Strain identifier
BacDive ID: 6113
Type strain: 
Species: Sulfurimonas denitrificans
Strain history: <- A. Timmer-ten Hoor
NCBI tax ID(s): 326298 (strain), 39766 (species)
version 8.1 (current version)
General
@ref: 595
BacDive-ID: 6113
DSM-Number: 1251
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, psychrophilic, motile
description: Sulfurimonas denitrificans DSM 1251 is an anaerobe, psychrophilic, motile bacterium that was isolated from estuarine mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 326298 | strain |
| 39766 | species |
strain history
- @ref: 595
- history: <- A. Timmer-ten Hoor
doi: 10.13145/bacdive6113.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Campylobacterales
- family: Helicobacteraceae
- genus: Sulfurimonas
- species: Sulfurimonas denitrificans
- full scientific name: Sulfurimonas denitrificans (Timmer-ten Hoor 1975) Takai et al. 2006
synonyms
- @ref: 20215
- synonym: Thiomicrospira denitrificans
@ref: 595
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Campylobacterales
family: Helicobacteraceae
genus: Sulfurimonas
species: Sulfurimonas denitrificans
full scientific name: Sulfurimonas denitrificans (Timmer-ten Hoor 1975) Takai et al. 2006
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.289 | |
| 69480 | 99.999 | negative |
Culture and growth conditions
culture medium
- @ref: 595
- name: THIOBACILLUS DENITRIFICANS MEDIUM (DSMZ Medium 113)
- growth: yes
- link: https://mediadive.dsmz.de/medium/113
- composition: Name: THIOBACILLUS DENITRIFICANS MEDIUM (DSMZ Medium 113) Composition: Agar 14.9551 g/l (optional) Na2S2O3 x 5 H2O 4.98504 g/l KH2PO4 1.99402 g/l KNO3 1.99402 g/l NaHCO3 0.997009 g/l NH4Cl 0.997008 g/l MgSO4 x 7 H2O 0.797607 g/l FeSO4 x 7 H2O 0.00199402 g/l Na2-EDTA 0.000997009 g/l H3BO3 0.000598205 g/l CoCl2 x 6 H2O 0.000398804 g/l ZnSO4 x 7 H2O 0.000199402 g/l MnCl2 x 4 H2O 5.98205e-05 g/l Na2MoO4 x 2 H2O 5.98205e-05 g/l NiCl2 x 6 H2O 3.98804e-05 g/l CuCl2 x 2 H2O 1.99402e-05 g/l H2SO4 Distilled water
culture temp
- @ref: 595
- growth: positive
- type: growth
- temperature: 21
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 595 | anaerobe | |
| 69480 | anaerobe | 94.779 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.996 |
Isolation, sampling and environmental information
isolation
- @ref: 595
- sample type: estuarine mud
- geographic location: Dollard
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Brackish |
| #Environmental | #Terrestrial | #Mud (Sludge) |
taxonmaps
- @ref: 69479
- File name: preview.99_671.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_133;96_413;97_468;98_539;99_671&stattab=map
- Last taxonomy: Sulfurimonas denitrificans subclade
- 16S sequence: L40808
- Sequence Identity:
- Total samples: 1342
- soil counts: 96
- aquatic counts: 1150
- animal counts: 84
- plant counts: 12
Safety information
risk assessment
- @ref: 595
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Thiomicrospira denitrificans 16S ribosomal RNA (16S rRNA) gene, partial sequence
- accession: L40808
- length: 1446
- database: ena
- NCBI tax ID: 326298
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sulfurimonas denitrificans DSM 1251 | GCA_000012965 | complete | ncbi | 326298 |
| 66792 | Sulfurimonas denitrificans DSM 1251 | 326298.21 | complete | patric | 326298 |
| 66792 | Sulfurimonas denitrificans DSM 1251 | 326298.7 | complete | patric | 326298 |
| 66792 | Sulfurimonas denitrificans DSM 1251 | 637000326 | complete | img | 326298 |
GC content
- @ref: 595
- GC-content: 34
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 90.586 | no |
| flagellated | yes | 72.085 | no |
| gram-positive | no | 99.134 | no |
| anaerobic | yes | 59.938 | yes |
| halophile | no | 80.238 | no |
| spore-forming | no | 95.204 | no |
| thermophile | no | 89.235 | yes |
| glucose-util | no | 82.557 | no |
| aerobic | no | 96.207 | yes |
| glucose-ferment | no | 90.464 | no |
External links
@ref: 595
culture collection no.: DSM 1251, ATCC 33889
straininfo link
- @ref: 75600
- straininfo: 40746
literature
| Pubmed-ID | title | authors | journal | DOI | year | mesh | topic | topic2 |
|---|---|---|---|---|---|---|---|---|
| 16817973 | Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales). | Gupta RS | BMC Genomics | 10.1186/1471-2164-7-167 | 2006 | Bacterial Proteins/*genetics, Campylobacter/*genetics, Conserved Sequence, Epsilonproteobacteria/genetics, *Open Reading Frames, RNA, Bacterial/genetics, RNA, Ribosomal/genetics | ||
| 16901999 | Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas. | Takai K, Suzuki M, Nakagawa S, Miyazaki M, Suzuki Y, Inagaki F, Horikoshi K | Int J Syst Evol Microbiol | 10.1099/ijs.0.64255-0 | 2006 | Anaerobiosis, Animals, Bacterial Typing Techniques/methods, Base Composition, Culture Media, DNA, Bacterial/chemistry/genetics, Epsilonproteobacteria/*classification/physiology, Hydrogen/metabolism, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, Piscirickettsiaceae/*classification/genetics, *Polychaeta, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Homology, Nucleic Acid, Species Specificity, Sulfur/metabolism, Temperature, *Water Microbiology | Phylogeny | Cultivation |
| 18065616 | Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. | Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hugler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, Simon J | Appl Environ Microbiol | 10.1128/AEM.01844-07 | 2007 | Base Sequence, Carbon/metabolism, Carboxy-Lyases/genetics, Chemoautotrophic Growth, Chemotaxis/genetics, Chromosome Mapping, Computational Biology, Electron Transport/physiology, Epsilonproteobacteria/*genetics, *Genome, Bacterial, Models, Biological, Molecular Sequence Data, Nitrogen/metabolism, Oxidative Stress/genetics, *Phylogeny, Sequence Analysis, DNA, Signal Transduction/*genetics | Genetics | Metabolism |
| 24750895 | Interactions between anaerobic ammonium and sulfur-oxidizing bacteria in a laboratory scale model system. | Russ L, Speth DR, Jetten MS, Op den Camp HJ, Kartal B | Environ Microbiol | 10.1111/1462-2920.12487 | 2014 | Ammonium Compounds/*metabolism, Anaerobiosis, Autotrophic Processes, Bacteria/drug effects/*metabolism, Coculture Techniques, *Denitrification, Epsilonproteobacteria/*metabolism, Gammaproteobacteria/metabolism, Microbial Interactions, Models, Biological, Nitrates/metabolism, Nitrites/metabolism, Oxidation-Reduction, Sulfides/metabolism/toxicity, Sulfur/*metabolism | Metabolism | Pathogenicity |
| 31639074 | Sulfurimonas crateris sp. nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano. | Ratnikova NM, Slobodkin AI, Merkel AY, Kopitsyn DS, Kevbrin VV, Bonch-Osmolovskaya EA, Slobodkina GB | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003779 | 2020 | Anaerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Helicobacteraceae/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, *Soil Microbiology, Sulfur/*metabolism, Sulfur-Reducing Bacteria/classification/isolation & purification, Thiosulfates | Phylogeny | Enzymology |
| 32134372 | Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov., hydrogen- and sulfur-oxidizing chemolithoautotrophs within the Epsilonproteobacteria isolated from coastal sediments, and an emended description of the genus Sulfurimonas. | Wang S, Jiang L, Liu X, Yang S, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004087 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Helicobacteraceae/*classification/isolation & purification, Hydrogen/metabolism, Nucleic Acid Hybridization, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur/metabolism | Phylogeny | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 595 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1251) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1251 | |||
| 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 | |||
| 75600 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40746.1 | StrainInfo: A central database for resolving microbial strain identifiers |