Strain identifier
BacDive ID: 4104
Type strain: 
Species: Nitratidesulfovibrio oxamicus
Strain history: <- NCIB <- J.R. Postgate, strain Monticello 2
NCBI tax ID(s): 32016 (species)
version 8.1 (current version)
General
@ref: 669
BacDive-ID: 4104
DSM-Number: 1925
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Nitratidesulfovibrio oxamicus DSM 1925 is an anaerobe, mesophilic, motile bacterium that was isolated from mud.
NCBI tax id
- NCBI tax id: 32016
- Matching level: species
strain history
- @ref: 669
- history: <- NCIB <- J.R. Postgate, strain Monticello 2
doi: 10.13145/bacdive4104.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Nitratidesulfovibrio
- species: Nitratidesulfovibrio oxamicus
- full scientific name: Nitratidesulfovibrio oxamicus (Postgate and Campbell 1966) Waite et al. 2020
synonyms
@ref synonym 20215 Cupidesulfovibrio oxamicus 20215 Desulfovibrio vulgaris subsp. oxamicus 20215 Desulfovibrio oxamicus
@ref: 669
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Cupidesulfovibrio
species: Cupidesulfovibrio oxamicus
full scientific name: Cupidesulfovibrio oxamicus (Postgate and Campbell 1966) Wan et al. 2021
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 98.599 | |
| 69480 | 99.997 | negative |
Culture and growth conditions
culture medium
- @ref: 669
- name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)
- growth: yes
- link: https://mediadive.dsmz.de/medium/63
- composition: Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) Composition: MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na2SO4 1.0 g/l FeSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Ascorbic acid 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 669
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 669 | anaerobe | |
| 69480 | anaerobe | 98.161 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.866
Isolation, sampling and environmental information
isolation
- @ref: 669
- sample type: mud
- geographic location: Illinois, Monticello near Urbana
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
taxonmaps
- @ref: 69479
- File name: preview.99_6970.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_288;96_1542;97_1841;98_2260;99_6970&stattab=map
- Last taxonomy: Desulfovibrionaceae
- 16S sequence: DQ122124
- Sequence Identity:
- Total samples: 35
- soil counts: 1
- aquatic counts: 25
- animal counts: 6
- plant counts: 3
Safety information
risk assessment
- @ref: 669
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Desulfovibrio oxamicus partial 16S rRNA gene, type strain DSM 1925T | AJ295677 | 1189 | ena | 32016 |
| 669 | Desulfovibrio oxamicus strain DSM 1925 16S ribosomal RNA gene, partial sequence | DQ122124 | 1513 | ena | 32016 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Cupidesulfovibrio oxamicus NCIMB 9442 | GCA_015731765 | contig | ncbi | 32016 |
| 66792 | Desulfovibrio oxamicus strain NCIMB 9442 strain not collected | 32016.3 | wgs | patric | 32016 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 79 | no |
| gram-positive | no | 98.828 | no |
| anaerobic | yes | 98.887 | no |
| halophile | no | 83.614 | no |
| spore-forming | no | 94.034 | no |
| glucose-util | no | 65.363 | no |
| motile | yes | 90.916 | no |
| flagellated | no | 50.764 | no |
| thermophile | no | 90.917 | yes |
| aerobic | no | 97.228 | no |
| glucose-ferment | no | 79.612 | no |
External links
@ref: 669
culture collection no.: DSM 1925, ATCC 33405, NCIMB 9442, VKM B-1766, Monticello 2
straininfo link
- @ref: 73607
- straininfo: 311074
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16825618 | Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov. | Lopez-Cortes A, Fardeau ML, Fauque G, Joulian C, Ollivier B | Int J Syst Evol Microbiol | 10.1099/ijs.0.64074-0 | 2006 | Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desulfovibrio/*classification/genetics/metabolism/physiology, Desulfovibrio vulgaris/*classification/genetics/metabolism/physiology, Genes, rRNA/genetics, Growth Inhibitors/pharmacology, Molecular Sequence Data, Nitrates/*metabolism, Oxidation-Reduction, Peptones/metabolism, Phylogeny, Quaternary Ammonium Compounds/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/pharmacology, Sulfates/*metabolism | Metabolism |
| Metabolism | 24467551 | Microbial ecology of arsenic-mobilizing Cambodian sediments: lithological controls uncovered by stable-isotope probing. | Hery M, Rizoulis A, Sanguin H, Cooke DA, Pancost RD, Polya DA, Lloyd JR | Environ Microbiol | 10.1111/1462-2920.12412 | 2014 | Acetates/metabolism, Arsenic/*metabolism/toxicity, Cambodia, Desulfovibrio/genetics/metabolism, Drinking Water/*chemistry, Geobacter/genetics/metabolism, Geologic Sediments/*microbiology, Groundwater/*microbiology, Isotope Labeling, Lactates/metabolism, Molecular Sequence Data, Proteobacteria/genetics/metabolism, RNA, Ribosomal, 16S/genetics, Water Pollution, Chemical | Genetics |
| Phylogeny | 33406030 | Cupidesulfovibrio liaohensis gen. nov., sp. nov., a novel sulphate-reducing bacterium isolated from an oil reservoir and reclassification of Desulfovibrio oxamicus and Desulfovibrio termitidis as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov. | Wan YY, Luo N, Liu XL, Lai QL, Goodfellow M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004618 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Desulfovibrio/classification, Desulfovibrionaceae/*classification/isolation & purification, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfates/metabolism, Sulfur-Reducing Bacteria/classification/isolation & purification | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 669 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1925) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1925 | |||
| 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) | |||
| 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) | |||
| 73607 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID311074.1 | StrainInfo: A central database for resolving microbial strain identifiers |