Strain identifier
BacDive ID: 16891
Type strain: 
Species: Thermodesulfobacterium commune
Strain Designation: YSRA-1
Strain history: <- J.G. Zeikus, YSRA-1
NCBI tax ID(s): 289377 (strain), 1741 (species)
version 8.1 (current version)
General
@ref: 995
BacDive-ID: 16891
DSM-Number: 2178
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-negative
description: Thermodesulfobacterium commune YSRA-1 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from thermal spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1741 | species |
| 289377 | strain |
strain history
- @ref: 995
- history: <- J.G. Zeikus, YSRA-1
doi: 10.13145/bacdive16891.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/thermodesulfobacteriota
- domain: Bacteria
- phylum: Thermodesulfobacteriota
- class: Thermodesulfobacteria
- order: Thermodesulfobacteriales
- family: Thermodesulfobacteriaceae
- genus: Thermodesulfobacterium
- species: Thermodesulfobacterium commune
- full scientific name: Thermodesulfobacterium commune Zeikus et al. 1995
@ref: 995
domain: Bacteria
phylum: Thermodesulfobacteria
class: Thermodesulfobacteria
order: Thermodesulfobacteriales
family: Thermodesulfobacteriaceae
genus: Thermodesulfobacterium
species: Thermodesulfobacterium commune
full scientific name: Thermodesulfobacterium commune Zeikus et al. 1995
strain designation: YSRA-1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.991
Culture and growth conditions
culture medium
- @ref: 995
- name: THERMODESULFOBACTERIUM MEDIUM (DSMZ Medium 206)
- growth: yes
- link: https://mediadive.dsmz.de/medium/206
- composition: Name: THERMODESULFOBACTERIUM MEDIUM (DSMZ Medium 206) Composition: Na-L-lactate 4.0 g/l Na2SO4 3.0 g/l Na2HPO4 x 12 H2O 2.0 g/l Yeast extract 1.0 g/l NH4Cl 1.0 g/l Na2S x 9 H2O 0.5 g/l KH2PO4 0.3 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.128 g/l NaCl 0.01 g/l FeCl2 x 4 H2O 0.002 g/l CoCl2 x 6 H2O 0.0017 g/l FeSO4 x 7 H2O 0.0015 g/l MnCl2 x 4 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l ZnCl2 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l Na2SeO3 x 5 H2O 0.0003 g/l CuCl2 0.0002 g/l H3BO3 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l Pyridoxine hydrochloride 5e-05 g/l Calcium D-(+)-pantothenate 2.5e-05 g/l p-Aminobenzoic acid 2.5e-05 g/l (DL)-alpha-Lipoic acid 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l Thiamine HCl 2.5e-05 g/l Riboflavin 2.5e-05 g/l Biotin 1e-05 g/l Folic acid 1e-05 g/l Vitamin B12 5e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 995 | positive | growth | 70 | thermophilic | |
| 69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 995 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 90 |
| 69480 | no | 99.946 |
Isolation, sampling and environmental information
isolation
- @ref: 995
- sample type: thermal spring
- geographic location: Wyoming, Yellowstone Natl. Park
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_5338.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_515;96_2584;97_3166;98_3978;99_5338&stattab=map
- Last taxonomy: Thermodesulfobacterium commune subclade
- 16S sequence: JQ346745
- Sequence Identity:
- Total samples: 477
- soil counts: 83
- aquatic counts: 280
- animal counts: 99
- plant counts: 15
Safety information
risk assessment
- @ref: 995
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thermodesulfobacterium commune strain YSRA-1 16S ribosomal RNA gene, partial sequence | JQ346745 | 1422 | ena | 1741 |
| 995 | Thermodesulfobacterium commune DSM 2178 16S ribosomal RNA gene, partial sequence | AF418169 | 1497 | ena | 289377 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermodesulfobacterium commune DSM 2178 | GCA_000734015 | complete | ncbi | 289377 |
| 66792 | Thermodesulfobacterium commune DSM 2178 | GCA_000746435 | scaffold | ncbi | 289377 |
| 66792 | Thermodesulfobacterium commune DSM 2178 | 289377.4 | wgs | patric | 289377 |
| 66792 | Thermodesulfobacterium commune DSM 2178 | 289377.5 | complete | patric | 289377 |
| 66792 | Thermodesulfobacterium commune DSM 2178 | 2574179772 | draft | img | 289377 |
| 66792 | Thermodesulfobacterium commune DSM 2178 | 2588253728 | complete | img | 289377 |
GC content
- @ref: 995
- GC-content: 34.4
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 90 | no |
| motile | yes | 90.863 | no |
| flagellated | no | 89.774 | no |
| gram-positive | no | 99.418 | no |
| anaerobic | yes | 99.998 | yes |
| aerobic | no | 99.646 | yes |
| halophile | no | 86.972 | no |
| spore-forming | no | 97.433 | no |
| thermophile | yes | 100 | yes |
| glucose-util | no | 64.06 | no |
| glucose-ferment | no | 85.296 | no |
External links
@ref: 995
culture collection no.: DSM 2178, ATCC 33708, VKM B-1767
straininfo link
- @ref: 85897
- straininfo: 47551
literature
- topic: Genetics
- Pubmed-ID: 25635017
- title: Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria).
- authors: Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA
- journal: Genome Announc
- DOI: 10.1128/genomeA.01490-14
- year: 2015
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 995 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2178) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2178 | |||
| 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) | |||
| 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 | |||
| 85897 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47551.1 | StrainInfo: A central database for resolving microbial strain identifiers |