Strain identifier
BacDive ID: 2037
Type strain:
Species: Cupriavidus oxalaticus
Strain Designation: Ox1
Strain history: CIP <- 2002, N. Sahin, Mugla Univ., Kotekli-Mugla, Turkey: strain Ox1 <- NEU <- DSMZ <- C. Friedrich <- NCIB <- J.V. Bath, Pseudomonas oxalaticus
NCBI tax ID(s): 1349762 (strain), 96344 (species)
General
@ref: 554
BacDive-ID: 2037
DSM-Number: 1105
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Cupriavidus oxalaticus Ox1 is a mesophilic, Gram-negative, motile bacterium that was isolated from garden soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1349762 | strain |
96344 | species |
strain history
@ref | history |
---|---|
554 | <- C. Friedrich <- NCIB <- J.V. Bath; Ox1 (Pseudomonas oxalaticus) |
67770 | LMG 2235 <-- W. Harder <-- J. Quale. |
121479 | CIP <- 2002, N. Sahin, Mugla Univ., Kotekli-Mugla, Turkey: strain Ox1 <- NEU <- DSMZ <- C. Friedrich <- NCIB <- J.V. Bath, Pseudomonas oxalaticus |
doi: 10.13145/bacdive2037.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiaceae
- genus: Cupriavidus
- species: Cupriavidus oxalaticus
- full scientific name: Cupriavidus oxalaticus (Sahin et al. 2000 ex Khambata and Bhat 1953) Vandamme and Coenye 2004
synonyms
@ref synonym 20215 Wautersia oxalatica 20215 Ralstonia oxalaticus 20215 Ralstonia oxalatica
@ref: 554
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Cupriavidus
species: Cupriavidus oxalaticus
full scientific name: Cupriavidus oxalaticus (Sahin et al. 2000) Vandamme and Coenye 2004
strain designation: Ox1
type strain: yes
Morphology
cell morphology
- @ref: 121479
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
554 | R2A MEDIUM (DSMZ Medium 830) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf | |
554 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf | |
554 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium220.pdf | |
554 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf | |
40709 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
121479 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
554 | positive | growth | 28 | mesophilic |
40709 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
121479 | positive | growth | 25-41 | |
121479 | no | growth | 5 | psychrophilic |
121479 | no | growth | 10 | psychrophilic |
Physiology and metabolism
compound production
- @ref: 554
- compound: polyhydroxyalkanoic acids
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121479 | NaCl | positive | growth | 0-2 % |
121479 | NaCl | no | growth | 4 % |
121479 | NaCl | no | growth | 6 % |
121479 | NaCl | no | growth | 8 % |
121479 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | + | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
121479 | 16947 | citrate | + | carbon source |
121479 | 4853 | esculin | + | hydrolysis |
121479 | 17632 | nitrate | + | reduction |
121479 | 16301 | nitrite | + | reduction |
121479 | 17632 | nitrate | + | respiration |
antibiotic resistance
- @ref: 121479
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121479 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
121479 | oxidase | + | |
121479 | beta-galactosidase | - | 3.2.1.23 |
121479 | alcohol dehydrogenase | - | 1.1.1.1 |
121479 | gelatinase | - | |
121479 | amylase | - | |
121479 | DNase | - | |
121479 | caseinase | - | 3.4.21.50 |
121479 | catalase | - | 1.11.1.6 |
121479 | tween esterase | + | |
121479 | lecithinase | - | |
121479 | lipase | - | |
121479 | lysine decarboxylase | - | 4.1.1.18 |
121479 | ornithine decarboxylase | - | 4.1.1.17 |
121479 | protease | - | |
121479 | tryptophan deaminase | - | |
121479 | urease | + | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121479 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
554 | + | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | + | + | + | + |
554 | + | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | + | + | + | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121479 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | + | + | - | - | - | + | - | - | + | - | - | - | + | + | + | + | + | + | + | + | - | + | - | - | - | + | - | + | + | + | - | + | + | + | + | - | - | - | + | + | + | + | + | + | + | + | + | - | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | isolation date |
---|---|---|---|---|---|
554 | garden soil | ||||
44481 | Indian earthworm,intestinal tract | India | IND | Asia | |
67770 | Alimentary tract of an Indian earthworm | ||||
121479 | Animal, Earthworm, intestine | India | IND | Asia | 1953 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Engineered | #Agriculture | #Garden |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
554 | 1 | Risk group (German classification) |
121479 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Cupriavidus oxalaticus partial 16S rRNA gene, type strain CCUG 2086T | FN597610 | 1392 | ena | 96344 |
20218 | Cupriavidus oxalaticus strain CIP 107389 16S ribosomal RNA gene, partial sequence | EU024156 | 1316 | ena | 96344 |
20218 | Ralstonia oxalatica 16S ribosomal RNA gene, complete sequence | AF155567 | 1469 | ena | 96344 |
20218 | Wautersia oxalatica 16S rRNA gene, 23S rRNA gene and ITS1, specimen voucher LMG2235 | AJ783980 | 895 | ena | 96344 |
20218 | Wautersia oxalatica 16S rRNA gene, 23S rRNA gene and ITS1, specimen voucher LMG2235 | AJ783981 | 714 | ena | 96344 |
20218 | Cupriavidus oxalaticus gene for 16S rRNA, partial sequence, strain: NBRC 13593 | AB680453 | 1459 | ena | 96344 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cupriavidus oxalaticus Ox1 | GCA_016894385 | complete | ncbi | 96344 |
66792 | Cupriavidus oxalaticus Cupriavidus oxalaticus LMG 2235 | GCA_900249725 | chromosome | ncbi | 96344 |
66792 | Cupriavidus oxalaticus NBRC 13593 | 1349762.5 | wgs | patric | 1349762 |
66792 | Cupriavidus oxalaticus strain Cupriavidus oxalaticus LMG 2235 | 96344.7 | wgs | patric | 96344 |
66792 | Cupriavidus oxalaticus NBRC 13593 | 2731957685 | draft | img | 1349762 |
67770 | Cupriavidus oxalaticus NBRC 13593 | GCA_001592245 | contig | ncbi | 1349762 |
GC content
- @ref: 67770
- GC-content: 68
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | yes | 59.965 | no |
gram-positive | no | 98.624 | no |
anaerobic | no | 98.606 | no |
aerobic | yes | 91.922 | no |
halophile | no | 94.489 | no |
spore-forming | no | 93.762 | no |
thermophile | no | 98.802 | no |
glucose-util | no | 62.389 | no |
motile | yes | 88.267 | no |
glucose-ferment | no | 90.318 | yes |
External links
@ref: 554
culture collection no.: CCUG 2086, LMG 2235, LMG 5121, DSM 1105, ATCC 11883, NCIB 8642, JCM 11285, IFO 13593, NBRC 13593, NCIMB 8642, CIP 107389
straininfo link
- @ref: 71684
- straininfo: 1693
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10930072 | Taxonomic position of "Pseudomonas oxalaticus" strain ox14T (DSM 1105T) (Khambata and Bhat, 1953) and its description in the genus Ralstonia as Ralstonia oxalatica comb. nov. | Sahin N, Isik K, Tamer AU, Goodfellow M | Syst Appl Microbiol | 10.1016/s0723-2020(00)80006-5 | 2000 | Bacterial Typing Techniques, DNA, Ribosomal/genetics, Gram-Negative Aerobic Rods and Cocci/*classification, Molecular Sequence Data, Oxalates/metabolism, Pseudomonas/*classification, RNA, Ribosomal, 16S/genetics | Genetics |
Phylogeny | 15545472 | Taxonomy of the genus Cupriavidus: a tale of lost and found. | Vandamme P, Coenye T | Int J Syst Evol Microbiol | 10.1099/ijs.0.63247-0 | 2004 | Bacterial Proteins/analysis/isolation & purification, Base Composition, Burkholderiaceae/*classification/genetics/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Proteome/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Enzymology |
Metabolism | 16821716 | Identification of oxalotrophic bacteria by neural network analysis of numerical phenetic data. | Sahin N, Aydin S | Folia Microbiol (Praha) | 10.1007/BF02932161 | 2006 | Gram-Negative Aerobic Bacteria/*classification/metabolism, *Neural Networks, Computer, Oxalates/metabolism | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
554 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1105) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1105 | |||
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 | |
40709 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4819 | ||||
44481 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 2086) | https://www.ccug.se/strain?id=2086 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
71684 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1693.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121479 | Curators of the CIP | Collection of Institut Pasteur (CIP 107389) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107389 |