Strain identifier
BacDive ID: 4070
Type strain: 
Species: Desulfovibrio piger
Strain history: <- N. Pfennig, Gesellschaft für Strahlen- und Umweltforschung mbH München in Göttingen, Germany; VPI 11112 <- W. E. C. Moore, Virginia Polytechnical Institute and State University, Blacksburg, V., USA
NCBI tax ID(s): 411464 (strain), 901 (species)
version 8.1 (current version)
General
@ref: 422
BacDive-ID: 4070
DSM-Number: 749
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Desulfovibrio piger DSM 749 is an anaerobe, mesophilic bacterium that was isolated from human faeces.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 901 | species |
| 411464 | strain |
strain history
- @ref: 422
- history: <- N. Pfennig, Gesellschaft für Strahlen- und Umweltforschung mbH München in Göttingen, Germany; VPI 11112 <- W. E. C. Moore, Virginia Polytechnical Institute and State University, Blacksburg, V., USA
doi: 10.13145/bacdive4070.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Desulfovibrio
- species: Desulfovibrio piger
- full scientific name: Desulfovibrio piger (Moore et al. 1976) Loubinoux et al. 2002
synonyms
- @ref: 20215
- synonym: Desulfomonas pigra
@ref: 422
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Desulfovibrio
species: Desulfovibrio piger
full scientific name: Desulfovibrio piger (Moore et al. 1976) Loubinoux et al. 2002
type strain: yes
Culture and growth conditions
culture medium
- @ref: 422
- name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)
- growth: yes
- link: https://mediadive.dsmz.de/medium/641
- composition: Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) Composition: Na-DL-lactate 2.49252 g/l Na2SO4 1.99402 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l Na2S2O3 x 5 H2O 0.997009 g/l KH2PO4 0.498504 g/l Na2S x 9 H2O 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
- @ref: 422
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 422
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 422
- sample type: human faeces
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Human | |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_13256.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_139;96_435;97_497;98_569;99_13256&stattab=map
- Last taxonomy: Desulfovibrio piger subclade
- 16S sequence: AF192152
- Sequence Identity:
- Total samples: 120767
- soil counts: 1726
- aquatic counts: 4606
- animal counts: 113854
- plant counts: 581
Safety information
risk assessment
- @ref: 422
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | D.pigra 16S ribosomal rRNA | M34404 | 1378 | ena | 901 |
| 422 | Desulfomonas pigra 16S ribosomal RNA gene, complete sequence | AF192152 | 1542 | ena | 411464 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfovibrio piger ATCC 29098 | GCA_000156375 | scaffold | ncbi | 411464 |
| 66792 | Desulfovibrio piger ATCC 29098 | 411464.8 | wgs | patric | 411464 |
| 66792 | Desulfovibrio piger ATCC 29098 | 642979316 | draft | img | 411464 |
GC content
- @ref: 422
- GC-content: 67.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 54.564 | no |
| flagellated | no | 87.328 | no |
| gram-positive | no | 97.535 | no |
| anaerobic | yes | 99.5 | yes |
| aerobic | no | 97.428 | yes |
| halophile | no | 82.884 | no |
| spore-forming | no | 95.185 | no |
| thermophile | no | 89.58 | yes |
| glucose-util | no | 64.981 | no |
| glucose-ferment | no | 74.706 | no |
External links
@ref: 422
culture collection no.: DSM 749, ATCC 29098, JCM 12224, VPI 11112, VPI C3-23
straininfo link
- @ref: 73573
- straininfo: 39351
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Cultivation | 9283136 | [Rapid identification of Bilophila wadsworthia]. | Sawamura H, Kato N, Sawa K, Watanabe K, Ueno K | Kansenshogaku Zasshi | 10.11150/kansenshogakuzasshi1970.71.614 | 1997 | Bacteriological Techniques, Culture Media, Gram-Negative Anaerobic Bacteria/*isolation & purification | Enzymology |
| Phylogeny | 12148644 | Reclassification of the only species of the genus Desulfomonas, Desulfomonas pigra, as Desulfovibrio piger comb. nov. | Loubinoux J, Valente FM, Pereira IA, Costa A, Grimont PA, Le Faou AE | Int J Syst Evol Microbiol | 10.1099/00207713-52-4-1305 | 2002 | Base Composition, DNA, Ribosomal/analysis, DNA, Ribosomal Spacer/analysis, Deltaproteobacteria/*classification/genetics/growth & development, Desulfovibrio/*classification/genetics/growth & development, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Species Specificity, Sulfur-Reducing Bacteria/classification/genetics/growth & development | Pathogenicity |
| Metabolism | 19732152 | Lactate has the potential to promote hydrogen sulphide formation in the human colon. | Marquet P, Duncan SH, Chassard C, Bernalier-Donadille A, Flint HJ | FEMS Microbiol Lett | 10.1111/j.1574-6968.2009.01750.x | 2009 | Bacteria/*metabolism, Butyrates/metabolism, Coculture Techniques, Colon/*microbiology, Humans, Hydrogen Sulfide/*metabolism, Lactic Acid/*metabolism | Pathogenicity |
| Genetics | 35468931 | Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice. | Jangid A, Fukuda S, Suzuki Y, Taylor TD, Ohno H, Prakash T | Sci Rep | 10.1038/s41598-022-10762-3 | 2022 | Animals, Cellulose/pharmacology, Diet, Dietary Fiber/pharmacology, Edible Grain, Lactobacillus/genetics, *Metagenome, Metagenomics, Mice, *Prebiotics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 422 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 749) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-749 | |||
| 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 | |||
| 73573 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39351.1 | StrainInfo: A central database for resolving microbial strain identifiers |