated | no | 97.189 | no |
| gram-positive | no | 90.054 | no |
| anaerobic | no | 98.598 | no |
| aerobic | yes | 88.808 | no |
| halophile | no | 90.503 | no |
| spore-forming | no | 92.61 | no |
| thermophile | yes | 99.999 | yes |
| glucose-util | yes | 90.695 | no |
| glucose-ferment | no | 90.294 | no |
External links
@ref: 6688
culture collection no.: DSM 17022, CIP 108604, LMG 22897, NBRC 103207
straininfo link
- @ref: 85726
- straininfo: 134623
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15796977 | Meiothermus timidus sp. nov., a new slightly thermophilic yellow-pigmented species. | Pires AL, Albuquerque L, Tiago I, Nobre MF, Empadinhas N, Verissimo A, da Costa MS | FEMS Microbiol Lett | 10.1016/j.femsle.2005.02.011 | 2005 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, *Hot Temperature, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, Pigments, Biological/*metabolism, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thermus/chemistry/*classification/genetics/metabolism | Stress |
| Phylogeny | 26219565 | Meiothermus roseus sp. nov., a thermophilic bacterium isolated from a geothermal area. | Ming H, Duan YY, Guo QQ, Yin YR, Zhou EM, Liu L, Li S, Nie GX, Li WJ | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0544-x | 2015 | Bacteria, Aerobic/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysis | Genetics |
| 26941711 | Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage phiOH3 Which Infects Thermus thermophilus HB8. | Nagayoshi Y, Kumagae K, Mori K, Tashiro K, Nakamura A, Fujino Y, Hiromasa Y, Iwamoto T, Kuhara S, Ohshima T, Doi K | Front Microbiol | 10.3389/fmicb.2016.00050 | 2016 | |||
| Enzymology | 31389242 | Thermostable Amylosucrase from Calidithermus timidus DSM 17022: Insight into Its Characteristics and Tetrameric Conformation. | Tian Y, Xu W, Guang C, Zhang W, Mu W | J Agric Food Chem | 10.1021/acs.jafc.9b04023 | 2019 | Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/metabolism, Enzyme Stability, Glucosyltransferases/*chemistry/genetics/metabolism, Hot Temperature, Hydrogen-Ion Concentration, Kinetics, Protein Conformation, Sequence Alignment, Thermus/chemistry/*enzymology/genetics | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6688 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17022) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17022 | |
| 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 | |
| 85726 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134623.1 | StrainInfo: A central database for resolving microbial strain identifiers |