Strain identifier

BacDive ID: 17770

Type strain: Yes

Species: Dethiosulfovibrio peptidovorans

Strain history: DSM 11002 <-- G. Ravot SEBR 4207.

NCBI tax ID(s): 469381 (strain), 47055 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
469381strain
47055species

strain history

@refhistory
4156<- G. Ravot, Université de Provence, Marseille, France; SEBR 4207 <- M. Magot {1992}
67770DSM 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

@refmotilityconfidencegram stain
69480yes92.579
6948099.952negative

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

@refgrowthtypetemperaturerange
4156positivegrowth42thermophilic
67770positivegrowth42thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4156anaerobe
69480anaerobe99.999

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.989

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4156offshore oil-producing wellEmeraude oil field (well BB325)Republic of the CongoCOGAfrica
67770Corroding offshore oil well in Congo

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dethiosulfovibrio peptidovorans DSM 11002469381.10wgspatric469381
66792Dethiosulfovibrio peptidovorans SEBR 4207, DSM 110022501533205draftimg469381
67770Dethiosulfovibrio peptidovorans DSM 11002GCA_000172975contigncbi469381

GC content

@refGC-contentmethod
415656.0
6777056high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno50no
gram-positiveno98.738no
anaerobicyes99.646yes
halophileno87.572no
spore-formingno83.845no
glucose-utilyes74.251no
aerobicno97.019yes
flagellatedno86.469no
thermophileyes72.997yes
motileyes88.883no
glucose-fermentno64.815no

External links

@ref: 4156

culture collection no.: DSM 11002, JCM 15826, SEBR 4207

straininfo link

  • @ref: 86761
  • straininfo: 48997

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9226912Dethiosulfovibrio 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 JLInt J Syst Bacteriol10.1099/00207713-47-3-8181997Bacteriological 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 MicrobiologyMetabolism
Genetics21304695Permanent 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 AStand Genomic Sci10.4056/sigs.10928652010

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4156Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11002)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11002
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
86761Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48997.1StrainInfo: A central database for resolving microbial strain identifiers