Strain identifier
BacDive ID: 11901
Type strain: 
Species: Picrophilus oshimae
Strain history: DSM 9790 <-- W. Zillig KAW2/3.
NCBI tax ID(s): 263820 (strain), 82076 (species)
version 8.1 (current version)
General
@ref: 3736
BacDive-ID: 11901
DSM-Number: 9790
keywords: genome sequence, 16S sequence, Archaea, spore-forming, thermophilic, Gram-negative
description: Picrophilus oshimae DSM 9790 is a spore-forming, thermophilic, Gram-negative archaeon that was isolated from solfataric field.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 82076 | species |
| 263820 | strain |
strain history
| @ref | history |
|---|---|
| 3736 | <- W. Zillig; KAW 2/3 |
| 67770 | DSM 9790 <-- W. Zillig KAW2/3. |
doi: 10.13145/bacdive11901.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Thermoplasmata
- order: Thermoplasmatales
- family: Picrophilaceae
- genus: Picrophilus
- species: Picrophilus oshimae
- full scientific name: Picrophilus oshimae Schleper et al. 1996
synonyms
- @ref: 20215
- synonym: Picrophilus torridus
@ref: 3736
domain: Archaea
phylum: Euryarchaeota
class: Thermoplasmata
order: Thermoplasmatales
family: Picrophilaceae
genus: Picrophilus
species: Picrophilus torridus
full scientific name: Picrophilus torridus Zillig et al. 1996
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.955
Culture and growth conditions
culture medium
- @ref: 3736
- name: SULFOLOBUS MEDIUM (DSMZ Medium 88)
- growth: yes
- link: https://mediadive.dsmz.de/medium/88
- composition: Name: SULFOLOBUS MEDIUM (DSMZ Medium 88; with strain-specific modifications) Composition: Yeast extract 1.9802 g/l (NH4)2SO4 1.28713 g/l KH2PO4 0.277228 g/l MgSO4 x 7 H2O 0.247525 g/l CaCl2 x 2 H2O 0.0693069 g/l FeCl3 x 6 H2O 0.019802 g/l Na2B4O7 x 10 H2O 0.00445545 g/l MnCl2 x 4 H2O 0.00178218 g/l ZnSO4 x 7 H2O 0.000217822 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Na2MoO4 x 2 H2O 2.9703e-05 g/l VOSO4 x 2 H2O 2.9703e-05 g/l CoSO4 x 7 H2O 9.90099e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 3736 | positive | growth | 55 | thermophilic | |
| 67770 | positive | growth | 55 | thermophilic | |
| 69480 | thermophilic | 98.383 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | no | 99.99 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 3736 | solfataric field | Hokkaido, Kawayu | Japan | JPN | Asia |
| 67770 | Dry, hot soil in the vicinity of Kawayu | Hokkaido | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Volcanic
taxonmaps
- @ref: 69479
- File name: preview.99_187095.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18356;96_68783;97_89425;98_121694;99_187095&stattab=map
- Last taxonomy: Picrophilus
- 16S sequence: NR_074187
- Sequence Identity:
- Total samples: 40
- soil counts: 1
- aquatic counts: 38
- plant counts: 1
Safety information
risk assessment
- @ref: 3736
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 67770
- description: Picrophilus torridus strain DSM 9790 16S ribosomal RNA, complete sequence
- accession: NR_074187
- length: 1469
- database: nuccore
- NCBI tax ID: 82076
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Picrophilus oshimae DSM 9789 DSM 9790 | GCA_000008265 | complete | ncbi | 1122961 |
| 66792 | Picrophilus torridus DSM 9790 | 638154512 | complete | img | 263820 |
| 66792 | Picrophilus torridus DSM 9790 | 263820.9 | complete | patric | 263820 |
GC content
- @ref: 3736
- GC-content: 35
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 85.598 | no |
| flagellated | no | 98.007 | no |
| gram-positive | no | 93.849 | no |
| anaerobic | yes | 58.566 | no |
| halophile | no | 84.606 | no |
| spore-forming | no | 95.963 | no |
| thermophile | yes | 99.999 | yes |
| glucose-util | yes | 87.734 | no |
| aerobic | no | 87.575 | no |
| glucose-ferment | no | 71.787 | no |
External links
@ref: 3736
culture collection no.: DSM 9790, JCM 10055, KAW 2/3, NBRC 100828
straininfo link
- @ref: 81116
- straininfo: 43735
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 15691337 | Properties of the recombinant glucose/galactose dehydrogenase from the extreme thermoacidophile, Picrophilus torridus. | Angelov A, Futterer O, Valerius O, Braus GH, Liebl W | FEBS J | 10.1111/j.1742-4658.2004.04539.x | 2005 | Cloning, Molecular, Galactose Dehydrogenases/genetics/*metabolism, Glucose 1-Dehydrogenase/genetics/isolation & purification/*metabolism, Hydrogen-Ion Concentration, NADP/metabolism, Recombinant Proteins/genetics/isolation & purification/metabolism, Sequence Analysis, Protein, Temperature, Thermoplasmales/*enzymology | Metabolism |
| Genetics | 15876567 | Identification of replication origins in archaeal genomes based on the Z-curve method. | Zhang R, Zhang CT | Archaea | 10.1155/2005/509646 | 2005 | Archaea/*genetics, DNA Replication/genetics, DNA, Archaeal/genetics, *Genome, Archaeal, Replication Origin/*genetics | |
| Phylogeny | 19628615 | Acidiplasma aeolicum gen. nov., sp. nov., a euryarchaeon of the family Ferroplasmaceae isolated from a hydrothermal pool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumulans comb. nov. | Golyshina OV, Yakimov MM, Lunsdorf H, Ferrer M, Nimtz M, Timmis KN, Wray V, Tindall BJ, Golyshin PN | Int J Syst Evol Microbiol | 10.1099/ijs.0.009639-0 | 2009 | DNA, Archaeal/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Thermoplasmales/*classification/genetics/*isolation & purification, *Water Microbiology | Genetics |
| Phylogeny | 23923548 | TRNomics: a comparative analysis of Picrophilus torridus with other archaeal thermoacidophiles. | Mallick B, Chakrabarti J, Das S, Ghosh Z | Indian J Biochem Biophys | 2005 | Base Pairing, Base Sequence, DNA, Archaeal/genetics, Molecular Sequence Data, RNA, Archaeal/*genetics, RNA, Transfer/*genetics, Species Specificity, Temperature, Thermococcus/classification/*genetics, Thermoplasmales/*genetics | Genetics | |
| Enzymology | 31549249 | Purification and characterization of a novel thermophilic beta-galactosidase from Picrophilus torridus of potential industrial application. | Murphy J, Walsh G | Extremophiles | 10.1007/s00792-019-01133-4 | 2019 | Archaeal Proteins/*chemistry/*isolation & purification, Enzyme Stability, *Hot Temperature, Industrial Microbiology, Thermoplasmales/*enzymology, beta-Galactosidase/*chemistry/*isolation & purification | Phylogeny |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3736 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9790) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9790 | |||
| 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) | |||
| 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 | |
| 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 | |||
| 81116 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43735.1 | StrainInfo: A central database for resolving microbial strain identifiers |