Strain identifier

BacDive ID: 14005

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
1085species
269796strain

strain history

@refhistory
120<- ATCC <- NCIB <- S.R. Elsden, S 1 <- C.B. van Niel
122298CIP <- 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

@refmotilityconfidencegram staincell shape
69480yes94.937
6948099.96negative
122298yesnegativerod-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

@refnamegrowthlinkcomposition
120RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)yeshttps://mediadive.dsmz.de/medium/27Name: 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
35750MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122298CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122298CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
120positivegrowth28mesophilic
35750positivegrowth30mesophilic
46704positivegrowth30mesophilic
122298positivegrowth15-30
122298nogrowth5psychrophilic
122298nogrowth37mesophilic
122298nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
120anaerobe
46704aerobe
122298obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.971

compound production

@refcompound
120carotenoids
120ubiquinone-10

halophily

@refsaltgrowthtested relationconcentration
122298NaClpositivegrowth0-2 %
122298NaClnogrowth4 %
122298NaClnogrowth6 %
122298NaClnogrowth8 %
122298NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12229816947citrate-carbon source
1222984853esculin+hydrolysis
12229817234glucose-fermentation
12229817716lactose-fermentation
12229817632nitrate-reduction
12229816301nitrite-reduction
122298132112sodium thiosulfate-builds gas from
12229817234glucose+/-degradation
12229817632nitrate-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

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12229815688acetoin-
12229817234glucose-

enzymes

@refvalueactivityec
122298oxidase+
122298beta-galactosidase-3.2.1.23
122298alcohol dehydrogenase-1.1.1.1
122298gelatinase-
122298amylase-
122298DNase-
122298caseinase-3.4.21.50
122298catalase+1.11.1.6
122298tween esterase-
122298gamma-glutamyltransferase+2.3.2.2
122298lecithinase-
122298lipase-
122298lysine decarboxylase-4.1.1.18
122298ornithine decarboxylase-4.1.1.17
122298phenylalanine ammonia-lyase-4.3.1.24
122298protease-
122298tryptophan deaminase-
122298urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122298----------+-++-+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
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

@refbiosafety levelbiosafety level comment
1201Risk group (German classification)
1222981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodospirillum rubrum gene for 16S ribosomal RNAD307781406ena269796
20218Rhodospirillum rubrum (ATCC 11170) 16S ribosomal RNA (partial)M55497263ena269796

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodospirillum rubrum DSM 467GCA_019134555completencbi1085
66792Rhodospirillum rubrum ATCC 11170GCA_000013085completencbi269796
66792Rhodospirillum rubrum ATCC 11170269796.21plasmidpatric269796
66792Rhodospirillum rubrum ATCC 11170269796.9completepatric269796
66792Rhodospirillum rubrum F111036743.4completepatric1036743
66792Rhodospirillum rubrum strain DSM 4671085.17completepatric1085
66792Rhodospirillum rubrum S1, ATCC 11170637000241completeimg269796

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes88.825no
flagellatedyes73.882no
gram-positiveno98.846no
anaerobicyes72.705no
halophileno94.889no
spore-formingno90.937no
thermophileno99.178yes
glucose-utilyes72.989no
aerobicno89.648no
glucose-fermentno85.385no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology7669805Electron paramagnetic resonance studies of ferric cytochrome c' from photosynthetic bacteria.Fujii S, Yoshimura T, Kamada H, Yamaguchi K, Suzuki S, Shidara S, Takakuwa SBiochim Biophys Acta10.1016/0167-4838(95)00092-91995Chromatium/*enzymology, Cytochrome-c Peroxidase/chemistry, Electron Spin Resonance Spectroscopy, Hydrogen-Ion Concentration, Peroxidases/*chemistry/isolation & purification, Rhodobacter capsulatus/*enzymology, Rhodopseudomonas/*enzymology, Rhodospirillum/*enzymologyPhylogeny
Metabolism8547347Spectroscopic 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 SBiochim Biophys Acta10.1016/0167-4838(95)00187-51996Cytochrome 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
Genetics16151144Whole-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 DCAppl Environ Microbiol10.1128/AEM.71.9.5511-5522.20052005Contig Mapping/methods, *Genome, Bacterial, Image Processing, Computer-Assisted, Restriction Mapping/*methods, Rhodospirillum rubrum/*genetics, Sequence Analysis, DNATranscriptome
Stress20544803Effects of ethanol, formaldehyde, and gentle heat fixation in confocal resonance Raman microscopy of purple nonsulfur bacteria.Kniggendorf AK, Gaul TW, Meinhardt-Wollweber MMicrosc Res Tech10.1002/jemt.208892011Ethanol/chemistry, Fixatives/chemistry, Formaldehyde/chemistry, Hot Temperature, Microscopy, Confocal, Rhodospirillaceae/*chemistry/cytology, Spectrum Analysis, Raman, Tissue Fixation/instrumentation/*methods
Metabolism20852980Aniline-induced tryptophan production and identification of indole derivatives from three purple bacteria.Mujahid M, Sasikala Ch, Ramana ChVCurr Microbiol10.1007/s00284-010-9609-22010Aniline 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 & purificationEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
120Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 467)https://www.dsmz.de/collection/catalogue/details/culture/DSM-467
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35750Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10536
46704Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 17859)https://www.ccug.se/strain?id=17859
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83175Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13840.1StrainInfo: A central database for resolving microbial strain identifiers
122298Curators of the CIPCollection of Institut Pasteur (CIP 70.61)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2070.61