Strain identifier

BacDive ID: 4132

Type strain: Yes

Species: Desulfovibrio litoralis

Strain history: <- H.-D. Babenzien, Institut für Gewässerökologie und Binnenfischerei, Abteilung Limnologie Geschichteter Seen, Neuglobsow, Germany; STL6 <- H. Sass {1994}

NCBI tax ID(s): 1121455 (strain), 466107 (species)

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General

@ref: 4345

BacDive-ID: 4132

DSM-Number: 11393

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile

description: Desulfovibrio litoralis DSM 11393 is an anaerobe, mesophilic, motile bacterium that was isolated from littoral sediment.

NCBI tax id

NCBI tax idMatching level
466107species
1121455strain

strain history

  • @ref: 4345
  • history: <- H.-D. Babenzien, Institut für Gewässerökologie und Binnenfischerei, Abteilung Limnologie Geschichteter Seen, Neuglobsow, Germany; STL6 <- H. Sass {1994}

doi: 10.13145/bacdive4132.20230509.8.1

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 litoralis
  • full scientific name: Desulfovibrio litoralis Sass et al. 1998

  • synonyms

    • @ref: 20215
    • synonym: Frigididesulfovibrio litoralis

@ref: 4345

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Desulfovibrio

species: Desulfovibrio litoralis

full scientific name: Desulfovibrio litoralis Sass et al. 1998

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes95.901
6948099.963negative

Culture and growth conditions

culture medium

  • @ref: 4345
  • 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: 4345
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4345anaerobe
69480anaerobe99.676

spore formation

@refspore formationconfidence
69481no100
69480no99.707

Isolation, sampling and environmental information

isolation

  • @ref: 4345
  • sample type: littoral sediment
  • geographic location: Lake Stechlin
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_181855.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9669;96_41842;97_53468;98_118546;99_181855&stattab=map
  • Last taxonomy: Desulfovibrio litoralis subclade
  • 16S sequence: X99504
  • Sequence Identity:
  • Total samples: 1697
  • soil counts: 246
  • aquatic counts: 831
  • animal counts: 587
  • plant counts: 33

Safety information

risk assessment

  • @ref: 4345
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4345
  • description: Desulfovibrio litoralis 16S rRNA gene, strain STL6
  • accession: X99504
  • length: 1503
  • database: ena
  • NCBI tax ID: 466107

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfovibrio litoralis DSM 11393GCA_900143255scaffoldncbi1121455
66792Desulfovibrio litoralis DSM 113931121455.3wgspatric1121455
66792Desulfovibrio litoralis DSM 113932582580730draftimg1121455

GC content

  • @ref: 4345
  • GC-content: 36.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.111no
flagellatedno75.725no
gram-positiveno99.325no
anaerobicyes99.545no
aerobicno99.016yes
halophileno85.54no
spore-formingno95.858no
thermophileno90.551yes
glucose-utilno61.94no
glucose-fermentno79.998no

External links

@ref: 4345

culture collection no.: DSM 11393, STL 6

straininfo link

  • @ref: 73635
  • straininfo: 49099

literature

  • topic: Phylogeny
  • Pubmed-ID: 9704109
  • title: Psychrotolerant sulfate-reducing bacteria from an oxic freshwater sediment, description of Desulfovibrio cuneatus sp. nov. and Desulfovibrio litoralis sp. nov.
  • authors: Sass H, Berchtold M, Branke J, Konig H, Cypionka H, Babenzien HD
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/S0723-2020(98)80025-8
  • year: 1998
  • mesh: Base Sequence, Cytochromes/analysis, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Desulfovibrio/*classification/metabolism/ultrastructure, Fresh Water/microbiology, Geologic Sediments/*microbiology, Germany, Hydrogensulfite Reductase, Microscopy, Electron, Microscopy, Phase-Contrast, Molecular Sequence Data, Nephelometry and Turbidimetry, Oxidation-Reduction, Oxidoreductases Acting on Sulfur Group Donors/analysis, Phylogeny, Polymerase Chain Reaction, Respiration, Sequence Analysis, DNA, Sulfates/chemistry/*metabolism, *Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4345Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11393)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11393
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)
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73635Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49099.1StrainInfo: A central database for resolving microbial strain identifiers