Strain identifier

BacDive ID: 17983

Type strain: Yes

Species: Dethiosulfatibacter aminovorans

Strain Designation: C/G2

Strain history: S. Takii C/G2.

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

@ref: 7012

BacDive-ID: 17983

DSM-Number: 17477

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-variable, rod-shaped

description: Dethiosulfatibacter aminovorans C/G2 is an anaerobe, mesophilic, Gram-variable bacterium that was isolated from coastal marine sediment.

NCBI tax id

NCBI tax idMatching level
332095species
1121476strain

strain history

@refhistory
7012<- S. Takii, Tokyo Metropolitan University, Hachioji, Japan; C/G2 <- S. Takii {2004}
67770S. Takii C/G2.

doi: 10.13145/bacdive17983.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Tissierellales
  • family: Dethiosulfatibacteraceae
  • genus: Dethiosulfatibacter
  • species: Dethiosulfatibacter aminovorans
  • full scientific name: Dethiosulfatibacter aminovorans Takii et al. 2007

@ref: 7012

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridia, not assigned to family

genus: Dethiosulfatibacter

species: Dethiosulfatibacter aminovorans

full scientific name: Dethiosulfatibacter aminovorans Takii et al. 2007

strain designation: C/G2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32052variable3.5 µm0.7 µmrod-shapedno
69480positive98.897

Culture and growth conditions

culture medium

  • @ref: 7012
  • name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/383
  • composition: Name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383; with strain-specific modifications) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Sodium glutamate monohydrate 1.89432 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7012positivegrowth28mesophilic
32052positivegrowth15-37
32052positiveoptimum29mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32052positivegrowth5.9-8.8alkaliphile
32052positiveoptimum7.8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7012anaerobe
32052anaerobe
69480anaerobe99.494

spore formation

@refspore formationconfidence
32052no
69481no97
69480no99.249

halophily

@refsaltgrowthtested relationconcentration
32052NaClpositivegrowth0.8-5.5 %
32052NaClpositiveoptimum2.0-3.0 %

observation

  • @ref: 32052
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3205229016arginine+carbon source
3205229987glutamate+carbon source
3205227570histidine+carbon source
3205224996lactate+carbon source
3205215361pyruvate+carbon source
3205217822serine+carbon source
3205226986threonine+carbon source

metabolite production

  • @ref: 32052
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 32052
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7012coastal marine sedimentTokyo BayJapanJPNAsia
67770Anoxic marine sediment from a highly eutrophic area of Tokyo BayJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_29344.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_994;96_12240;97_14845;98_21885;99_29344&stattab=map
  • Last taxonomy: Dethiosulfatibacter aminovorans subclade
  • 16S sequence: AB218661
  • Sequence Identity:
  • Total samples: 165
  • soil counts: 3
  • aquatic counts: 75
  • animal counts: 76
  • plant counts: 11

Safety information

risk assessment

  • @ref: 7012
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7012
  • description: Dethiosulfatibacter aminovorans gene for 16S rRNA
  • accession: AB218661
  • length: 1479
  • database: ena
  • NCBI tax ID: 332095

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dethiosulfatibacter aminovorans DSM 174771121476.3wgspatric1121476
66792Dethiosulfatibacter aminovorans DSM 174772585428150draftimg1121476
67770Dethiosulfatibacter aminovorans DSM 17477GCA_900142005scaffoldncbi1121476

GC content

@refGC-contentmethod
701241.0
3205241
6777041high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileno88.145yes
flagellatedno94.233yes
gram-positiveyes53.351no
anaerobicyes99.425yes
halophileno74.242no
spore-formingno83.037yes
thermophileno96.187yes
glucose-utilyes85.178no
aerobicno96.662yes
glucose-fermentyes55.674no

External links

@ref: 7012

culture collection no.: DSM 17477, JCM 13356, NBRC 101112

straininfo link

  • @ref: 86970
  • straininfo: 310969

literature

  • topic: Phylogeny
  • Pubmed-ID: 17911304
  • title: Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids.
  • authors: Takii S, Hanada S, Tamaki H, Ueno Y, Sekiguchi Y, Ibe A, Matsuura K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64882-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Bacteriological Techniques/*methods, Base Composition, Carbon/metabolism, Chlorates/metabolism, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Glutamic Acid/metabolism, Gram-Positive Bacteria/*classification/cytology/*isolation & purification/physiology, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Nitrogen/metabolism, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Thiosulfates/*metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7012Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17477)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17477
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
32052Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2830228776041
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
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)
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
86970Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310969.1StrainInfo: A central database for resolving microbial strain identifiers