Strain identifier
BacDive ID: 132490
Type strain: 
Species: Caldimicrobium thiodismutans
Strain Designation: TF1
Strain history: <- T. Watanabe, Univ. Hokkaido; TF1 <- H. Kojima {2014}
NCBI tax ID(s): 1653476 (species)
version 8.1 (current version)
General
@ref: 24279
BacDive-ID: 132490
DSM-Number: 29380
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, chemoautolithotroph, spore-forming, thermophilic, Gram-negative, motile, rod-shaped
description: Caldimicrobium thiodismutans TF1 is an anaerobe, chemoautolithotroph, spore-forming bacterium that was isolated from slightly alkaline hot spring.
NCBI tax id
- NCBI tax id: 1653476
- Matching level: species
strain history
- @ref: 24279
- history: <- T. Watanabe, Univ. Hokkaido; TF1 <- H. Kojima {2014}
doi: 10.13145/bacdive132490.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/thermodesulfobacteriota
- domain: Bacteria
- phylum: Thermodesulfobacteriota
- class: Thermodesulfobacteria
- order: Thermodesulfobacteriales
- family: Thermodesulfobacteriaceae
- genus: Caldimicrobium
- species: Caldimicrobium thiodismutans
- full scientific name: Caldimicrobium thiodismutans Kojima et al. 2016
@ref: 24279
domain: Bacteria
phylum: Thermodesulfobacteria
class: Thermodesulfobacteria
order: Thermodesulfobacteriales
family: Thermodesulfobacteriaceae
genus: Caldimicrobium
species: Caldimicrobium thiodismutans
full scientific name: Caldimicrobium thiodismutans Kojima et al. 2016
strain designation: TF1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 43669 | negative | 1-2 µm | 0.5-0.6 µm | rod-shaped | yes | |
| 69480 | yes | 92.816 | ||||
| 69480 | negative | 99.998 |
Culture and growth conditions
culture medium
- @ref: 24279
- name: CALDIMICROBIUM THIODISMUTANS MEDIUM (DSMZ Medium 1277b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1277b
- composition: Name: CALDIMICROBIUM THIODISMUTANS MEDIUM (DSMZ Medium 1277b) Composition: Na2CO3 2.5 g/l Na2S2O5 0.9 g/l NaOH 0.36 g/l MgCl2 x 6 H2O 0.2 g/l KH2PO4 0.1 g/l (NH4)2SO4 0.1 g/l CaCl2 x 2 H2O 0.1 g/l KCl 0.1 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Pyridoxine hydrochloride 0.0003 g/l Thiamine-HCl x 2 H2O 0.0002 g/l Nicotinic acid 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l Calcium pantothenate 0.0001 g/l Vitamin B12 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l D-(+)-biotin 2e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l FeCl3 x 6 H2O Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 43669 | positive | growth | 40-77 | thermophilic | |
| 43669 | positive | optimum | 75 | thermophilic | |
| 24279 | positive | growth | 75 | thermophilic | |
| 69480 | thermophilic | 99.999 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 43669 | positive | growth | 5.9-9.5 | alkaliphile |
| 43669 | positive | optimum | 7.5-8.8 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 43669 | anaerobe | |
| 69480 | anaerobe | 99.999 |
nutrition type
- @ref: 43669
- type: chemoautolithotroph
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 97 |
| 69480 | no | 99.941 |
halophily
- @ref: 43669
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %(w/v)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43669 | 18276 | dihydrogen | - | electron donor |
| 43669 | 25115 | malate | - | electron donor |
| 43669 | 16236 | ethanol | - | electron donor |
| 43669 | 29806 | fumarate | - | electron donor |
| 43669 | 30031 | succinate | - | electron donor |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 24279 | slightly alkaline hot spring | Nakabusa | Japan | JPN | Asia | 36.3833 | 137.75 |
| 43669 | a neutral to slightly alkaline hot spring | Nakabusa | Japan | JPN | Asia | 36.383 | 137.75 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Condition | #Alkaline | |
| #Condition | #Thermophilic (>45°C) | |
| #Environmental | #Aquatic | #Thermal spring |
taxonmaps
- @ref: 69479
- File name: preview.99_6202.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_515;96_2952;97_3633;98_4598;99_6202&stattab=map
- Last taxonomy: Caldimicrobium thiodismutans subclade
- 16S sequence: LC055107
- Sequence Identity:
- Total samples: 82
- soil counts: 1
- aquatic counts: 79
- animal counts: 2
Safety information
risk assessment
- @ref: 24279
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24279
- description: Caldimicrobium thiodismutans gene for 16S ribosomal RNA, partial sequence
- accession: LC055107
- length: 1494
- database: ena
- NCBI tax ID: 1653476
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Caldimicrobium thiodismutans TF1 | GCA_001548275 | complete | ncbi | 1653476 |
| 66792 | Caldimicrobium thiodismutans TF1 | 2751185666 | complete | img | 1653476 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 43669 | 38.3 | |
| 24279 | 38.3 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 97 | no |
| flagellated | no | 91.154 | no |
| gram-positive | no | 99.562 | yes |
| anaerobic | yes | 99.435 | no |
| halophile | no | 82.949 | no |
| spore-forming | no | 95.497 | no |
| thermophile | yes | 99.999 | no |
| glucose-util | no | 67.153 | no |
| motile | yes | 90.592 | yes |
| aerobic | no | 99.372 | no |
| glucose-ferment | no | 85.93 | no |
External links
@ref: 24279
culture collection no.: DSM 29380, NBRC 110713
straininfo link
- @ref: 90820
- straininfo: 408156
literature
- topic: Phylogeny
- Pubmed-ID: 26842785
- title: Caldimicrobium thiodismutans sp. nov., a sulfur-disproportionating bacterium isolated from a hot spring, and emended description of the genus Caldimicrobium.
- authors: Kojima H, Umezawa K, Fukui M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000947
- year: 2016
- mesh: Autotrophic Processes, Bacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/*microbiology, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/*metabolism
- topic2: Genetics
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 | |||
| 24279 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29380 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29380) | |||
| 43669 | Hisaya Kojima, Kazuhiro Umezawa, Manabu Fukui | Caldimicrobium thiodismutans sp. nov., a sulfur-disproportionating bacterium isolated from a hot spring, and emended description of the genus Caldimicrobium | 10.1099/ijsem.0.000947 | IJSEM 66: 1828-1831 2016 | 26842785 | |
| 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 | |||
| 90820 | 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-ID408156.1 |