Strain identifier

BacDive ID: 17057

Type strain: Yes

Species: Thermosipho atlanticus

Strain Designation: DV1140

Strain history: <- G. Barbier, IFREMER; DV1140 <- V. Cueff-Gauchard and L. Urios {2002}

NCBI tax ID(s): 1123380 (strain), 238991 (species)

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General

@ref: 6117

BacDive-ID: 17057

DSM-Number: 15807

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, rod-shaped

description: Thermosipho atlanticus DV1140 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from hydrothermal vent.

NCBI tax id

NCBI tax idMatching level
1123380strain
238991species

strain history

  • @ref: 6117
  • history: <- G. Barbier, IFREMER; DV1140 <- V. Cueff-Gauchard and L. Urios {2002}

doi: 10.13145/bacdive17057.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/thermotogota
  • domain: Bacteria
  • phylum: Thermotogota
  • class: Thermotogae
  • order: Thermotogales
  • family: Fervidobacteriaceae
  • genus: Thermosipho
  • species: Thermosipho atlanticus
  • full scientific name: Thermosipho atlanticus Urios et al. 2004

@ref: 6117

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Fervidobacteriaceae

genus: Thermosipho

species: Thermosipho atlanticus

full scientific name: Thermosipho atlanticus Urios et al. 2004

strain designation: DV1140

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31217negative1.8 µm0.4 µmrod-shapedno
69480negative99.866

Culture and growth conditions

culture medium

  • @ref: 6117
  • name: MARINITOGA HYDROGENITOLERANS MEDIUM (DSMZ Medium 904a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/904a
  • composition: Name: MARINITOGA HYDROGENITOLERANS MEDIUM (DSMZ Medium 904a) Composition: Sea Salt 30.0 g/l MES 4.0 g/l D-Glucose 2.5 g/l Tryptone 1.0 g/l Yeast extract 1.0 g/l Na2S x 9 H2O 0.5 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
6117positivegrowth65thermophilic
31217positivegrowth45-80hyperthermophilic
31217positiveoptimum60thermophilic
69480thermophilic100

culture pH

@refabilitytypepHPH range
31217positivegrowth05-09alkaliphile
31217positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6117anaerobe
31217anaerobe
69480anaerobe100

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.994

halophily

@refsaltgrowthtested relationconcentration
31217NaClpositivegrowth02-06 %
31217NaClpositiveoptimum3 %

observation

  • @ref: 31217
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3121722599arabinose+carbon source
3121717057cellobiose+carbon source
3121728260galactose+carbon source
312175291gelatin+carbon source
3121717234glucose+carbon source
3121727082trehalose+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 6117
  • sample type: hydrothermal vent
  • geographic location: Mid. Atlantic Ridge, Menez-Gwen hydrothermal site
  • country: Portugal
  • origin.country: PRT
  • continent: Europe
  • latitude: 37.85
  • longitude: -31.5167

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_104275.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_93;96_2192;97_2651;98_3287;99_104275&stattab=map
  • Last taxonomy: Thermosipho atlanticus subclade
  • 16S sequence: AJ577471
  • Sequence Identity:
  • Total samples: 1
  • aquatic counts: 1

Safety information

risk assessment

  • @ref: 6117
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
31217Thermosipho atlanticus partial 16S rRNA gene, strain DV1140AJ5774711511nuccore238991
6117AJ57471ena

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermosipho atlanticus DSM 15807GCA_900129985contigncbi1123380
66792Thermosipho atlanticus DSM 158071123380.4wgspatric1123380
66792Thermosipho atlanticus DSM 158072585428073draftimg1123380

GC content

  • @ref: 6117
  • GC-content: 33

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes52no
motileno81.614no
flagellatedno98.747yes
gram-positiveno92.371yes
anaerobicyes99.034yes
aerobicno98.878yes
halophileno84.748no
spore-formingno96.46no
glucose-utilyes88.333yes
thermophileyes100yes
glucose-fermentno52.778no

External links

@ref: 6117

culture collection no.: DSM 15807, CIP 108053

straininfo link

  • @ref: 86057
  • straininfo: 134463

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545417Thermosipho atlanticus sp. nov., a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent.Urios L, Cueff-Gauchard V, Pignet P, Postec A, Fardeau ML, Ollivier B, Barbier GInt J Syst Evol Microbiol10.1099/ijs.0.63069-02004Acetic Acid/metabolism, Anaerobiosis, Bacteria/*classification/cytology/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fermentation, Genes, rRNA, Hemiterpenes, Hot Temperature, Hydrogen/metabolism, Hydrogen-Ion Concentration, Mid-Atlantic Region, Molecular Sequence Data, Movement, Organic Chemicals/metabolism, Pentanoic Acids/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic, Sequence Analysis, DNA, *Water MicrobiologyMetabolism
Phylogeny34328826Thermosipho ferrireducens sp.nov., an anaerobic thermophilic iron(III)-reducing bacterium isolated from a deep-sea hydrothermal sulfide deposits.Chen Y, He Y, Shao Z, Han X, Chen D, Yang J, Zeng XInt J Syst Evol Microbiol10.1099/ijsem.0.0049292021Anaerobiosis, Bacteria, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Iron, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, SulfidesTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6117Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15807)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15807
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
31217Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2754328776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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)
86057Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134463.1StrainInfo: A central database for resolving microbial strain identifiers