Strain identifier
BacDive ID: 131401
Type strain: 
Species: Sedimenticola thiotaurini
Strain Designation: SIP-G1
Strain history: <- B. Flood, Univ. Minnesota; SIP-G1 <- B. Flood, Univ. of Southern California, USA
NCBI tax ID(s): 1543721 (species)
version 8.1 (current version)
General
@ref: 22628
BacDive-ID: 131401
DSM-Number: 28581
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Sedimenticola thiotaurini SIP-G1 is a mesophilic, motile bacterium that was isolated from salt marsh sediment.
NCBI tax id
- NCBI tax id: 1543721
- Matching level: species
strain history
- @ref: 22628
- history: <- B. Flood, Univ. Minnesota; SIP-G1 <- B. Flood, Univ. of Southern California, USA
doi: 10.13145/bacdive131401.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Sedimenticolaceae
- genus: Sedimenticola
- species: Sedimenticola thiotaurini
- full scientific name: Sedimenticola thiotaurini Flood et al. 2015
@ref: 22628
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Gammaproteobacteria, not assigned to family
genus: Sedimenticola
species: Sedimenticola thiotaurini
full scientific name: Sedimenticola thiotaurini Flood et al. 2015
strain designation: SIP-G1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 98.316 | |
| 69480 | 100 | negative |
Culture and growth conditions
culture medium
- @ref: 22628
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
- @ref: 22628
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.99 |
Isolation, sampling and environmental information
isolation
- @ref: 22628
- sample type: salt marsh sediment
- geographic location: Massachusetts, Falmouth, Sippiwissett Salt Marsh
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Salt marsh |
| #Environmental | #Terrestrial | #Sediment |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_4188.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_159;96_2117;97_2550;98_3160;99_4188&stattab=map
- Last taxonomy: Sedimenticola thiotaurini
- 16S sequence: JN882289
- Sequence Identity:
- Total samples: 251
- soil counts: 24
- aquatic counts: 206
- animal counts: 4
- plant counts: 17
Safety information
risk assessment
- @ref: 22628
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22628
- description: Sedimenticola thiotaurini strain SIP-G1 16S ribosomal RNA gene, partial sequence
- accession: JN882289
- length: 1405
- database: ena
- NCBI tax ID: 1543721
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sedimenticola thiotaurini SIP-G1 | GCA_001007875 | complete | ncbi | 1543721 |
| 66792 | Sedimenticola thiotaurini SIP-G1 | 2654588029 | complete | img | 1543721 |
| 66792 | Sedimenticola thiotaurini SIP-G1 | 2609459601 | complete | img | 349742 |
GC content
- @ref: 22628
- GC-content: 57
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 90.381 | no |
| flagellated | yes | 82.369 | no |
| gram-positive | no | 99.447 | no |
| anaerobic | no | 73.361 | no |
| aerobic | no | 79.249 | no |
| halophile | no | 73.189 | no |
| spore-forming | no | 95.602 | no |
| thermophile | no | 97.933 | no |
| glucose-util | no | 56.528 | no |
| glucose-ferment | no | 90.748 | no |
External links
@ref: 22628
culture collection no.: DSM 28581, ATCC BAA 2640
straininfo link
- @ref: 89834
- straininfo: 404143
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25944805 | Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens. | Flood BE, Jones DS, Bailey JV | Int J Syst Evol Microbiol | 10.1099/ijs.0.000295 | 2015 | DNA, Bacterial/genetics, Gammaproteobacteria/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Massachusetts, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/metabolism, Sulfur-Reducing Bacteria/classification/genetics/isolation & purification, Thiosulfates/metabolism, Vitamin K 2/chemistry, *Wetlands | Enzymology |
| Genetics | 26089430 | Complete Genome Sequence of Sedimenticola thiotaurini Strain SIP-G1, a Polyphosphate- and Polyhydroxyalkanoate-Accumulating Sulfur-Oxidizing Gammaproteobacterium Isolated from Salt Marsh Sediments. | Flood BE, Jones DS, Bailey JV | Genome Announc | 10.1128/genomeA.00671-15 | 2015 | Phylogeny |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 22628 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28581 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28581) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 89834 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID404143.1 |