Strain identifier

BacDive ID: 16894

Type strain: Yes

Species: Thermodesulfobacterium hydrogeniphilum

Strain Designation: SL6

Strain history: <- C. Jeanthon, Centre National de la Recherche Scientifique, and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Plouzané, France; SL6 <- S. L'Haridon {1998}

NCBI tax ID(s): 161156 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5301

BacDive-ID: 16894

DSM-Number: 14290

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile

description: Thermodesulfobacterium hydrogeniphilum SL6 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from deep-sea hydrothermal vent sulfides, 2000 m depth.

NCBI tax id

  • NCBI tax id: 161156
  • Matching level: species

strain history

  • @ref: 5301
  • history: <- C. Jeanthon, Centre National de la Recherche Scientifique, and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Plouzané, France; SL6 <- S. L'Haridon {1998}

doi: 10.13145/bacdive16894.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/thermodesulfobacteriota
  • domain: Bacteria
  • phylum: Thermodesulfobacteriota
  • class: Thermodesulfobacteria
  • order: Thermodesulfobacteriales
  • family: Thermodesulfobacteriaceae
  • genus: Thermodesulfobacterium
  • species: Thermodesulfobacterium hydrogeniphilum
  • full scientific name: Thermodesulfobacterium hydrogeniphilum Jeanthon et al. 2002

@ref: 5301

domain: Bacteria

phylum: Thermodesulfobacteria

class: Thermodesulfobacteria

order: Thermodesulfobacteriales

family: Thermodesulfobacteriaceae

genus: Thermodesulfobacterium

species: Thermodesulfobacterium hydrogeniphilum

full scientific name: Thermodesulfobacterium hydrogeniphilum Jeanthon et al. 2002

strain designation: SL6

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes92.641
6948099.979negative

Culture and growth conditions

culture medium

  • @ref: 5301
  • name: THERMODESULFOBACTERIUM HYDROGENIPHILUM MEDIUM (DSMZ Medium 829b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/829b
  • composition: Name: THERMODESULFOBACTERIUM HYDROGENIPHILUM MEDIUM (DSMZ Medium 829b) Composition: Sea Salt 29.8507 g/l MES [2-(N-morpholino) ethane sulfonic acid] 1.9403 g/l NH4Cl 0.995025 g/l Na2CO3 0.497512 g/l Yeast extract 0.497512 g/l KH2PO4 0.348259 g/l Na2S2O4 0.0497512 g/l NaHCO3 0.0497512 g/l Succinic acid 0.00597015 g/l 3-Methylbutyric acid 0.00497512 g/l Valeric acid 0.00497512 g/l Isobutyric acid 0.00497512 g/l 2-Methylbutyric acid 0.00497512 g/l HCl 0.00248756 g/l Caproic acid 0.00199005 g/l FeCl2 x 4 H2O 0.00149254 g/l NaOH 0.000497512 g/l Sodium resazurin 0.000497512 g/l Pyridoxine hydrochloride 0.000298507 g/l Nicotinic acid 0.000199005 g/l Thiamine-HCl x 2 H2O 0.000199005 g/l CoCl2 x 6 H2O 0.000189055 g/l MnCl2 x 4 H2O 9.95025e-05 g/l Calcium pantothenate 9.95025e-05 g/l Vitamin B12 9.95025e-05 g/l p-Aminobenzoic acid 7.9602e-05 g/l ZnCl2 6.96517e-05 g/l Na2MoO4 x 2 H2O 3.58209e-05 g/l NiCl2 x 6 H2O 2.38806e-05 g/l D-(+)-biotin 1.99005e-05 g/l H3BO3 5.97015e-06 g/l Na2WO4 x 2 H2O 3.9801e-06 g/l Na2SeO3 x 5 H2O 2.98507e-06 g/l CuCl2 x 2 H2O 1.99005e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
5301positivegrowth70thermophilic
69480thermophilic100

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5301anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481yes100
69480no99.922

Isolation, sampling and environmental information

isolation

  • @ref: 5301
  • sample type: deep-sea hydrothermal vent sulfides, 2000 m depth
  • geographic location: Guaymas Basin hydrothermal vent field
  • country: Mexico
  • origin.country: MEX
  • continent: North America
  • latitude: 27.0167
  • longitude: -111.4

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Marine
#Condition#Sulfuric
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6135.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_515;96_2920;97_3595;98_4550;99_6135&stattab=map
  • Last taxonomy: Thermodesulfobacterium hydrogeniphilum subclade
  • 16S sequence: AF332514
  • Sequence Identity:
  • Total samples: 60
  • soil counts: 1
  • aquatic counts: 58
  • animal counts: 1

Safety information

risk assessment

  • @ref: 5301
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5301
  • description: Thermodesulfobacterium hydrogeniphilum 16S ribosomal RNA gene, partial sequence
  • accession: AF332514
  • length: 1497
  • database: ena
  • NCBI tax ID: 161156

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermodesulfobacterium hydrogeniphilum DSM 14290GCA_000746255scaffoldncbi161156
66792Thermodesulfobacterium hydrogeniphilum strain DSM 14290161156.3wgspatric161156
66792Thermodesulfobacterium hydrogeniphilum DSM 142902579779159draftimg161156

GC content

  • @ref: 5301
  • GC-content: 28
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes87.095no
flagellatedno93.922no
gram-positiveno99.585no
anaerobicyes99.999yes
aerobicno99.481yes
halophileno87.753no
spore-formingno96.111no
glucose-utilno65.801no
thermophileyes100no
glucose-fermentno85.661no

External links

@ref: 5301

culture collection no.: DSM 14290, JCM 11239

straininfo link

  • @ref: 85900
  • straininfo: 101010

literature

  • topic: Phylogeny
  • Pubmed-ID: 12054236
  • title: Thermodesulfobacterium hydrogeniphilum sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a deep-sea hydrothermal vent at Guaymas Basin, and emendation of the genus Thermodesulfobacterium.
  • authors: Jeanthon C, L'Haridon S, Cueff V, Banta A, Reysenbach AL, Prieur D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-3-765
  • year: 2002
  • mesh: Bacterial Typing Techniques, Base Composition, Culture Media, DNA, Ribosomal/analysis, *Hot Temperature, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/*genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfates/metabolism, Sulfur-Reducing Bacteria/*classification/genetics/*growth & development/isolation & purification
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitle
5301Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14290)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14290
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)
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
85900Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID101010.1StrainInfo: A central database for resolving microbial strain identifiers