Strain identifier
BacDive ID: 11762
Type strain: 
Species: Desulfitobacterium dehalogenans
Strain Designation: JW/IU-DC1
Strain history: <- J. Wiegel; JW/IU-DC1 <- I. Utkin and J. Wiegel {1993}
NCBI tax ID(s): 756499 (strain), 36854 (species)
version 8.1 (current version)
General
@ref: 3497
BacDive-ID: 11762
DSM-Number: 9161
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile
description: Desulfitobacterium dehalogenans JW/IU-DC1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from freshwater pond sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 756499 | strain |
| 36854 | species |
strain history
- @ref: 3497
- history: <- J. Wiegel; JW/IU-DC1 <- I. Utkin and J. Wiegel {1993}
doi: 10.13145/bacdive11762.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Desulfitobacteriaceae
- genus: Desulfitobacterium
- species: Desulfitobacterium dehalogenans
- full scientific name: Desulfitobacterium dehalogenans Utkin et al. 1994
@ref: 3497
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptococcaceae
genus: Desulfitobacterium
species: Desulfitobacterium dehalogenans
full scientific name: Desulfitobacterium dehalogenans Utkin et al. 1994
strain designation: JW/IU-DC1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.915 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 3497 | DESULFITOBACTERIUM HAFNIENSE MEDIUM (DSMZ Medium 720) | yes | https://mediadive.dsmz.de/medium/720 | Name: DESULFITOBACTERIUM HAFNIENSE MEDIUM (DSMZ Medium 720) Composition: NaHCO3 2.59222 g/l Na-pyruvate 2.49252 g/l Na2S2O3 x 5 H2O 1.24626 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l K2HPO4 x 3 H2O 0.398804 g/l Na2S x 9 H2O 0.299103 g/l MgCl2 x 6 H2O 0.0997009 g/l NaCl 0.0997009 g/l CaCl2 x 2 H2O 0.0498504 g/l Na2-EDTA x 2 H2O 0.00518445 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water |
| 3497 | DESULFITOBACTERIUM MEDIUM (DSMZ Medium 663) | yes | https://mediadive.dsmz.de/medium/663 | Name: DESULFITOBACTERIUM MEDIUM (DSMZ Medium 663) Composition: KH2PO4 5.40218 g/l Na-pyruvate 2.48262 g/l Na2S2O3 x 5 H2O 1.9861 g/l Yeast extract 0.993049 g/l NH4Cl 0.496524 g/l L-Cysteine HCl x H2O 0.397219 g/l Na2S x 9 H2O 0.397219 g/l MgCl2 x 2 H2O 0.178749 g/l Nitrilotriacetic acid 0.0635551 g/l NaCl 0.00496524 g/l FeCl2 x 4 H2O 0.000993049 g/l CoCl2 x 6 H2O 0.000844091 g/l MnCl2 x 4 H2O 0.000496524 g/l ZnCl2 0.000496524 g/l Sodium resazurin 0.000496524 g/l CaCl2 x 2 H2O 0.000496524 g/l Pyridoxine hydrochloride 0.00019861 g/l NiCl2 x 6 H2O 0.000148957 g/l Na2SeO3 x 5 H2O 0.000148957 g/l p-Aminobenzoic acid 9.93049e-05 g/l (DL)-alpha-Lipoic acid 9.93049e-05 g/l CuCl2 9.93049e-05 g/l Nicotinic acid 9.93049e-05 g/l Thiamine HCl 9.93049e-05 g/l Riboflavin 9.93049e-05 g/l Calcium D-(+)-pantothenate 9.93049e-05 g/l H3BO3 4.96524e-05 g/l Na2MoO4 x 2 H2O 4.96524e-05 g/l Biotin 3.97219e-05 g/l Folic acid 3.97219e-05 g/l Vitamin B12 1.9861e-06 g/l Distilled water |
culture temp
- @ref: 3497
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 3497 | anaerobe | |
| 69480 | anaerobe | 98.323 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 93 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 3497
- sample type: freshwater pond sediment
- geographic location: Athens, Ga., Sandy Creek Nature Park
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 3497
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Desulfitobacterium dehalogenans strain DSM 9161 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | DQ834677 | 662 | ena | 756499 |
| 3497 | Desulfitobacterium dehalogenans 16S ribosomal RNA | L28946 | 1514 | ena | 756499 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfitobacterium dehalogenans ATCC 51507 | GCA_000243155 | complete | ncbi | 756499 |
| 66792 | Desulfitobacterium dehalogenans ATCC 51507 | 756499.4 | wgs | patric | 756499 |
| 66792 | Desulfitobacterium dehalogenans JW/IU-DC1, ATCC 51507 | 2507262031 | complete | img | 756499 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 3497 | 44 | thermal denaturation, midpoint method (Tm) |
| 3497 | 45 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 93 | no |
| motile | yes | 86.371 | no |
| flagellated | no | 73.029 | no |
| gram-positive | no | 80.887 | no |
| anaerobic | yes | 97.524 | yes |
| aerobic | no | 97.139 | yes |
| halophile | no | 95.05 | no |
| spore-forming | yes | 94.834 | no |
| thermophile | no | 99.059 | yes |
| glucose-util | yes | 58.827 | no |
| glucose-ferment | no | 80.84 | no |
External links
@ref: 3497
culture collection no.: DSM 9161, ATCC 51507
straininfo link
- @ref: 80980
- straininfo: 43024
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 7887614 | Specificity of reductive dehalogenation of substituted ortho-chlorophenols by Desulfitobacterium dehalogenans JW/IU-DC1. | Utkin I, Dalton DD, Wiegel J | Appl Environ Microbiol | 10.1128/aem.61.1.346-351.1995 | 1995 | Bacteria, Anaerobic/*metabolism, Chlorophenols/*metabolism, Electron Transport, Halogens/metabolism, Phenylacetates/metabolism, Substrate Specificity | |
| Phylogeny | 7981092 | Isolation and characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an anaerobic bacterium which reductively dechlorinates chlorophenolic compounds. | Utkin I, Woese C, Wiegel J | Int J Syst Bacteriol | 10.1099/00207713-44-4-612 | 1994 | Bacteria, Anaerobic/growth & development/*isolation & purification, Chlorophenols/*metabolism, Fermentation, Gram-Positive Bacteria/growth & development/*isolation & purification | Enzymology |
| Phylogeny | 8863430 | Isolation and characterization of Desulfitobacterium frappieri sp. nov., an anaerobic bacterium which reductively dechlorinates pentachlorophenol to 3-chlorophenol. | Bouchard B, Beaudet R, Villemur R, McSween G, Lepine F, Bisaillon JG | Int J Syst Bacteriol | 10.1099/00207713-46-4-1010 | 1996 | Bacteria, Anaerobic/*metabolism, Base Sequence, Chlorophenols/*metabolism, Gram-Positive Bacteria/classification/*metabolism, Molecular Sequence Data, Pentachlorophenol/*metabolism, Phylogeny | Metabolism |
| Metabolism | 11525991 | Energy yield of respiration on chloroaromatic compounds in Desulfitobacterium dehalogenans. | van de Pas BA, Jansen S, Dijkema C, Schraa G, de Vos WM, Stams AJ | Appl Environ Microbiol | 10.1128/AEM.67.9.3958-3963.2001 | 2001 | Bacteria, Anaerobic/*enzymology/growth & development, Biomass, Carbon Dioxide/metabolism, Culture Media, Electron Transport, *Energy Metabolism, Magnetic Resonance Spectroscopy, Oxidation-Reduction, Phenylacetates/*metabolism, Phosphorylation | Cultivation |
| 16535014 | Specificity of Reductive Dehalogenation of Substituted ortho-Chlorophenols by Desulfitobacterium dehalogenans JW/IU-DC1. | Utkin I, Dalton DD, Wiegel J | Appl Environ Microbiol | 10.1128/aem.61.4.1677-1677c.1995 | 1995 | |||
| Genetics | 25512312 | Genomic, proteomic, and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. | Kruse T, van de Pas BA, Atteia A, Krab K, Hagen WR, Goodwin L, Chain P, Boeren S, Maphosa F, Schraa G, de Vos WM, van der Oost J, Smidt H, Stams AJ | J Bacteriol | 10.1128/JB.02370-14 | 2014 | Bacterial Proteins/chemistry/genetics/metabolism, Desulfitobacterium/chemistry/enzymology/*genetics/*metabolism, Electron Transport, Formates/metabolism, Fumarates/metabolism, Genome, Bacterial, *Genomics, Halogens/*metabolism, Molecular Sequence Data, Operon, *Proteomics | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3497 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9161) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9161 | |||
| 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) | |||
| 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 | |||
| 80980 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43024.1 | StrainInfo: A central database for resolving microbial strain identifiers |