Strain identifier
BacDive ID: 132336
Type strain: 
Species: Calidithermus roseus
Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 71031.
NCBI tax ID(s): 1644118 (species)
version 8.1 (current version)
General
@ref: 24125
BacDive-ID: 132336
DSM-Number: 29972
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Calidithermus roseus DSM 29972 is a thermophilic, Gram-negative bacterium that was isolated from geothermally heated sediment from a hot spring.
NCBI tax id
- NCBI tax id: 1644118
- Matching level: species
strain history
| @ref | history |
|---|---|
| 24125 | <- W.-J. Li, YIM; YIM 71031 <- Y. Duan |
| 67770 | W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 71031. |
doi: 10.13145/bacdive132336.20230509.8.1
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 roseus
- full scientific name: Calidithermus roseus (Ming et al. 2016) Raposo et al. 2019
synonyms
- @ref: 20215
- synonym: Meiothermus roseus
@ref: 24125
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Thermales
family: Thermaceae
genus: Calidithermus
species: Calidithermus roseus
full scientific name: Calidithermus roseus (Ming et al. 2016) Raposo et al. 2019
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.806
Culture and growth conditions
culture medium
- @ref: 24125
- name: T 5 MEDIUM (DSMZ Medium 1573)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1573
- composition: Name: T 5 MEDIUM (DSMZ Medium 1573) Composition: Yeast extract 2.0 g/l Peptone 1.0 g/l D(+)-Glucose 1.0 g/l CaCO3 1.0 g/l Tryptone 0.5 g/l MgSO4 x 7 H2O 0.003 g/l Nitrilotriacetic acid 0.0015 g/l NaCl 0.001 g/l MnSO4 x H2O 0.0005 g/l CoSO4 x 7 H2O 0.00018 g/l ZnSO4 x 7 H2O 0.00018 g/l FeSO4 x 7 H2O 0.0001 g/l CaCl2 x 2 H2O 0.0001 g/l NiCl2 x 6 H2O 3e-05 g/l AlK(SO4)2 x 12 H2O 2e-05 g/l H3BO3 1e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l CuSO4 x 5 H2O 1e-05 g/l Na2WO4 x 2 H2O 4e-07 g/l Na2SeO3 x 5 H2O 3e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 24125 | positive | growth | 50 | thermophilic | |
| 67770 | positive | growth | 50 | thermophilic | |
| 69480 | thermophilic | 99.122 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 99.748 |
observation
- @ref: 67770
- observation: quinones: MK-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 24125 | geothermally heated sediment from a hot spring | Yunnan province, Tengchong county | China | CHN | Asia |
| 67770 | Hot spring in Tengchong county | Yunnan Province | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_180893.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16211;96_3394;97_4166;98_5327;99_180893&stattab=map
- Last taxonomy: Calidithermus roseus
- 16S sequence: KP232921
- Sequence Identity:
- Total samples: 4
- animal counts: 4
Safety information
risk assessment
- @ref: 24125
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24125
- description: Meiothermus roseus strain YIM 71031 16S ribosomal RNA gene, partial sequence
- accession: KP232921
- length: 1538
- database: ena
- NCBI tax ID: 1644118
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Meiothermus roseus strain NBRC 110900 | 1644118.3 | wgs | patric | 1644118 |
| 66792 | Calidithermus roseus NBRC 110900 | 2887030614 | draft | img | 1644118 |
| 67770 | Calidithermus roseus NBRC 110900 | GCA_003574095 | contig | ncbi | 1644118 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 24125 | 64.0 | high performance liquid chromatography (HPLC) |
| 67770 | 64 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 89.694 | no |
| gram-positive | no | 88.663 | no |
| anaerobic | no | 98.268 | no |
| aerobic | yes | 86.689 | no |
| halophile | no | 93.614 | no |
| spore-forming | no | 91.515 | no |
| thermophile | yes | 99.999 | yes |
| glucose-util | yes | 88.539 | no |
| flagellated | no | 97.464 | no |
| glucose-ferment | no | 91.172 | no |
External links
@ref: 24125
culture collection no.: DSM 29972, KCTC 42495, NBRC 110900, YIM 71031, JCM 30647
straininfo link
- @ref: 90683
- straininfo: 404729
literature
- topic: Phylogeny
- Pubmed-ID: 26219565
- title: Meiothermus roseus sp. nov., a thermophilic bacterium isolated from a geothermal area.
- authors: Ming H, Duan YY, Guo QQ, Yin YR, Zhou EM, Liu L, Li S, Nie GX, Li WJ
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-015-0544-x
- year: 2015
- mesh: 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
- 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 | |||
| 24125 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29972 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29972) | |||
| 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 | |
| 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. | 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 | |||
| 90683 | 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-ID404729.1 |