Strain identifier
BacDive ID: 16670
Type strain: 
Species: Syntrophobacter fumaroxidans
Strain Designation: MPOB
Strain history: <- H. J. M. Harmsen; MPOB <- H. J. M. Harmsen and C. M. Plugge {1994}
NCBI tax ID(s): 335543 (strain), 119484 (species)
version 8.1 (current version)
General
@ref: 3779
BacDive-ID: 16670
DSM-Number: 10017
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Syntrophobacter fumaroxidans MPOB is an anaerobe, mesophilic bacterium that was isolated from methanogenic granular sludge, anaerobic reactor.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 119484 | species |
| 335543 | strain |
strain history
- @ref: 3779
- history: <- H. J. M. Harmsen; MPOB <- H. J. M. Harmsen and C. M. Plugge {1994}
doi: 10.13145/bacdive16670.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Syntrophobacterales
- family: Syntrophobacteraceae
- genus: Syntrophobacter
- species: Syntrophobacter fumaroxidans
- full scientific name: Syntrophobacter fumaroxidans Harmsen et al. 1998
synonyms
- @ref: 20215
- synonym: Syntrophobacterium fumaroxidans
@ref: 3779
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Syntrophobacterales
family: Syntrophobacteraceae
genus: Syntrophobacter
species: Syntrophobacter fumaroxidans
full scientific name: Syntrophobacter fumaroxidans Harmsen et al. 1998
strain designation: MPOB
type strain: yes
Morphology
colony morphology
- @ref: 3779
- incubation period: 8-14 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 3779 | SYNTROPHOBACTER (MPOB) MEDIUM (DSMZ Medium 684) | yes | https://mediadive.dsmz.de/medium/684 | Name: SYNTROPHOBACTER (MPOB) MEDIUM (DSMZ Medium 684) Composition: Na2-fumarate 3.19043 g/l Na2CO3 1.49551 g/l Na2HPO4 x 2 H2O 0.528415 g/l Na2S x 9 H2O 0.498504 g/l KH2PO4 0.408774 g/l NaCl 0.299103 g/l NH4Cl 0.299103 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.109671 g/l MgCl2 x 6 H2O 0.0997009 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 Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l p-Aminobenzoic 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 |
| 3779 | DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium641.pdf |
culture temp
- @ref: 3779
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 3779
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 3779
- sample type: methanogenic granular sludge, anaerobic reactor
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Bioreactor | |
| #Engineered | #Waste | #Activated sludge |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_6500.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_574;96_3074;97_3774;98_4794;99_6500&stattab=map
- Last taxonomy: Syntrophobacter fumaroxidans subclade
- 16S sequence: JQ346744
- Sequence Identity:
- Total samples: 1834
- soil counts: 618
- aquatic counts: 1077
- animal counts: 35
- plant counts: 104
Safety information
risk assessment
- @ref: 3779
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Syntrophobacter fumaroxidans MPOB 16S ribosomal RNA gene, partial sequence
- accession: JQ346744
- length: 1415
- database: ena
- NCBI tax ID: 335543
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Syntrophobacter fumaroxidans MPOB | GCA_000014965 | complete | ncbi | 335543 |
| 66792 | Syntrophobacter fumaroxidans MPOB | 335543.9 | complete | patric | 335543 |
| 66792 | Syntrophobacter fumaroxidans MPOB | 639633063 | complete | img | 335543 |
GC content
- @ref: 3779
- GC-content: 59
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 85.666 | no |
| flagellated | no | 97.385 | no |
| gram-positive | no | 99.12 | no |
| anaerobic | yes | 99.349 | yes |
| halophile | no | 88.168 | no |
| spore-forming | no | 88.391 | no |
| thermophile | no | 91.955 | yes |
| glucose-util | no | 65.133 | no |
| aerobic | no | 98.277 | yes |
| glucose-ferment | no | 85.864 | no |
External links
@ref: 3779
culture collection no.: DSM 10017
straininfo link
- @ref: 85691
- straininfo: 48732
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 9828440 | Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium. | Harmsen HJ, Van Kuijk BL, Plugge CM, Akkermans AD, De Vos WM, Stams AJ | Int J Syst Bacteriol | 10.1099/00207713-48-4-1383 | 1998 | Anaerobiosis, Biodegradation, Environmental, Bioreactors, Culture Media, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Gram-Negative Anaerobic Bacteria/classification/*isolation & purification/*metabolism/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, Propionates/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sulfates/*metabolism, Terminology as Topic, Waste Disposal, Fluid | Metabolism |
| Phylogeny | 15879275 | Syntrophobacter sulfatireducens sp. nov., a novel syntrophic, propionate-oxidizing bacterium isolated from UASB reactors. | Chen S, Liu X, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.63565-0 | 2005 | Acetic Acid/metabolism, Anaerobiosis, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Deltaproteobacteria/*classification/cytology/*isolation & purification/physiology, Fumarates/metabolism, Genes, rRNA, Gentian Violet, Hydrogen-Ion Concentration, Methane/metabolism, Molecular Sequence Data, Oxidation-Reduction, Phenazines, Phylogeny, Propionates/*metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sulfates/metabolism, Temperature, Thiosulfates/metabolism, *Water Microbiology | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3779 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10017) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10017 | |||
| 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) | |||
| 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 | |||
| 85691 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48732.1 | StrainInfo: A central database for resolving microbial strain identifiers |