Strain identifier
BacDive ID: 17983
Type strain:
Species: Dethiosulfatibacter aminovorans
Strain Designation: C/G2
Strain history: S. Takii C/G2.
NCBI tax ID(s): 1121476 (strain), 332095 (species)
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 id | Matching level |
---|---|
332095 | species |
1121476 | strain |
strain history
@ref | history |
---|---|
7012 | <- S. Takii, Tokyo Metropolitan University, Hachioji, Japan; C/G2 <- S. Takii {2004} |
67770 | S. 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32052 | variable | 3.5 µm | 0.7 µm | rod-shaped | no | |
69480 | positive | 98.897 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
7012 | positive | growth | 28 | mesophilic |
32052 | positive | growth | 15-37 | |
32052 | positive | optimum | 29 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32052 | positive | growth | 5.9-8.8 | alkaliphile |
32052 | positive | optimum | 7.8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
7012 | anaerobe | |
32052 | anaerobe | |
69480 | anaerobe | 99.494 |
spore formation
@ref | spore formation | confidence |
---|---|---|
32052 | no | |
69481 | no | 97 |
69480 | no | 99.249 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32052 | NaCl | positive | growth | 0.8-5.5 % |
32052 | NaCl | positive | optimum | 2.0-3.0 % |
observation
- @ref: 32052
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32052 | 29016 | arginine | + | carbon source |
32052 | 29987 | glutamate | + | carbon source |
32052 | 27570 | histidine | + | carbon source |
32052 | 24996 | lactate | + | carbon source |
32052 | 15361 | pyruvate | + | carbon source |
32052 | 17822 | serine | + | carbon source |
32052 | 26986 | threonine | + | 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
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7012 | coastal marine sediment | Tokyo Bay | Japan | JPN | Asia |
67770 | Anoxic marine sediment from a highly eutrophic area of Tokyo Bay | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dethiosulfatibacter aminovorans DSM 17477 | 1121476.3 | wgs | patric | 1121476 |
66792 | Dethiosulfatibacter aminovorans DSM 17477 | 2585428150 | draft | img | 1121476 |
67770 | Dethiosulfatibacter aminovorans DSM 17477 | GCA_900142005 | scaffold | ncbi | 1121476 |
GC content
@ref | GC-content | method |
---|---|---|
7012 | 41.0 | |
32052 | 41 | |
67770 | 41 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 97 | no |
motile | no | 88.145 | yes |
flagellated | no | 94.233 | yes |
gram-positive | yes | 53.351 | no |
anaerobic | yes | 99.425 | yes |
halophile | no | 74.242 | no |
spore-forming | no | 83.037 | yes |
thermophile | no | 96.187 | yes |
glucose-util | yes | 85.178 | no |
aerobic | no | 96.662 | yes |
glucose-ferment | yes | 55.674 | no |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7012 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17477) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17477 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
32052 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28302 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
69479 | João 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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
86970 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID310969.1 | StrainInfo: A central database for resolving microbial strain identifiers |