Strain identifier

BacDive ID: 18094

Type strain: Yes

Species: Thermosulfidibacter takaii

Strain Designation: ABI70S6

Strain history: T. Nunoura ABI70S6.

NCBI tax ID(s): 412593 (species)

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General

@ref: 6985

BacDive-ID: 18094

DSM-Number: 17441

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

description: Thermosulfidibacter takaii ABI70S6 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from deep-sea hydrothermal field.

NCBI tax id

  • NCBI tax id: 412593
  • Matching level: species

strain history

@refhistory
6985<- T. Nunoura, Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC); ABI70S6 <- T. Nunoura {2004}
67770T. Nunoura ABI70S6.

doi: 10.13145/bacdive18094.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/aquificota
  • domain: Bacteria
  • phylum: Aquificota
  • class: Aquificia
  • order: Thermosulfidibacterales
  • family: Thermosulfidibacteraceae
  • genus: Thermosulfidibacter
  • species: Thermosulfidibacter takaii
  • full scientific name: Thermosulfidibacter takaii Nunoura et al. 2008

@ref: 6985

domain: Bacteria

phylum: Aquificae

class: Aquificae

order: Aquificales

family: Aquificae, not assigned to family

genus: Thermosulfidibacter

species: Thermosulfidibacter takaii

full scientific name: Thermosulfidibacter takaii Nunoura et al. 2008

strain designation: ABI70S6

type strain: yes

Morphology

cell morphology

  • @ref: 32341
  • gram stain: negative
  • cell length: 1.45 µm
  • cell width: 0.6 µm
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

  • @ref: 6985
  • name: THERMOSULFIDIBACTER MEDIUM (DSMZ Medium 1092)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1092
  • composition: Name: THERMOSULFIDIBACTER MEDIUM (DSMZ Medium 1092) Composition: Sea Salt 29.9103 g/l Sulfur 2.99103 g/l NaHCO3 2.49252 g/l Yeast extract 1.99402 g/l Na2S x 9 H2O 0.498504 g/l MgSO4 x 7 H2O 0.0299103 g/l NaCl 0.00997009 g/l MnSO4 x H2O 0.00498504 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00279163 g/l ZnSO4 x 7 H2O 0.00179462 g/l CoCl2 x 6 H2O 0.00179462 g/l CaCl2 x 2 H2O 0.000997009 g/l FeSO4 x 7 H2O 0.000997009 g/l Sodium resazurin 0.000498504 g/l Pyridoxine hydrochloride 0.000199402 g/l AlK(SO4)2 x 12 H2O 0.000179462 g/l CuSO4 x 5 H2O 9.97009e-05 g/l H3BO3 9.97009e-05 g/l Na2MoO4 x 2 H2O 9.97009e-05 g/l Nicotinic acid 9.97009e-05 g/l Riboflavin 9.97009e-05 g/l Thiamine HCl 9.97009e-05 g/l Calcium D-(+)-pantothenate 9.97009e-05 g/l p-Aminobenzoic acid 9.97009e-05 g/l (DL)-alpha-Lipoic acid 9.97009e-05 g/l Na2SeO4 9.97009e-05 g/l Na2WO4 x 2 H2O 9.97009e-05 g/l Biotin 3.98804e-05 g/l Folic acid 3.98804e-05 g/l Vitamin B12 1.99402e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6985positivegrowth70thermophilic
32341positivegrowth55-78thermophilic
32341positiveoptimum70thermophilic
67770positivegrowth70thermophilic

culture pH

@refabilitytypepH
32341positivegrowth5-7.5
32341positiveoptimum5.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6985anaerobe
32341anaerobe

spore formation

  • @ref: 32341
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32341NaClpositivegrowth0.5-4.5 %
32341NaClpositiveoptimum3 %

metabolite production

  • @ref: 32341
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
6985deep-sea hydrothermal fieldYonaguni Knoll IV hydrothermal field, Southern Okinawa TroughJapanJPNAsia24.8461122.701
67770Deep-sea hydrothermal field at the Yonaguni Knoll IVSouthern Okinawa Trough

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7210.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_629;96_3370;97_4138;98_5294;99_7210&stattab=map
  • Last taxonomy: Thermosulfidibacter takaii subclade
  • 16S sequence: AB282756
  • Sequence Identity:
  • Total samples: 96
  • soil counts: 8
  • aquatic counts: 84
  • animal counts: 4

Safety information

risk assessment

  • @ref: 6985
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6985
  • description: Thermosulfidibacter takaii gene for 16S rRNA, partial sequence, strain: ABI70S6
  • accession: AB282756
  • length: 1450
  • database: ena
  • NCBI tax ID: 1298851

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermosulfidibacter takaii ABI70S6GCA_001547735completencbi1298851
66792Thermosulfidibacter takaii ABI70S61298851.4completepatric1298851

GC content

@refGC-contentmethod
698544.2high performance liquid chromatography (HPLC)
3234144.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno87.542no
gram-positiveno99.572yes
anaerobicyes99.323no
halophileno76.394no
spore-formingno96.27yes
thermophileyes100no
glucose-utilno54.248no
motileyes88.665yes
aerobicno98.988yes
glucose-fermentno84.231no

External links

@ref: 6985

culture collection no.: DSM 17441, JCM 13301, NBRC 103674

straininfo link

  • @ref: 87082
  • straininfo: 343471

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18319474Thermosulfidibacter takaii gen. nov., sp. nov., a thermophilic, hydrogen-oxidizing, sulfur-reducing chemolithoautotroph isolated from a deep-sea hydrothermal field in the Southern Okinawa Trough.Nunoura T, Oida H, Miyazaki M, Suzuki YInt J Syst Evol Microbiol10.1099/ijs.0.65349-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Gram-Negative Chemolithotrophic Bacteria/*classification/genetics/growth & development/physiology, Hot Temperature, Hydrogen/*metabolism, Japan, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity, Sulfur-Reducing Bacteria/*classification/genetics/growth & development/physiologyStress
Metabolism29420286A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile.Nunoura T, Chikaraishi Y, Izaki R, Suwa T, Sato T, Harada T, Mori K, Kato Y, Miyazaki M, Shimamura S, Yanagawa K, Shuto A, Ohkouchi N, Fujita N, Takaki Y, Atomi H, Takai KScience10.1126/science.aao34072018Bacteria/*metabolism, *Carbon Cycle, *Chemoautotrophic Growth, *Citric Acid Cycle

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6985Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17441)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17441
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
32341Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2857328776041
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)
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
87082Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343471.1StrainInfo: A central database for resolving microbial strain identifiers