Strain identifier
BacDive ID: 14005
Type strain:
Species: Rhodospirillum rubrum
Strain Designation: S 1, S1
Strain history: CIP <- 1970, F. Gasser, Inst. Pasteur, Paris, France <- NCIB <- S.R. Elsden: strain S1 <- C.B. van Niel: strain ATH 1.1.1
NCBI tax ID(s): 269796 (strain), 1085 (species)
General
@ref: 120
BacDive-ID: 14005
DSM-Number: 467
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Rhodospirillum rubrum S 1 is an anaerobe, mesophilic, motile bacterium of the family Rhodospirillaceae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1085 | species |
269796 | strain |
strain history
@ref | history |
---|---|
120 | <- ATCC <- NCIB <- S.R. Elsden, S 1 <- C.B. van Niel |
122298 | CIP <- 1970, F. Gasser, Inst. Pasteur, Paris, France <- NCIB <- S.R. Elsden: strain S1 <- C.B. van Niel: strain ATH 1.1.1 |
doi: 10.13145/bacdive14005.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Rhodospirillaceae
- genus: Rhodospirillum
- species: Rhodospirillum rubrum
- full scientific name: Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Spirillum rubrum
@ref: 120
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodospirillales
family: Rhodospirillaceae
genus: Rhodospirillum
species: Rhodospirillum rubrum
full scientific name: Rhodospirillum rubrum (Esmarch 1887) Molisch 1907
strain designation: S 1, S1
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 94.937 | ||
69480 | 99.96 | negative | ||
122298 | yes | negative | rod-shaped |
colony morphology
- @ref: 46704
- incubation period: 5 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_467_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
120 | RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) | yes | https://mediadive.dsmz.de/medium/27 | Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 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 |
35750 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
122298 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
122298 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
120 | positive | growth | 28 | mesophilic |
35750 | positive | growth | 30 | mesophilic |
46704 | positive | growth | 30 | mesophilic |
122298 | positive | growth | 15-30 | |
122298 | no | growth | 5 | psychrophilic |
122298 | no | growth | 37 | mesophilic |
122298 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
120 | anaerobe |
46704 | aerobe |
122298 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.971 |
compound production
@ref | compound |
---|---|
120 | carotenoids |
120 | ubiquinone-10 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
122298 | NaCl | positive | growth | 0-2 % |
122298 | NaCl | no | growth | 4 % |
122298 | NaCl | no | growth | 6 % |
122298 | NaCl | no | growth | 8 % |
122298 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
122298 | 16947 | citrate | - | carbon source |
122298 | 4853 | esculin | + | hydrolysis |
122298 | 17234 | glucose | - | fermentation |
122298 | 17716 | lactose | - | fermentation |
122298 | 17632 | nitrate | - | reduction |
122298 | 16301 | nitrite | - | reduction |
122298 | 132112 | sodium thiosulfate | - | builds gas from |
122298 | 17234 | glucose | +/- | degradation |
122298 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 122298
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 122298
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
122298 | 15688 | acetoin | - | |
122298 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
122298 | oxidase | + | |
122298 | beta-galactosidase | - | 3.2.1.23 |
122298 | alcohol dehydrogenase | - | 1.1.1.1 |
122298 | gelatinase | - | |
122298 | amylase | - | |
122298 | DNase | - | |
122298 | caseinase | - | 3.4.21.50 |
122298 | catalase | + | 1.11.1.6 |
122298 | tween esterase | - | |
122298 | gamma-glutamyltransferase | + | 2.3.2.2 |
122298 | lecithinase | - | |
122298 | lipase | - | |
122298 | lysine decarboxylase | - | 4.1.1.18 |
122298 | ornithine decarboxylase | - | 4.1.1.17 |
122298 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
122298 | protease | - | |
122298 | tryptophan deaminase | - | |
122298 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122298 | - | - | - | - | - | - | - | - | - | - | + | - | + | + | - | + | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122298 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | + | - | - | - | - | - | - | - | + | + | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_6089.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_319;96_2902;97_3569;98_4518;99_6089&stattab=map
- Last taxonomy: Rhodospirillum rubrum subclade
- 16S sequence: D30778
- Sequence Identity:
- Total samples: 1489
- soil counts: 261
- aquatic counts: 1019
- animal counts: 135
- plant counts: 74
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
120 | 1 | Risk group (German classification) |
122298 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rhodospirillum rubrum gene for 16S ribosomal RNA | D30778 | 1406 | ena | 269796 |
20218 | Rhodospirillum rubrum (ATCC 11170) 16S ribosomal RNA (partial) | M55497 | 263 | ena | 269796 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhodospirillum rubrum DSM 467 | GCA_019134555 | complete | ncbi | 1085 |
66792 | Rhodospirillum rubrum ATCC 11170 | GCA_000013085 | complete | ncbi | 269796 |
66792 | Rhodospirillum rubrum ATCC 11170 | 269796.21 | plasmid | patric | 269796 |
66792 | Rhodospirillum rubrum ATCC 11170 | 269796.9 | complete | patric | 269796 |
66792 | Rhodospirillum rubrum F11 | 1036743.4 | complete | patric | 1036743 |
66792 | Rhodospirillum rubrum strain DSM 467 | 1085.17 | complete | patric | 1085 |
66792 | Rhodospirillum rubrum S1, ATCC 11170 | 637000241 | complete | img | 269796 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | yes | 88.825 | no |
flagellated | yes | 73.882 | no |
gram-positive | no | 98.846 | no |
anaerobic | yes | 72.705 | no |
halophile | no | 94.889 | no |
spore-forming | no | 90.937 | no |
thermophile | no | 99.178 | yes |
glucose-util | yes | 72.989 | no |
aerobic | no | 89.648 | no |
glucose-ferment | no | 85.385 | no |
External links
@ref: 120
culture collection no.: DSM 467, ATCC 11170, NCIB 8255, CCUG 17859, CIP 70.61, LMG 4362, NCIMB 8255, ATH 1.1.1
straininfo link
- @ref: 83175
- straininfo: 13840
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Enzymology | 7669805 | Electron paramagnetic resonance studies of ferric cytochrome c' from photosynthetic bacteria. | Fujii S, Yoshimura T, Kamada H, Yamaguchi K, Suzuki S, Shidara S, Takakuwa S | Biochim Biophys Acta | 10.1016/0167-4838(95)00092-9 | 1995 | Chromatium/*enzymology, Cytochrome-c Peroxidase/chemistry, Electron Spin Resonance Spectroscopy, Hydrogen-Ion Concentration, Peroxidases/*chemistry/isolation & purification, Rhodobacter capsulatus/*enzymology, Rhodopseudomonas/*enzymology, Rhodospirillum/*enzymology | Phylogeny |
Metabolism | 8547347 | Spectroscopic characterization of nitrosylheme in nitric oxide complexes of ferric and ferrous cytochrome c' from photosynthetic bacteria. | Yoshimura T, Fujii S, Kamada H, Yamaguchi K, Suzuki S, Shidara S, Takakuwa S | Biochim Biophys Acta | 10.1016/0167-4838(95)00187-5 | 1996 | Cytochrome c Group/chemistry/*metabolism, Electron Spin Resonance Spectroscopy, Ferric Compounds/metabolism, Ferrous Compounds/metabolism, Heme/*analogs & derivatives/chemistry, Nitric Oxide/*metabolism, Photosynthesis, Rhodospirillales/*chemistry, Spectrophotometry | |
Genetics | 16151144 | Whole-genome shotgun optical mapping of Rhodospirillum rubrum. | Reslewic S, Zhou S, Place M, Zhang Y, Briska A, Goldstein S, Churas C, Runnheim R, Forrest D, Lim A, Lapidus A, Han CS, Roberts GP, Schwartz DC | Appl Environ Microbiol | 10.1128/AEM.71.9.5511-5522.2005 | 2005 | Contig Mapping/methods, *Genome, Bacterial, Image Processing, Computer-Assisted, Restriction Mapping/*methods, Rhodospirillum rubrum/*genetics, Sequence Analysis, DNA | Transcriptome |
Stress | 20544803 | Effects of ethanol, formaldehyde, and gentle heat fixation in confocal resonance Raman microscopy of purple nonsulfur bacteria. | Kniggendorf AK, Gaul TW, Meinhardt-Wollweber M | Microsc Res Tech | 10.1002/jemt.20889 | 2011 | Ethanol/chemistry, Fixatives/chemistry, Formaldehyde/chemistry, Hot Temperature, Microscopy, Confocal, Rhodospirillaceae/*chemistry/cytology, Spectrum Analysis, Raman, Tissue Fixation/instrumentation/*methods | |
Metabolism | 20852980 | Aniline-induced tryptophan production and identification of indole derivatives from three purple bacteria. | Mujahid M, Sasikala Ch, Ramana ChV | Curr Microbiol | 10.1007/s00284-010-9609-2 | 2010 | Aniline Compounds/*metabolism, Betaproteobacteria/*metabolism, Biodegradation, Environmental, Chromatography, High Pressure Liquid, Chromatography, Liquid, Indoleacetic Acids/isolation & purification, Indoles/analysis/isolation & purification/*metabolism, Industrial Waste, Mass Spectrometry, Metabolic Networks and Pathways, Rhodobacter sphaeroides/*metabolism, Rhodospirillum rubrum/*metabolism, Tandem Mass Spectrometry, Tryptophan/*metabolism, ortho-Aminobenzoates/isolation & purification | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
120 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 467) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-467 | |||
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 | |
35750 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/10536 | ||||
46704 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 17859) | https://www.ccug.se/strain?id=17859 | |||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
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 | |
68382 | Automatically annotated from API zym | |||||
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 | |||
83175 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13840.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122298 | Curators of the CIP | Collection of Institut Pasteur (CIP 70.61) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2070.61 |