Strain identifier
BacDive ID: 13742
Type strain: 
Species: Rhodovulum sulfidophilum
Strain Designation: W4
Strain history: <- T.A. Hansen, W4
NCBI tax ID(s): 1188256 (strain), 35806 (species)
version 8.1 (current version)
General
@ref: 754
BacDive-ID: 13742
DSM-Number: 1374
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Rhodovulum sulfidophilum W4 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from mud from intertidal flats.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1188256 | strain |
| 35806 | species |
strain history
- @ref: 754
- history: <- T.A. Hansen, W4
doi: 10.13145/bacdive13742.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Rhodovulum
- species: Rhodovulum sulfidophilum
- full scientific name: Rhodovulum sulfidophilum (Hansen and Veldkamp 1973) Hiraishi and Ueda 1994
synonyms
@ref synonym 20215 Rhodopseudomonas sulfidophila 20215 Rhodobacter sulfidophilus
@ref: 754
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Rhodovulum
species: Rhodovulum sulfidophilum
full scientific name: Rhodovulum sulfidophilum (Hansen and Veldkamp 1973) Hiraishi and Ueda 1994
strain designation: W4
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.999
Culture and growth conditions
culture medium
- @ref: 754
- 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: NaCl 25.0 g/l Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NH4Cl 0.4 g/l L-Cysteine HCl 0.3 g/l Yeast extract 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: 754
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 754
- oxygen tolerance: anaerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.81
compound production
| @ref | compound |
|---|---|
| 754 | ubiquinone-10 |
| 754 | hydrogen |
Isolation, sampling and environmental information
isolation
- @ref: 754
- sample type: mud from intertidal flats
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Environmental | #Terrestrial | #Tidal flat |
taxonmaps
- @ref: 69479
- File name: preview.99_1133.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_663;97_767;98_887;99_1133&stattab=map
- Last taxonomy: Rhodovulum sulfidophilum
- 16S sequence: D16423
- Sequence Identity:
- Total samples: 6072
- soil counts: 533
- aquatic counts: 4467
- animal counts: 971
- plant counts: 101
Safety information
risk assessment
- @ref: 754
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Rhodovulum sulfidophilum strain ATCC 35886 16S ribosomal RNA gene, partial sequence | DQ342323 | 1389 | ena | 1188256 |
| 20218 | Rhodovulum sulfidophilum gene for 16S ribosomal RNA, partial sequence and upstream region, strain: DSM 1374 | AB513346 | 726 | ena | 1188256 |
| 20218 | Rhodovulum sulfidophilum gene for 16S rRNA, strain: DSM1374 | D16423 | 1389 | ena | 1188256 |
| 20218 | Rhodovulum sulfidophilum 16S rRNA | D13475 | 1378 | ena | 35806 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodovulum sulfidophilum DSM 1374 | GCA_001633165 | complete | ncbi | 1188256 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | GCA_000520135 | chromosome | ncbi | 1188256 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | 1188256.8 | complete | patric | 1188256 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | 1188256.18 | plasmid | patric | 1188256 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | 1188256.19 | plasmid | patric | 1188256 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | 1188256.3 | complete | patric | 1188256 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | 1188256.20 | plasmid | patric | 1188256 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | 1188256.21 | plasmid | patric | 1188256 |
| 66792 | Rhodovulum sulfidophilum strain SNK001 | 35806.25 | plasmid | patric | 35806 |
| 66792 | Rhodovulum sulfidophilum strain TUT | 35806.7 | complete | patric | 35806 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | 2687453592 | complete | img | 1188256 |
| 66792 | Rhodovulum sulfidophilum DSM 1374 | 2667527571 | complete | img | 1188256 |
GC content
- @ref: 754
- GC-content: 70.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 69 | no |
| flagellated | no | 73.144 | no |
| gram-positive | no | 99.108 | no |
| anaerobic | yes | 74.655 | no |
| halophile | yes | 54.582 | no |
| spore-forming | no | 94.709 | no |
| glucose-util | yes | 86.105 | no |
| motile | yes | 75.142 | no |
| aerobic | no | 90.154 | yes |
| thermophile | no | 95.717 | yes |
| glucose-ferment | no | 85.545 | no |
External links
@ref: 754
culture collection no.: DSM 1374, ATCC 35886, LMG 5202
straininfo link
- @ref: 82924
- straininfo: 4840
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17684252 | Rhodovulum visakhapatnamense sp. nov. | Srinivas TNR, Anil Kumar P, Sasikala C, Ramana CV, Imhoff JF | Int J Syst Evol Microbiol | 10.1099/ijs.0.65076-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, India, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodovulum/*classification/genetics/physiology, Seawater/*microbiology | Genetics |
| 31979033 | Distribution of Phototrophic Purple Nonsulfur Bacteria in Massive Blooms in Coastal and Wastewater Ditch Environments. | Hiraishi A, Nagao N, Yonekawa C, Umekage S, Kikuchi Y, Eki T, Hirose Y | Microorganisms | 10.3390/microorganisms8020150 | 2020 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 754 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1374) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1374 | |||
| 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 | |||
| 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) | |||
| 82924 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4840.1 | StrainInfo: A central database for resolving microbial strain identifiers |