Strain identifier
BacDive ID: 17663
Type strain: 
Species: Steroidobacter denitrificans
Strain Designation: FS
Strain history: <- M. Fahrbach, Univ. Aachen; FS
NCBI tax ID(s): 465721 (species)
version 8.1 (current version)
General
@ref: 7577
BacDive-ID: 17663
DSM-Number: 18526
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Steroidobacter denitrificans FS is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from anoxic sewage sludge.
NCBI tax id
- NCBI tax id: 465721
- Matching level: species
strain history
- @ref: 7577
- history: <- M. Fahrbach, Univ. Aachen; FS
doi: 10.13145/bacdive17663.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Nevskiales
- family: Steroidobacteraceae
- genus: Steroidobacter
- species: Steroidobacter denitrificans
- full scientific name: Steroidobacter denitrificans Fahrbach et al. 2008
@ref: 7577
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Steroidobacteraceae
genus: Steroidobacter
species: Steroidobacter denitrificans
full scientific name: Steroidobacter denitrificans Fahrbach et al. 2008
strain designation: FS
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32337 | negative | 0.61 µm | 0.3-0.5 µm | rod-shaped | yes | |
| 69480 | yes | 91.985 | ||||
| 69480 | negative | 100 |
colony morphology
- @ref: 7577
- incubation period: >14 days
pigmentation
- @ref: 32337
- production: yes
Culture and growth conditions
culture medium
- @ref: 7577
- name: STEROIDOBACTER MEDIUM (DSMZ Medium 1116)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1116
- composition: Name: STEROIDOBACTER MEDIUM (DSMZ Medium 1116) Composition: NaCl 1.0 g/l KCl 0.5 g/l NaNO3 0.42 g/l MgCl2 x 6 H2O 0.4 g/l NH4Cl 0.25 g/l KH2PO4 0.2 g/l CaCl2 x 2 H2O 0.15 g/l Na2SO4 0.07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7577 | positive | growth | 28 | mesophilic |
| 32337 | positive | growth | 20-38 | |
| 32337 | positive | optimum | 28-30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 32337 | positive | growth | 6.1-7.8 |
| 32337 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 7577 | anaerobe |
| 32337 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32337 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.999 |
observation
- @ref: 32337
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32337 | 30089 | acetate | + | carbon source |
| 32337 | 29987 | glutamate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32337 | catalase | + | 1.11.1.6 |
| 32337 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 7577
- sample type: anoxic sewage sludge
- geographic location: Aachen-Soers
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Sewage sludge |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_7120.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_626;96_3339;97_4096;98_5238;99_7120&stattab=map
- Last taxonomy: Steroidobacter denitrificans subclade
- 16S sequence: EF605262
- Sequence Identity:
- Total samples: 4646
- soil counts: 3121
- aquatic counts: 1017
- animal counts: 228
- plant counts: 280
Safety information
risk assessment
- @ref: 7577
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7577
- description: Steroidobacter denitrificans strain FS 16S ribosomal RNA gene, partial sequence
- accession: EF605262
- length: 1407
- database: ena
- NCBI tax ID: 465721
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Steroidobacter denitrificans DSM 18526 | GCA_001579945 | complete | ncbi | 465721 |
| 66792 | Steroidobacter denitrificans strain DSM 18526 | 465721.9 | complete | patric | 465721 |
| 66792 | Steroidobacter denitrificans DSM 18526 | 2721755797 | complete | img | 465721 |
GC content
- @ref: 32337
- GC-content: 61.9
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 79.907 | no |
| gram-positive | no | 98.472 | yes |
| anaerobic | no | 94.518 | no |
| aerobic | no | 50.618 | no |
| halophile | no | 92.929 | no |
| spore-forming | no | 93.029 | yes |
| thermophile | no | 90.588 | yes |
| glucose-util | no | 53.791 | no |
| motile | yes | 86.016 | yes |
| glucose-ferment | no | 87.275 | no |
External links
@ref: 7577
culture collection no.: DSM 18526, JCM 14622
straininfo link
- @ref: 86654
- straininfo: 403599
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 18768632 | Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium. | Fahrbach M, Kuever J, Remesch M, Huber BE, Kampfer P, Dott W, Hollender J | Int J Syst Evol Microbiol | 10.1099/ijs.0.65342-0 | 2008 | Anaerobiosis, Bacterial Typing Techniques, Catalase/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/metabolism, Gammaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Genes, rRNA, Glutamic Acid/metabolism, Gonadal Steroid Hormones/*metabolism, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nitrates/metabolism, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Sodium Chloride/metabolism, Spores, Bacterial/cytology, Temperature | Phylogeny |
| Phylogeny | 24844263 | Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes. | Nogi Y, Yoshizumi M, Hamana K, Miyazaki M, Horikoshi K | Int J Syst Evol Microbiol | 10.1099/ijs.0.062620-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fruit/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polyamines/chemistry, Polyvinyl Alcohol/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Vitis/*microbiology | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 7577 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18526) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18526 | ||||
| 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 | ||||
| 32337 | 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 | 28569 | 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 | ||||
| 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 | ||||
| 86654 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403599.1 | StrainInfo: A central database for resolving microbial strain identifiers |