Strain identifier
BacDive ID: 11792
Type strain: 
Species: Desulfotomaculum nigrificans
Strain history: <- F. Hollaus <- NCIB <- K.R. Butlin (Desulfovibrio desulfuricans) <- J. Senez <- R.L. Starkey, Delft 74
NCBI tax ID(s): 696369 (strain), 1565 (species)
version 8.1 (current version)
General
@ref: 291
BacDive-ID: 11792
DSM-Number: 574
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile
description: Desulfotomaculum nigrificans DSM 574 is an anaerobe, spore-forming, thermophilic bacterium of the family Peptococcaceae.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1565 | species |
| 696369 | strain |
strain history
- @ref: 291
- history: <- F. Hollaus <- NCIB <- K.R. Butlin (Desulfovibrio desulfuricans) <- J. Senez <- R.L. Starkey, Delft 74
doi: 10.13145/bacdive11792.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Peptococcaceae
- genus: Desulfotomaculum
- species: Desulfotomaculum nigrificans
- full scientific name: Desulfotomaculum nigrificans (Werkman and Weaver 1927) Campbell and Postgate 1965 (Approved Lists 1980)
synonyms
@ref synonym 20215 Clostridium nigrificans 20215 Desulfotomaculum carboxydivorans
@ref: 291
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptococcaceae
genus: Desulfotomaculum
species: Desulfotomaculum nigrificans
full scientific name: Desulfotomaculum nigrificans (Werkman and Weaver 1927) Campbell and Postgate 1965 emend. Visser et al. 2014
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.718 | |
| 69480 | 99.999 | positive |
multimedia
- @ref: 66793
- multimedia content: EM_DSM_574_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 291
- 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 | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 291 | positive | growth | 55 | thermophilic | |
| 69480 | thermophilic | 97.162 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 291 | anaerobe | |
| 69480 | anaerobe | 99.246 |
spore formation
- @ref: 69480
- spore formation: yes
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 291
- geographic location: freshwater
- country: Netherlands
- origin.country: NLD
- continent: Europe
taxonmaps
- @ref: 69479
- File name: preview.99_2442.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15838;96_1321;97_1568;98_1907;99_2442&stattab=map
- Last taxonomy: Desulfotomaculum nigrificans subclade
- 16S sequence: HG005352
- Sequence Identity:
- Total samples: 6931
- soil counts: 516
- aquatic counts: 688
- animal counts: 5582
- plant counts: 145
Safety information
risk assessment
- @ref: 291
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Sulphate-reducing bacteria ATCC 19858 16S rRNA region | A30643 | 1346 | ena | 77133 |
| 291 | Desulfotomaculum nigrificans partial 16S rRNA gene, type strain NCIMB 8395T | HG005352 | 1521 | ena | 1565 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfotomaculum nigrificans DSM 574 | GCA_000189755 | contig | ncbi | 696369 |
| 66792 | Desulfotomaculum nigrificans DSM 574 | 696369.3 | wgs | patric | 696369 |
| 66792 | Desulfotomaculum nigrificans DSM 574 | 2507262026 | draft | img | 696369 |
GC content
- @ref: 291
- GC-content: 46
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 77 | no |
| motile | yes | 89.677 | no |
| flagellated | no | 89.47 | no |
| gram-positive | no | 85.984 | no |
| anaerobic | yes | 99.306 | yes |
| aerobic | no | 96.29 | yes |
| halophile | no | 94.83 | no |
| spore-forming | yes | 95.037 | no |
| glucose-util | yes | 89.842 | no |
| thermophile | yes | 98.632 | yes |
| glucose-ferment | no | 73.106 | no |
External links
@ref: 291
culture collection no.: DSM 574, ATCC 19858, ATCC 19998, CIP 111238, NCIMB 8395, WDCM 00081, Delft 74
straininfo link
- @ref: 81010
- straininfo: 92880
literature
- topic: Phylogeny
- Pubmed-ID: 16166725
- title: Desulfotomaculum carboxydivorans sp. nov., a novel sulfate-reducing bacterium capable of growth at 100% CO.
- authors: Parshina SN, Sipma J, Nakashimada Y, Henstra AM, Smidt H, Lysenko AM, Lens PNL, Lettinga G, Stams AJM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63780-0
- year: 2005
- mesh: Anaerobiosis, Bioreactors, Carbon Monoxide/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Desulfotomaculum/*classification/genetics/*growth & development/isolation & purification, Genes, rRNA, Molecular Sequence Data, Oxidation-Reduction, Paper, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal/methods, Sequence Analysis, DNA, Sewage/*microbiology, Sulfates/*metabolism, Sulfur-Reducing Bacteria/classification/genetics/isolation & purification
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 291 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 574) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-574 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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) | |||
| 81010 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92880.1 | StrainInfo: A central database for resolving microbial strain identifiers |