Strain identifier
BacDive ID: 16690
Type strain: 
Species: Syntrophomonas zehnderi
Strain Designation: OL-4
Strain history: <- D. Z. Sousa, IBB-Institute for Biotechnology and Bioengineering, University of Minho, Braga, Portugal; OL-4 <- D. Z. Sousa {2005}
NCBI tax ID(s): 690567 (strain), 404335 (species)
version 8.1 (current version)
General
@ref: 7135
BacDive-ID: 16690
DSM-Number: 17840
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-variable, motile, rod-shaped
description: Syntrophomonas zehnderi OL-4 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from anaerobic sludge sampled from an EGSB reactor to treat oleate-based effluent.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 404335 | species |
| 690567 | strain |
strain history
- @ref: 7135
- history: <- D. Z. Sousa, IBB-Institute for Biotechnology and Bioengineering, University of Minho, Braga, Portugal; OL-4 <- D. Z. Sousa {2005}
doi: 10.13145/bacdive16690.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Syntrophomonadaceae
- genus: Syntrophomonas
- species: Syntrophomonas zehnderi
- full scientific name: Syntrophomonas zehnderi Sousa et al. 2007
@ref: 7135
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Syntrophomonadaceae
genus: Syntrophomonas
species: Syntrophomonas zehnderi
full scientific name: Syntrophomonas zehnderi Sousa et al. 2007
strain designation: OL-4
type strain: yes
Morphology
cell morphology
- @ref: 31971
- gram stain: variable
- cell length: 5.25 µm
- cell width: 0.4 µm
- cell shape: rod-shaped
- motility: yes
colony morphology
- @ref: 7135
- incubation period: >14 days
Culture and growth conditions
culture medium
- @ref: 7135
- name: SYNTROPHOMONAS ZEHNDERI MEDIUM (DSMZ Medium 347a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/347a
- composition: Name: SYNTROPHOMONAS ZEHNDERI MEDIUM (DSMZ Medium 347a) Composition: PIPES 14.8957 g/l Na2SO4 2.78053 g/l Na-laurate 2.76068 g/l CaCl2 x 2 H2O 1.82721 g/l Na2CO3 1.48957 g/l KH2PO4 0.496524 g/l NH4Cl 0.39722 g/l NaCl 0.39722 g/l MgCl2 x 6 H2O 0.327706 g/l Na2S x 9 H2O 0.297915 g/l L-Cysteine HCl x H2O 0.297915 g/l HCl 0.00248262 g/l FeCl2 x 4 H2O 0.00148957 g/l Sodium resazurin 0.000496524 g/l Pyridoxine hydrochloride 0.000297915 g/l Nicotinic acid 0.00019861 g/l Thiamine-HCl x 2 H2O 0.00019861 g/l CoCl2 x 6 H2O 0.000188679 g/l MnCl2 x 4 H2O 9.93049e-05 g/l Calcium pantothenate 9.93049e-05 g/l Vitamin B12 9.93049e-05 g/l p-Aminobenzoic acid 7.94439e-05 g/l ZnCl2 6.95134e-05 g/l Na2MoO4 x 2 H2O 3.57498e-05 g/l NiCl2 x 6 H2O 2.38332e-05 g/l D-(+)-biotin 1.9861e-05 g/l H3BO3 5.95829e-06 g/l CuCl2 x 2 H2O 1.9861e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7135 | positive | growth | 37 | mesophilic |
| 31971 | positive | growth | 25-40 | |
| 31971 | positive | optimum | 31 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31971 | positive | growth | 6.5-7.5 |
| 31971 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 7135 | anaerobe |
| 31971 | anaerobe |
spore formation
- @ref: 31971
- spore formation: yes
metabolite utilization
- @ref: 31971
- Chebi-ID: 27689
- metabolite: decanoate
- utilization activity: +
- kind of utilization tested: carbon source
Isolation, sampling and environmental information
isolation
- @ref: 7135
- sample type: anaerobic sludge sampled from an EGSB reactor to treat oleate-based effluent
- geographic location: Braga
- country: Portugal
- origin.country: PRT
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Biodegradation | #Anaerobic digestor |
| #Engineered | #Waste | #Industrial wastewater |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_8288.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_397;96_3804;97_4693;98_6032;99_8288&stattab=map
- Last taxonomy: Syntrophomonas zehnderi subclade
- 16S sequence: DQ898277
- Sequence Identity:
- Total samples: 2432
- soil counts: 289
- aquatic counts: 729
- animal counts: 1295
- plant counts: 119
Safety information
risk assessment
- @ref: 7135
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7135
- description: Syntrophomonas zehnderi strain OL-4 16S ribosomal RNA gene, partial sequence
- accession: DQ898277
- length: 1467
- database: ena
- NCBI tax ID: 690567
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Syntrophomonas zehnderi OL-4 | GCA_000983115 | scaffold | ncbi | 690567 |
| 66792 | Syntrophomonas zehnderi OL-4 | 690567.3 | wgs | patric | 690567 |
| 66792 | Syntrophomonas zehnderi OL-4 | 2675903293 | draft | img | 690567 |
GC content
- @ref: 31971
- GC-content: 37.6
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 75.885 | no |
| flagellated | no | 92.038 | no |
| gram-positive | no | 90.879 | yes |
| anaerobic | yes | 99.406 | yes |
| aerobic | no | 97.408 | no |
| halophile | no | 95.892 | no |
| spore-forming | yes | 90.548 | no |
| thermophile | no | 50.527 | yes |
| glucose-util | yes | 62.541 | no |
| glucose-ferment | no | 83.337 | no |
External links
@ref: 7135
culture collection no.: DSM 17840, JCM 13948
straininfo link
- @ref: 85709
- straininfo: 397085
literature
- topic: Phylogeny
- Pubmed-ID: 17329794
- title: Syntrophomonas zehnderi sp. nov., an anaerobe that degrades long-chain fatty acids in co-culture with Methanobacterium formicicum.
- authors: Sousa DZ, Smidt H, Alves MM, Stams AJM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64734-0
- year: 2007
- mesh: Anaerobiosis, Bacteria, Anaerobic/*classification/*metabolism, Bioreactors, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/*metabolism, Methanobacterium/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 7135 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17840) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17840 | ||||
| 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 | ||||
| 31971 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28226 | 28776041 | ||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | ||||
| 85709 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397085.1 | StrainInfo: A central database for resolving microbial strain identifiers |