Strain identifier
BacDive ID: 436
Type strain: 
Species: Kyrpidia tusciae
Strain Designation: T2
Strain history: <- M. Aragno, strain T2
NCBI tax ID(s): 562970 (strain), 33943 (species)
version 9.3 (current version)
General
@ref: 1245
BacDive-ID: 436
DSM-Number: 2912
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, thermophilic
description: Kyrpidia tusciae T2 is a spore-forming, thermophilic bacterium that was isolated from solfatara.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 33943 | species |
| 562970 | strain |
strain history
- @ref: 1245
- history: <- M. Aragno, strain T2
doi: 10.13145/bacdive436.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Alicyclobacillaceae
- genus: Kyrpidia
- species: Kyrpidia tusciae
- full scientific name: Kyrpidia tusciae (Bonjour and Aragno 1985) Klenk et al. 2012
synonyms
- @ref: 20215
- synonym: Bacillus tusciae
@ref: 1245
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Alicyclobacillaceae
genus: Kyrpidia
species: Kyrpidia tusciae
full scientific name: Kyrpidia tusciae (Bonjour and Aragno 1985) Klenk et al. 2012
strain designation: T2
type strain: yes
Morphology
multimedia
- @ref: 66793
- multimedia content: EM_DSM_2912_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1245
- name: BACILLUS TUSCIAE MEDIUM (DSMZ Medium 369)
- growth: yes
- link: https://mediadive.dsmz.de/medium/369
- composition: Name: BACILLUS TUSCIAE MEDIUM (DSMZ Medium 369) Composition: Agar 15.0 g/l Na2HPO4 x 2 H2O 4.5 g/l KH2PO4 1.5 g/l NH4Cl 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.01 g/l CaCl2 x 2 H2O 0.01 g/l Ferric ammonium citrate 0.005 g/l H3BO3 0.0009 g/l CoCl2 x 6 H2O 0.0006 g/l ZnSO4 x 7 H2O 0.0003 g/l MnCl2 x 4 H2O 9e-05 g/l Na2MoO4 x 2 H2O 9e-05 g/l NiCl2 x 6 H2O 6e-05 g/l CuCl2 x 2 H2O 3e-05 g/l Distilled water
culture temp
- @ref: 1245
- growth: positive
- type: growth
- temperature: 50
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: facultative anaerobe
- confidence: 91.7
Isolation, sampling and environmental information
isolation
- @ref: 1245
- sample type: solfatara
- geographic location: Tuscany, Grosseto, near Lago, Solfatara of S. Frederigo
- country: Italy
- origin.country: ITA
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Volcanic
taxonmaps
- @ref: 69479
- File name: preview.99_3381.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_399;96_1762;97_2110;98_2590;99_3381&stattab=map
- Last taxonomy: Kyrpidia tusciae subclade
- 16S sequence: Z26933
- Sequence Identity:
- Total samples: 469
- soil counts: 287
- aquatic counts: 41
- animal counts: 133
- plant counts: 8
Safety information
risk assessment
- @ref: 1245
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Kyrpidia tusciae gene for 16S rRNA, partial sequence, strain: NBRC 15312 | AB680831 | 1465 | nuccore | 562970 |
| 20218 | Kyrpidia tusciae DSM 2912 partial 16S rRNA gene | Z26933 | 1491 | nuccore | 562970 |
| 124043 | Kyrpidia tusciae DSM 2912 gene for 16S ribosomal RNA, partial sequence. | AB042062 | 1512 | nuccore | 562970 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Kyrpidia tusciae DSM 2912 | GCA_000092905 | complete | ncbi | 562970 |
| 66792 | Kyrpidia tusciae DSM 2912 | 562970.4 | complete | patric | 562970 |
| 66792 | Kyrpidia tusciae T2, DSM 2912 | 646564511 | complete | img | 562970 |
GC content
- @ref: 1245
- GC-content: 57.0-58.0
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 55.768 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 79.671 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 52.365 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 89.89 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | yes | 64.04 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 69.46 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 75.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 57.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 75.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | facultative anaerobe | 91.7 |
External links
@ref: 1245
culture collection no.: DSM 2912, IFO 15312, NBRC 15312
straininfo link
- @ref: 70115
- straininfo: 1209
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | topic2 | mesh |
|---|---|---|---|---|---|---|---|---|
| Genetics | 22180816 | Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. | Klenk HP, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Mavromatis K, Daum C, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Jeffries CD, Detter JC, Rohde M, Abt B, Pukall R, Goker M, Bristow J, Markowitz V, Hugenholtz P, Eisen JA | Stand Genomic Sci | 10.4056/sigs.2144922 | 2011 | Phylogeny | |
| Metabolism | 25911482 | Thermophilic Coenzyme B12-Dependent Acyl Coenzyme A (CoA) Mutase from Kyrpidia tusciae DSM 2912 Preferentially Catalyzes Isomerization of (R)-3-Hydroxybutyryl-CoA and 2-Hydroxyisobutyryl-CoA. | Weichler MT, Kurteva-Yaneva N, Przybylski D, Schuster J, Muller RH, Harms H, Rohwerder T | Appl Environ Microbiol | 10.1128/AEM.00716-15 | 2015 | Enzymology | Acyl Coenzyme A/chemistry/*metabolism, Bacillales/chemistry/*enzymology/genetics/metabolism, Bacterial Proteins/*chemistry/genetics/*metabolism, Catalysis, Cobamides/*metabolism, Enzyme Stability, Intramolecular Transferases/*chemistry/genetics/*metabolism, Stereoisomerism, Substrate Specificity |
| Metabolism | 27836853 | Production of 2-Hydroxyisobutyric Acid from Methanol by Methylobacterium extorquens AM1 Expressing (R)-3-Hydroxybutyryl Coenzyme A-Isomerizing Enzymes. | Rohde MT, Tischer S, Harms H, Rohwerder T | Appl Environ Microbiol | 10.1128/AEM.02622-16 | 2017 | Enzymology | Acyl Coenzyme A/*metabolism, Bacterial Proteins/*metabolism, Bioreactors, Hydroxybutyrates/*metabolism, Methanol/*metabolism, Methylobacterium extorquens/enzymology/*metabolism |
| Metabolism | 32351493 | Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction. | Rohwerder T, Rohde MT, Jehmlich N, Purswani J | Front Microbiol | 10.3389/fmicb.2020.00691 | 2020 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1245 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2912) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2912 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 70115 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1209.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | ||||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |