Strain identifier
BacDive ID: 1797
Type strain:
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)
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 id | Matching level |
---|---|
40137 | species |
504832 | strain |
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
@ref synonym 20215 Pseudomonas carboxydovorans 20215 Oligotropha 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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 91.776 | |
69480 | 99.999 | negative |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
542 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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 |
542 | CARBON MONOXIDE OXIDIZER MEDIUM (DSMZ Medium 133) | yes | https://mediadive.dsmz.de/medium/133 | Name: 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
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.995 |
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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Afipia carboxidovorans OM5 | GCA_000218565 | complete | ncbi | 504832 |
66792 | Afipia carboxidovorans OM5 OM5; ATCC 49405 | GCA_000021365 | complete | ncbi | 504832 |
66792 | Oligotropha carboxidovorans OM5 | 504832.19 | complete | patric | 504832 |
66792 | Oligotropha carboxidovorans OM5 | 504832.21 | plasmid | patric | 504832 |
66792 | Oligotropha carboxidovorans OM5 | 504832.5 | complete | patric | 504832 |
66792 | Oligotropha carboxidovorans OM5 | 504832.20 | plasmid | patric | 504832 |
66792 | Oligotropha carboxidovorans OM5 strain OM5; ATCC 49405 | 504832.18 | complete | patric | 504832 |
66792 | Afipia carboxidovorans OM5 | 2510065041 | complete | img | 504832 |
66792 | Afipia carboxidovorans OM5 | 2576861421 | complete | img | 504832 |
GC content
- @ref: 542
- GC-content: 60.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 81.168 | no |
flagellated | no | 77.209 | no |
gram-positive | no | 98.447 | no |
anaerobic | no | 94.045 | no |
aerobic | yes | 72.147 | no |
halophile | no | 95.849 | no |
spore-forming | no | 95.66 | no |
thermophile | no | 93.713 | yes |
glucose-util | no | 55.301 | no |
glucose-ferment | no | 92.856 | no |
External links
@ref: 542
culture collection no.: DSM 1227, ATCC 49405, KCTC 32145
straininfo link
- @ref: 71444
- straininfo: 42455
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 18539730 | Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T. | Paul D, Bridges S, Burgess SC, Dandass Y, Lawrence ML | J Bacteriol | 10.1128/JB.00614-08 | 2008 | Base Sequence, Bradyrhizobiaceae/*genetics, *Genome, Bacterial, Molecular Sequence Data, Sequence Analysis, DNA | Transcriptome |
Genetics | 20863402 | Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5. | Paul D, Bridges SM, Burgess SC, Dandass YS, Lawrence ML | BMC Genomics | 10.1186/1471-2164-11-511 | 2010 | Bacterial 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/genetics | Metabolism |
Proteome | 21386900 | Proteome 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 SC | PLoS One | 10.1371/journal.pone.0017111 | 2011 | Bacterial 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/*analysis | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
542 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1227) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1227 | |||
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) | |||
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 | |||
71444 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42455.1 | StrainInfo: A central database for resolving microbial strain identifiers |