Strain identifier
BacDive ID: 11789
Type strain: 
Species: Desulfofarcimen acetoxidans
Strain Designation: 5575
Strain history: <- N. Pfennig, 5575
NCBI tax ID(s): 485916 (strain), 58138 (species)
version 8.1 (current version)
General
@ref: 438
BacDive-ID: 11789
DSM-Number: 771
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile
description: Desulfofarcimen acetoxidans 5575 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from piggery waste.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 485916 | strain |
| 58138 | species |
strain history
- @ref: 438
- history: <- N. Pfennig, 5575
doi: 10.13145/bacdive11789.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Peptococcaceae
- genus: Desulfofarcimen
- species: Desulfofarcimen acetoxidans
- full scientific name: Desulfofarcimen acetoxidans (Widdel and Pfennig 1977) Watanabe et al. 2018
synonyms
- @ref: 20215
- synonym: Desulfotomaculum acetoxidans
@ref: 438
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptococcaceae
genus: Desulfofarcimen
species: Desulfofarcimen acetoxidans
full scientific name: Desulfofarcimen acetoxidans (Widdel and Pfennig 1977) Watanabe et al. 2018
strain designation: 5575
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 93.086 | |
| 69480 | 99.719 | positive |
colony morphology
- @ref: 438
- incubation period: 2-3 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_771_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 438
- name: DESULFOFARCIMEN MEDIUM (DSMZ Medium 124)
- growth: yes
- link: https://mediadive.dsmz.de/medium/124
- composition: Name: DESULFOFARCIMEN MEDIUM (DSMZ Medium 124) Composition: NaHCO3 4.48654 g/l Na2SO4 2.83151 g/l Na-acetate 1.39581 g/l Na-butyrate 1.39581 g/l NaCl 1.1665 g/l Yeast extract 0.997009 g/l MgCl2 x 6 H2O 0.398804 g/l Na2S x 9 H2O 0.398804 g/l KCl 0.299103 g/l NH4Cl 0.269192 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 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 p-Aminobenzoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 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 Folic acid 1.99402e-05 g/l Biotin 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
culture temp
- @ref: 438
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 438 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
- @ref: 69480
- spore formation: yes
- confidence: 99.448
Isolation, sampling and environmental information
isolation
- @ref: 438
- sample type: piggery waste
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | |
| #Host | #Mammals | #Suidae (Pig,Swine) |
taxonmaps
- @ref: 69479
- File name: preview.99_2045.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_287;96_1128;97_1324;98_1600;99_2045&stattab=map
- Last taxonomy: Desulfofarcimen acetoxidans subclade
- 16S sequence: Y11566
- Sequence Identity:
- Total samples: 67
- soil counts: 1
- aquatic counts: 7
- animal counts: 56
- plant counts: 3
Safety information
risk assessment
- @ref: 438
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: D.acetoxidans 16S rRNA gene
- accession: Y11566
- length: 1523
- database: ena
- NCBI tax ID: 485916
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfofarcimen acetoxidans DSM 771 | GCA_000024205 | complete | ncbi | 485916 |
| 66792 | Desulfotomaculum acetoxidans DSM 771 | 485916.5 | complete | patric | 485916 |
| 66792 | Desulfofarcimen acetoxidans DSM 771 | 644736351 | complete | img | 485916 |
GC content
- @ref: 438
- GC-content: 37.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 57 | no |
| motile | yes | 78.401 | no |
| flagellated | no | 81.168 | no |
| gram-positive | no | 85.229 | no |
| anaerobic | yes | 98.473 | yes |
| aerobic | no | 94.761 | yes |
| halophile | no | 98.092 | no |
| spore-forming | yes | 92.9 | no |
| thermophile | no | 91.75 | yes |
| glucose-util | yes | 65.404 | no |
| glucose-ferment | no | 85.412 | no |
External links
@ref: 438
culture collection no.: DSM 771, ATCC 49208, VKM B-1644
straininfo link
- @ref: 81007
- straininfo: 42351
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 16212113 | The uptake and accumulation of iron by the intestinal bacterium Desulfotomaculum acetoxidans DSM 771. | Pado R, Pawlowska-Cwiek L | Folia Biol (Krakow) | 10.3409/1734916054663519 | 2005 | Animals, Desulfotomaculum/*metabolism, Intestines/*microbiology, Iron/*metabolism | |
| Metabolism | 16265594 | The role of benzoate secreted by Desulfotomaculum acetoxidans DSM 771 in sulfate uptake. | Pawlowska-Cwiek L, Pado R | Acta Biochim Pol | 20050897 | 2005 | Benzoates/*metabolism, Hydrogen Sulfide/metabolism, Kinetics, Oxidation-Reduction, Peptococcaceae/growth & development/*metabolism, Spectrophotometry, Sulfates/*metabolism | Enzymology |
| Metabolism | 18062655 | Growth and antioxidant activity of Desulfotomaculum acetoxidans DSM 771 cultivated in acetate or lactate containing media. | Pawlowska-Cwiek L, Pado R | Pol J Microbiol | 2007 | Acetic Acid/chemistry/*metabolism, Antioxidants/*metabolism, Cell Proliferation, Culture Media/*chemistry, Desulfotomaculum/*growth & development/*metabolism, Glutathione, Hydrogen Sulfide, Lactic Acid/chemistry/*metabolism, Time Factors | Cultivation | |
| Metabolism | 21466042 | Peroxidase activity in the sulfate-reducing bacterium Desulfotomaculum acetoxidans DSM 771. | Pawlowska-Cwiek L | Pol J Microbiol | 2010 | Benzoates/analysis/metabolism, Cell Wall/enzymology, Desulfotomaculum/*enzymology/metabolism, Hydrogen Peroxide/analysis/metabolism, Hydrogen Sulfide/analysis/metabolism, Oxygen/analysis/metabolism, Peroxidases/isolation & purification/*metabolism, Sulfates/metabolism, Time Factors | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 438 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 771) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-771 | |||
| 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) | |||
| 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) | |||
| 81007 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42351.1 | StrainInfo: A central database for resolving microbial strain identifiers |