Strain identifier
BacDive ID: 4218
Type strain: 
Species: Syntrophotalea carbinolica
Strain Designation: Bd1, GraBd1
Strain history: <- B. Schink, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; GraBd1 <- B. Schink {1982}
NCBI tax ID(s): 338963 (strain), 19 (species)
version 9.1 (current version)
General
@ref: 1062
BacDive-ID: 4218
DSM-Number: 2380
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative
description: Syntrophotalea carbinolica Bd1 is an anaerobe, Gram-negative bacterium that was isolated from mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 338963 | strain |
| 19 | species |
strain history
- @ref: 1062
- history: <- B. Schink, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; GraBd1 <- B. Schink {1982}
doi: 10.13145/bacdive4218.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfuromonadales
- family: Syntrophotaleaceae
- genus: Syntrophotalea
- species: Syntrophotalea carbinolica
- full scientific name: Syntrophotalea carbinolica (Schink 1984) Waite et al. 2020
synonyms
- @ref: 20215
- synonym: Pelobacter carbinolicus
@ref: 1062
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfuromonadales
family: Syntrophotaleaceae
genus: Syntrophotalea
species: Syntrophotalea carbinolica
full scientific name: Syntrophotalea carbinolica (Schink 1984) Waite et al. 2020
strain designation: Bd1, GraBd1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 97.673
Culture and growth conditions
culture medium
- @ref: 1062
- name: PROPIONIGENIUM MODESTUM MEDIUM (MARINE) (DSMZ Medium 293)
- growth: yes
- link: https://mediadive.dsmz.de/medium/293
- composition: Name: PROPIONIGENIUM MODESTUM MEDIUM (MARINE) (DSMZ Medium 293; with strain-specific modifications) Composition: NaCl 19.98 g/l MgCl2 x 6 H2O 2.997 g/l Na2CO3 1.24875 g/l 2,3-butanediol 0.899101 g/l KCl 0.499501 g/l Na2S x 9 H2O 0.35964 g/l NH4Cl 0.24975 g/l KH2PO4 0.1998 g/l CaCl2 x 2 H2O 0.14985 g/l HCl 0.0024975 g/l FeCl2 x 4 H2O 0.0014985 g/l Sodium resazurin 0.0004995 g/l CoCl2 x 6 H2O 0.00018981 g/l MnCl2 x 4 H2O 9.99001e-05 g/l ZnCl2 6.99301e-05 g/l Na2MoO4 x 2 H2O 3.5964e-05 g/l NiCl2 x 6 H2O 2.3976e-05 g/l H3BO3 5.99401e-06 g/l CuCl2 x 2 H2O 1.998e-06 g/l Distilled water
culture temp
- @ref: 1062
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 1062
- oxygen tolerance: anaerobe
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 1062
- sample type: mud
- geographic location: Venice, Canale Grande
- country: Italy
- origin.country: ITA
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
taxonmaps
- @ref: 69479
- File name: preview.99_309.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_50;96_214;97_233;98_262;99_309&stattab=map
- Last taxonomy: Syntrophotalea carbinolica subclade
- 16S sequence: X79413
- Sequence Identity:
- Total samples: 300
- soil counts: 20
- aquatic counts: 275
- animal counts: 5
Safety information
risk assessment
- @ref: 1062
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Pelobacter carbinolicus 16S ribosomal RNA gene, partial sequence | U23141 | 1414 | nuccore | 19 |
| 20218 | P.carbinolicus 16S rDNA | X79413 | 1476 | nuccore | 338963 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Syntrophotalea carbinolica DSM 2380 | GCA_000012885 | complete | ncbi | 338963 |
| 66792 | Pelobacter carbinolicus DSM 2380 | 338963.6 | complete | patric | 338963 |
| 66792 | Syntrophotalea carbinolica DSM 2380 | 2518285547 | draft | img | 338963 |
| 66792 | Syntrophotalea carbinolica DSM 2380 | 2518285546 | draft | img | 338963 |
| 66792 | Syntrophotalea carbinolica DSM 2380 | 637000204 | complete | img | 338963 |
GC content
- @ref: 1062
- GC-content: 55.1
- method: sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.673 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 67.679 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 76.774 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 82.658 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 83.175 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 72.568 | no |
External links
@ref: 1062
culture collection no.: DSM 2380, NBRC 103641
straininfo link
- @ref: 73718
- straininfo: 47605
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 2792735 | Evidence for oxidative thiolytic cleavage of acetoin in Pelobacter carbinolicus analogous to aerobic oxidative decarboxylation of pyruvate. | Oppermann FB, Steinbuchel A, Schlegel HG | FEMS Microbiol Lett | 10.1016/0378-1097(89)90087-6 | 1989 | Acetoin/*metabolism, Acetyl Coenzyme A/biosynthesis, Acetyltransferases/metabolism, Bacteria, Anaerobic/*metabolism, Butanones/*metabolism, Chromatography, Decarboxylation, Dihydrolipoamide Dehydrogenase/metabolism, Dihydrolipoyllysine-Residue Acetyltransferase, Electrophoresis, Polyacrylamide Gel, Ethylene Glycol, Ethylene Glycols/metabolism, Metronidazole/metabolism, Models, Chemical, Oxidation-Reduction, *Pyruvate Dehydrogenase Complex, Pyruvates/*metabolism, Pyruvic Acid | Enzymology |
| Phylogeny | 33570486 | Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments. | Baesman SM, Sutton JM, Fierst JL, Akob DM, Oremland RS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004698 | 2021 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1062 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2380) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2380 | |||
| 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 | |||
| 73718 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47605.1 | StrainInfo: A central database for resolving microbial strain identifiers |