Strain identifier
BacDive ID: 17770
Type strain:
Species: Dethiosulfovibrio peptidovorans
Strain history: DSM 11002 <-- G. Ravot SEBR 4207.
NCBI tax ID(s): 469381 (strain), 47055 (species)
General
@ref: 4156
BacDive-ID: 17770
DSM-Number: 11002
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, motile
description: Dethiosulfovibrio peptidovorans DSM 11002 is an anaerobe, thermophilic, motile bacterium that was isolated from offshore oil-producing well.
NCBI tax id
NCBI tax id | Matching level |
---|---|
469381 | strain |
47055 | species |
strain history
@ref | history |
---|---|
4156 | <- G. Ravot, Université de Provence, Marseille, France; SEBR 4207 <- M. Magot {1992} |
67770 | DSM 11002 <-- G. Ravot SEBR 4207. |
doi: 10.13145/bacdive17770.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/synergistota
- domain: Bacteria
- phylum: Synergistota
- class: Synergistia
- order: Synergistales
- family: Dethiosulfovibrionaceae
- genus: Dethiosulfovibrio
- species: Dethiosulfovibrio peptidovorans
- full scientific name: Dethiosulfovibrio peptidovorans Magot et al. 1997
@ref: 4156
domain: Bacteria
phylum: Synergistetes
class: Synergistia
order: Synergistales
family: Synergistaceae
genus: Dethiosulfovibrio
species: Dethiosulfovibrio peptidovorans
full scientific name: Dethiosulfovibrio peptidovorans Magot et al. 1997
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 92.579 | |
69480 | 99.952 | negative |
multimedia
- @ref: 66793
- multimedia content: EM_DSM_11002_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 4156
- name: DETHIOSULFOVIBRIO PEPTIDOVORANS MEDIUM (DSMZ Medium 786)
- growth: yes
- link: https://mediadive.dsmz.de/medium/786
- composition: Name: DETHIOSULFOVIBRIO PEPTIDOVORANS MEDIUM (DSMZ Medium 786) Composition: Trypticase peptone 5.0 g/l Na2S2O3 x 5 H2O 5.0 g/l MgCl2 x 6 H2O 3.0 g/l Na2CO3 1.5 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na-acetate 0.5 g/l Na2S x 9 H2O 0.5 g/l L-Cysteine HCl x H2O 0.5 g/l KH2PO4 0.3 g/l K2HPO4 0.3 g/l KCl 0.1 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l H3BO3 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4156 | positive | growth | 42 | thermophilic |
67770 | positive | growth | 42 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
4156 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.989
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
4156 | offshore oil-producing well | Emeraude oil field (well BB325) | Republic of the Congo | COG | Africa |
67770 | Corroding offshore oil well in Congo |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Industrial | #Engineered product |
#Engineered | #Industrial | #Oil reservoir |
taxonmaps
- @ref: 69479
- File name: preview.99_61322.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_366;96_2096;97_2526;98_43520;99_61322&stattab=map
- Last taxonomy: Dethiosulfovibrio
- 16S sequence: U52817
- Sequence Identity:
- Total samples: 28
- aquatic counts: 25
- animal counts: 3
Safety information
risk assessment
- @ref: 4156
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4156
- description: Desulfothiovibrio peptidovorans 16S ribosomal RNA, partial sequence
- accession: U52817
- length: 1505
- database: ena
- NCBI tax ID: 469381
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dethiosulfovibrio peptidovorans DSM 11002 | 469381.10 | wgs | patric | 469381 |
66792 | Dethiosulfovibrio peptidovorans SEBR 4207, DSM 11002 | 2501533205 | draft | img | 469381 |
67770 | Dethiosulfovibrio peptidovorans DSM 11002 | GCA_000172975 | contig | ncbi | 469381 |
GC content
@ref | GC-content | method |
---|---|---|
4156 | 56.0 | |
67770 | 56 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 50 | no |
gram-positive | no | 98.738 | no |
anaerobic | yes | 99.646 | yes |
halophile | no | 87.572 | no |
spore-forming | no | 83.845 | no |
glucose-util | yes | 74.251 | no |
aerobic | no | 97.019 | yes |
flagellated | no | 86.469 | no |
thermophile | yes | 72.997 | yes |
motile | yes | 88.883 | no |
glucose-ferment | no | 64.815 | no |
External links
@ref: 4156
culture collection no.: DSM 11002, JCM 15826, SEBR 4207
straininfo link
- @ref: 86761
- straininfo: 48997
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9226912 | Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a new anaerobic, slightly halophilic, thiosulfate-reducing bacterium from corroding offshore oil wells. | Magot M, Ravot G, Campaignolle X, Ollivier B, Patel BK, Fardeau ML, Thomas P, Crolet JL, Garcia JL | Int J Syst Bacteriol | 10.1099/00207713-47-3-818 | 1997 | Bacteriological Techniques, Congo, DNA, Bacterial/analysis, Gram-Negative Anaerobic Bacteria/*classification/genetics/metabolism, Molecular Sequence Data, Oils, Phylogeny, RNA, Ribosomal, 16S/analysis, Salts/metabolism, Sulfur-Reducing Bacteria/*classification/genetics/metabolism, Thiosulfates/metabolism, *Water Microbiology | Metabolism |
Genetics | 21304695 | Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207). | Labutti K, Mayilraj S, Clum A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A | Stand Genomic Sci | 10.4056/sigs.1092865 | 2010 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4156 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11002) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11002 | |||
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 | |||
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 | |
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 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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) | |||
86761 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48997.1 | StrainInfo: A central database for resolving microbial strain identifiers |