Strain identifier

BacDive ID: 1797

Type strain: Yes

Species: Afipia carboxidovorans

Strain Designation: OM5

Strain history: <- O. Meyer, Universität Göttingen, Institut für Mikrobiologie, Germany; OM5 (Pseudomonas carboxydovorans) <- O. Meyer {1976}

NCBI tax ID(s): 504832 (strain), 40137 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 542

BacDive-ID: 1797

DSM-Number: 1227

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Afipia carboxidovorans OM5 is a mesophilic, motile bacterium that was isolated from waste water.

NCBI tax id

NCBI tax idMatching level
40137species
504832strain

strain history

  • @ref: 542
  • history: <- O. Meyer, Universität Göttingen, Institut für Mikrobiologie, Germany; OM5 (Pseudomonas carboxydovorans) <- O. Meyer {1976}

doi: 10.13145/bacdive1797.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Afipia
  • species: Afipia carboxidovorans
  • full scientific name: Afipia carboxidovorans (Meyer et al. 1994 ex Meyer and Schlegel 1978) Hördt et al. 2020
  • synonyms

    @refsynonym
    20215Pseudomonas carboxydovorans
    20215Oligotropha carboxidovorans

@ref: 542

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Afipia

species: Afipia carboxidovorans

full scientific name: Afipia carboxidovorans (Meyer et al. 1994) Hördt et al. 2020

strain designation: OM5

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes91.776
6948099.999negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
542R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
542CARBON MONOXIDE OXIDIZER MEDIUM (DSMZ Medium 133)yeshttps://mediadive.dsmz.de/medium/133Name: CARBON MONOXIDE OXIDIZER MEDIUM (DSMZ Medium 133) Composition: Agar 12.0 g/l Na2HPO4 x 12 H2O 4.5 g/l NH4Cl 1.5 g/l KH2PO4 0.75 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.03 g/l Ferric ammonium citrate 0.018 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 Distilled water

culture temp

  • @ref: 542
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

Isolation, sampling and environmental information

isolation

  • @ref: 542
  • sample type: waste water
  • geographic location: Göttingen
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_1530.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_1207;99_1530&stattab=map
  • Last taxonomy: Afipia
  • 16S sequence: FR733697
  • Sequence Identity:
  • Total samples: 807
  • soil counts: 269
  • aquatic counts: 275
  • animal counts: 203
  • plant counts: 60

Safety information

risk assessment

  • @ref: 542
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Oligotropha carboxidovorans partial 16S rRNA gene, type strain DSM1227T
  • accession: FR733697
  • length: 1477
  • database: ena
  • NCBI tax ID: 40137

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Afipia carboxidovorans OM5GCA_000218565completencbi504832
66792Afipia carboxidovorans OM5 OM5; ATCC 49405GCA_000021365completencbi504832
66792Oligotropha carboxidovorans OM5504832.19completepatric504832
66792Oligotropha carboxidovorans OM5504832.21plasmidpatric504832
66792Oligotropha carboxidovorans OM5504832.5completepatric504832
66792Oligotropha carboxidovorans OM5504832.20plasmidpatric504832
66792Oligotropha carboxidovorans OM5 strain OM5; ATCC 49405504832.18completepatric504832
66792Afipia carboxidovorans OM52510065041completeimg504832
66792Afipia carboxidovorans OM52576861421completeimg504832

GC content

  • @ref: 542
  • GC-content: 60.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes81.168no
flagellatedno77.209no
gram-positiveno98.447no
anaerobicno94.045no
aerobicyes72.147no
halophileno95.849no
spore-formingno95.66no
thermophileno93.713yes
glucose-utilno55.301no
glucose-fermentno92.856no

External links

@ref: 542

culture collection no.: DSM 1227, ATCC 49405, KCTC 32145

straininfo link

  • @ref: 71444
  • straininfo: 42455

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics18539730Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T.Paul D, Bridges S, Burgess SC, Dandass Y, Lawrence MLJ Bacteriol10.1128/JB.00614-082008Base Sequence, Bradyrhizobiaceae/*genetics, *Genome, Bacterial, Molecular Sequence Data, Sequence Analysis, DNATranscriptome
Genetics20863402Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5.Paul D, Bridges SM, Burgess SC, Dandass YS, Lawrence MLBMC Genomics10.1186/1471-2164-11-5112010Bacterial Proteins/genetics/metabolism, Bradyrhizobiaceae/enzymology/*genetics, Carbohydrate Metabolism/genetics, Chemoautotrophic Growth/*genetics, DNA, Circular/genetics, Energy Metabolism/genetics, Extrachromosomal Inheritance/genetics, Fatty Acids/biosynthesis, Genome, Bacterial/*genetics, Genomics, Interspersed Repetitive Sequences/genetics, Metabolic Networks and Pathways/genetics, Oxidation-Reduction, Phylogeny, Protein Binding, Protein Transport, RNA, Ribosomal, 16S/genetics, RNA, Untranslated/genetics, Sequence Homology, Amino Acid, Synteny/geneticsMetabolism
Proteome21386900Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions.Paul D, Kumar R, Nanduri B, French T, Pendarvis K, Brown A, Lawrence ML, Burgess SCPLoS One10.1371/journal.pone.00171112011Bacterial Proteins/analysis, Bradyrhizobiaceae/enzymology/genetics/*growth & development/metabolism, Chemoautotrophic Growth/*physiology, Cluster Analysis, Fatty Acids/*analysis, Gene Regulatory Networks/physiology, Genes, Bacterial, Glyoxylates/metabolism, Heterotrophic Processes/*physiology, Membrane Lipids/analysis, Metabolic Networks and Pathways/genetics, Oxidation-Reduction, Proteome/*analysisMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
542Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1227)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1227
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
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)
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
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
71444Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42455.1StrainInfo: A central database for resolving microbial strain identifiers