Strain identifier
BacDive ID: 17063
Type strain: 
Species: Pseudothermotoga thermarum
Strain Designation: LA3
Strain history: <- K. O. Stetter, Univ. Regensburg, Germany; LA3 <- R. Huber and E. Windberger {1987}
NCBI tax ID(s): 688269 (strain), 119394 (species)
version 8.1 (current version)
General
@ref: 1921
BacDive-ID: 17063
DSM-Number: 5069
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative
description: Pseudothermotoga thermarum LA3 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from continental solfataric spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 688269 | strain |
| 119394 | species |
strain history
- @ref: 1921
- history: <- K. O. Stetter, Univ. Regensburg, Germany; LA3 <- R. Huber and E. Windberger {1987}
doi: 10.13145/bacdive17063.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/thermotogota
- domain: Bacteria
- phylum: Thermotogota
- class: Thermotogae
- order: Thermotogales
- family: Thermotogaceae
- genus: Pseudothermotoga
- species: Pseudothermotoga thermarum
- full scientific name: Pseudothermotoga thermarum (Windberger et al. 1992) Bhandari and Gupta 2014
synonyms
- @ref: 20215
- synonym: Thermotoga thermarum
@ref: 1921
domain: Bacteria
phylum: Thermotogae
class: Thermotogae
order: Thermotogales
family: Thermotogaceae
genus: Pseudothermotoga
species: Pseudothermotoga thermarum
full scientific name: Pseudothermotoga thermarum (Windberger et al. 1992) Bhandari and Gupta 2014
strain designation: LA3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.908
multimedia
- @ref: 66793
- multimedia content: EM_DSM_5069_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1921
- name: PSEUDOTHERMOTOGA MEDIUM (DSMZ Medium 498)
- growth: yes
- link: https://mediadive.dsmz.de/medium/498
- composition: Name: PSEUDOTHERMOTOGA MEDIUM (DSMZ Medium 498) Composition: Starch 5.0 g/l NaCl 3.46 g/l MgSO4 x 7 H2O 0.88 g/l Na2-EDTA 0.77 g/l MgCl2 x 6 H2O 0.69 g/l Na2S x 9 H2O 0.5 g/l Yeast extract 0.5 g/l KH2PO4 0.5 g/l CaCl2 x 2 H2O 0.14 g/l KCl 0.08 g/l Nitrilotriacetic acid 0.0225 g/l NaBr 0.0125 g/l MnSO4 x H2O 0.0075 g/l H3BO3 0.004 g/l (NH4)2Ni(SO4)2 0.003 g/l CoSO4 x 7 H2O 0.0027 g/l ZnSO4 x 7 H2O 0.0027 g/l SrCl2 x 6 H2O 0.0019 g/l FeSO4 x 7 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.00045 g/l AlK(SO4)2 x 12 H2O 0.0003 g/l CuSO4 x 5 H2O 0.00015 g/l Na2MoO4 x 2 H2O 0.00015 g/l KI 1e-05 g/l Na2WO4 x 2 H2O 6e-06 g/l Na2SeO3 x 5 H2O 4.5e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 1921 | positive | growth | 70 | thermophilic | |
| 69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1921 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.694
Isolation, sampling and environmental information
isolation
- @ref: 1921
- sample type: continental solfataric spring
- geographic location: Lac Abbe
- country: Djibouti
- origin.country: DJI
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Spring |
| #Environmental | #Terrestrial | #Geologic |
| #Condition | #Sulfuric |
taxonmaps
- @ref: 69479
- File name: preview.99_8183.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_177;96_3766;97_4636;98_5952;99_8183&stattab=map
- Last taxonomy: Pseudothermotoga thermarum subclade
- 16S sequence: AB039769
- Sequence Identity:
- Total samples: 38
- soil counts: 1
- aquatic counts: 35
- animal counts: 1
- plant counts: 1
Safety information
risk assessment
- @ref: 1921
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 1921
- description: Thermotoga thermarum gene for 16S rRNA
- accession: AB039769
- length: 1471
- database: ena
- NCBI tax ID: 688269
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudothermotoga thermarum DSM 5069 | GCA_000217815 | complete | ncbi | 688269 |
| 66792 | Thermotoga thermarum DSM 5069 | 688269.3 | complete | patric | 688269 |
| 66792 | Pseudothermotoga thermarum DSM 5069 | 2503508007 | complete | img | 688269 |
GC content
- @ref: 1921
- GC-content: 40.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 87 | no |
| motile | yes | 81.338 | no |
| flagellated | no | 93.871 | no |
| gram-positive | no | 95.955 | no |
| anaerobic | yes | 99.463 | yes |
| aerobic | no | 98.457 | yes |
| halophile | no | 89.248 | no |
| spore-forming | no | 88.259 | no |
| thermophile | yes | 100 | yes |
| glucose-util | yes | 88.611 | no |
| glucose-ferment | yes | 51.388 | no |
External links
@ref: 1921
culture collection no.: DSM 5069, NBRC 107925
straininfo link
- @ref: 86063
- straininfo: 47895
literature
| Pubmed-ID | title | authors | journal | DOI | year | topic | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| 23422003 | Biochemical properties of a novel thermostable and highly xylose-tolerant beta-xylosidase/alpha-arabinosidase from Thermotoga thermarum. | Shi H, Li X, Gu H, Zhang Y, Huang Y, Wang L, Wang F | Biotechnol Biofuels | 10.1186/1754-6834-6-27 | 2013 | |||
| 24099409 | High-level expression of a novel thermostable and mannose-tolerant beta-mannosidase from Thermotoga thermarum DSM 5069 in Escherichia coli. | Shi H, Huang Y, Zhang Y, Li W, Li X, Wang F | BMC Biotechnol | 10.1186/1472-6750-13-83 | 2013 | Enzymology | Amino Acid Sequence, Bacterial Proteins/*biosynthesis/genetics, Cloning, Molecular, Computational Biology, DNA, Bacterial/genetics, Escherichia coli/genetics/*metabolism, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*enzymology/genetics, Half-Life, Hydrogen-Ion Concentration, Mannans/chemistry, Mannose/metabolism, Molecular Sequence Data, Phylogeny, Plasmids/genetics, Polysaccharides/chemistry, Substrate Specificity, Temperature, beta-Mannosidase/*biosynthesis/genetics | Metabolism |
| 24563323 | Characterization of a novel GH2 family alpha-L-arabinofuranosidase from hyperthermophilic bacterium Thermotoga thermarum. | Shi H, Zhang Y, Xu B, Tu M, Wang F | Biotechnol Lett | 10.1007/s10529-014-1493-6 | 2014 | Enzymology | Arabinose/analogs & derivatives, Bacteria/*enzymology/genetics, Copper/metabolism, Enzyme Inhibitors/metabolism, Enzyme Stability, Glycoside Hydrolases/chemistry/genetics/isolation & purification/*metabolism, Hydrogen-Ion Concentration, Kinetics, Molecular Weight, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Temperature, Zinc/metabolism | Metabolism |
| 26725313 | Characterization of a novel arabinose-tolerant alpha-L-arabinofuranosidase with high ginsenoside Rc to ginsenoside Rd bioconversion productivity. | Xie J, Zhao D, Zhao L, Pei J, Xiao W, Ding G, Wang Z, Xu J | J Appl Microbiol | 10.1111/jam.13040 | 2016 | Metabolism | Arabinose/*metabolism, Bacterial Proteins/*chemistry/genetics/*metabolism, Biotransformation, Enzyme Stability, Ginsenosides/*metabolism, Glycoside Hydrolases/*chemistry/genetics/*metabolism, Gram-Negative Anaerobic Bacteria/chemistry/*enzymology/genetics, Molecular Weight, Substrate Specificity | Enzymology |
| 27209035 | Expression and Characterization of Hyperthermostable Exo-polygalacturonase TtGH28 from Thermotoga thermophilus. | Wagschal K, Rose Stoller J, Chan VJ, Lee CC, Grigorescu AA, Jordan DB | Mol Biotechnol | 10.1007/s12033-016-9948-8 | 2016 | Metabolism | Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/metabolism, Catalytic Domain, Cloning, Molecular, Conserved Sequence, *Gene Expression, Genes, Synthetic, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/chemistry/*enzymology/genetics/metabolism, Models, Molecular, Polygalacturonase/chemistry/*genetics/*metabolism, Protein Multimerization | Enzymology |
| 29500062 | Thermostable xylanase-aided two-stage hydrolysis approach enhances sugar release of pretreated lignocellulosic biomass. | Long L, Tian D, Zhai R, Li X, Zhang Y, Hu J, Wang F, Saddler J | Bioresour Technol | 10.1016/j.biortech.2018.02.104 | 2018 | *Biomass, Cellulase, Cellulases, Hydrolysis, *Sugars | ||
| 29751706 | [Comparison of three different thermophilic beta-glucosidases for baicalin transformation]. | Wu T, Zhang SS, Pei JJ, Xiao W, Wang ZZ, Zhao LG | Zhongguo Zhong Yao Za Zhi | 10.19540/j.cnki.cjcmm.20180201.002 | 2018 | Metabolism | Flavonoids, Hydrogen-Ion Concentration, beta-Glucosidase/*metabolism | |
| 36399304 | Expression and Characterization of a GH38 alpha-Mannosidase from the Hyperthermophile Pseudothermotoga thermarum. | Yan X, Nie X, Li Q, Gao F, Liu P, Tan Z, Shi H | Appl Biochem Biotechnol | 10.1007/s12010-022-04243-6 | 2022 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1921 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5069) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5069 | |||
| 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) | |||
| 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 | |||
| 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) | |||
| 86063 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47895.1 | StrainInfo: A central database for resolving microbial strain identifiers |