Strain identifier
BacDive ID: 2989
Type strain: 
Species: Rhodoferax fermentans
Strain Designation: FR 2
Strain history: A. Hiraishi FR2.
NCBI tax ID(s): 28066 (species)
version 8.1 (current version)
General
@ref: 3815
BacDive-ID: 2989
DSM-Number: 10138
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Rhodoferax fermentans FR 2 is an anaerobe, mesophilic, motile bacterium that was isolated from sewage ditch.
NCBI tax id
- NCBI tax id: 28066
- Matching level: species
strain history
| @ref | history |
|---|---|
| 3815 | <- J. H. Klemme <- JCM <- A. Hiraishi, strain Fr 2 |
| 67770 | A. Hiraishi FR2. |
doi: 10.13145/bacdive2989.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Rhodoferax
- species: Rhodoferax fermentans
- full scientific name: Rhodoferax fermentans Hiraishi et al. 1992
@ref: 3815
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Rhodoferax
species: Rhodoferax fermentans
full scientific name: Rhodoferax fermentans Hiraishi et al. 1992
strain designation: FR 2
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.417 | |
| 69480 | 99.981 | negative |
Culture and growth conditions
culture medium
- @ref: 3815
- name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
- growth: yes
- link: https://mediadive.dsmz.de/medium/27
- composition: Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27; with strain-specific modifications) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Yeast extract 0.5 g/l Ammonium acetate 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NH4Cl 0.4 g/l NaCl 0.4 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Resazurin 0.005 g/l Fe(III) citrate 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 3815 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 3815
- oxygen tolerance: anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.982 |
observation
- @ref: 67770
- observation: quinones: Q-8, RQ-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 3815 | sewage ditch | Japan | JPN | Asia |
| 56743 | Sewage ditch | |||
| 67770 | Sewage ditch |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Wastewater
Safety information
risk assessment
- @ref: 3815
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3815
- description: Rhodoferax fermentans gene for 16S ribosomal RNA, partial sequence, strain: FR2
- accession: D16211
- length: 1457
- database: ena
- NCBI tax ID: 28066
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodoferax fermentans JCM 7819 | GCA_002017865 | contig | ncbi | 28066 |
| 66792 | Rhodoferax fermentans DSM 10138 | GCA_016583655 | scaffold | ncbi | 28066 |
| 66792 | Rhodoferax fermentans strain DSM 10138 | 28066.15 | wgs | patric | 28066 |
| 66792 | Rhodoferax fermentans strain JCM 7819 | 28066.3 | wgs | patric | 28066 |
| 66792 | Rhodoferax fermentans JCM 7819 | 2894787282 | draft | img | 28066 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 3815 | 60.1 | |
| 67770 | 60.1 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 87.406 | no |
| gram-positive | no | 99.067 | no |
| anaerobic | yes | 57.823 | yes |
| aerobic | no | 87.392 | yes |
| halophile | no | 94.735 | no |
| spore-forming | no | 95.762 | no |
| thermophile | no | 99.335 | yes |
| glucose-util | yes | 68.444 | no |
| motile | yes | 91.864 | no |
| glucose-ferment | no | 82.648 | no |
External links
@ref: 3815
culture collection no.: DSM 10138, ATCC 49787, JCM 7819, CCUG 45364, NBRC 16659, IFO 16659
straininfo link
- @ref: 72511
- straininfo: 42686
literature
- topic: Phylogeny
- Pubmed-ID: 28956356
- title: Rhodoferax koreense sp. nov, an obligately aerobic bacterium within the family Comamonadaceae, and emended description of the genus Rhodoferax.
- authors: Farh ME, Kim YJ, Singh P, Jung SY, Kang JP, Yang DC
- journal: J Microbiol
- DOI: 10.1007/s12275-017-7033-z
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/*genetics/*isolation & purification/physiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial/genetics, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/microbiology, Ubiquinone/analysis
- topic2: Transcriptome
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3815 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10138) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10138 | |||
| 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 | |||
| 56743 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 45364) | https://www.ccug.se/strain?id=45364 | |||
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 72511 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42686.1 | StrainInfo: A central database for resolving microbial strain identifiers |