Strain identifier
BacDive ID: 14074
Type strain:
Species: Shewanella sediminis
Strain Designation: A010-1, HAW-EB3
Strain history: CIP <- 2005, NCIMB
NCBI tax ID(s): 271097 (species)
General
@ref: 6724
BacDive-ID: 14074
DSM-Number: 17055
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Shewanella sediminis A010-1 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediment of Emerald Basin in 215 meter deep.
NCBI tax id
- NCBI tax id: 271097
- Matching level: species
strain history
@ref | history |
---|---|
6724 | <- J.-S. Zhao; HAW-EB3 |
38368 | 2005, NCIMB |
122537 | CIP <- 2005, NCIMB |
doi: 10.13145/bacdive14074.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Shewanellaceae
- genus: Shewanella
- species: Shewanella sediminis
- full scientific name: Shewanella sediminis Zhao et al. 2005
@ref: 6724
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Shewanellaceae
genus: Shewanella
species: Shewanella sediminis
full scientific name: Shewanella sediminis Zhao et al. 2005
strain designation: A010-1, HAW-EB3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31456 | negative | 1.7 µm | 0.7 µm | rod-shaped | yes | |
69480 | yes | 98.125 | ||||
69480 | negative | 99.999 |
pigmentation
- @ref: 31456
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6724 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
38368 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
122537 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6724 | positive | growth | 10-20 | psychrophilic |
31456 | positive | growth | 04-25 | |
31456 | positive | optimum | 10 | psychrophilic |
38368 | positive | growth | 15 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 31456
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31456 | no | |
69481 | no | 100 |
69480 | no | 99.99 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31456 | NaCl | positive | growth | 01-04 % |
31456 | NaCl | positive | optimum | 2 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31456 | 30089 | acetate | + | carbon source |
31456 | 16449 | alanine | + | carbon source |
31456 | 35391 | aspartate | + | carbon source |
31456 | 29987 | glutamate | + | carbon source |
31456 | 17596 | inosine | + | carbon source |
31456 | 24996 | lactate | + | carbon source |
31456 | 51850 | methyl pyruvate | + | carbon source |
31456 | 506227 | N-acetylglucosamine | + | carbon source |
31456 | 18257 | ornithine | + | carbon source |
31456 | 26271 | proline | + | carbon source |
31456 | 17272 | propionate | + | carbon source |
31456 | 15361 | pyruvate | + | carbon source |
31456 | 17822 | serine | + | carbon source |
31456 | 30031 | succinate | + | carbon source |
31456 | 17748 | thymidine | + | carbon source |
31456 | 53424 | tween 20 | + | carbon source |
31456 | 53423 | tween 40 | + | carbon source |
31456 | 53426 | tween 80 | + | carbon source |
31456 | 16199 | urea | + | carbon source |
31456 | 31011 | valerate | + | carbon source |
31456 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31456 | alkaline phosphatase | + | 3.1.3.1 |
31456 | catalase | + | 1.11.1.6 |
31456 | cytochrome oxidase | + | 1.9.3.1 |
31456 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6724 | marine sediment of Emerald Basin in 215 meter deep | Halifax | Canada | CAN | North America |
122537 | Environment, Sediment | Halifax harbour, Nova Scotia | Canada | CAN | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_789.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_479;97_547;98_630;99_789&stattab=map
- Last taxonomy: Shewanella sediminis
- 16S sequence: FR733715
- Sequence Identity:
- Total samples: 3109
- soil counts: 163
- aquatic counts: 2554
- animal counts: 381
- plant counts: 11
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6724 | 1 | Risk group (German classification) |
122537 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Shewanella sediminis partial 16S rRNA gene, type strain DSM17055T | FR733715 | 1530 | ena | 271097 |
31456 | Shewanella sediminis strain HAW-EB3 16S ribosomal RNA gene, partial sequence | AY579750 | 1288 | nuccore | 425104 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Shewanella sediminis HAW-EB3 | GCA_000018025 | complete | ncbi | 425104 |
66792 | Shewanella sediminis HAW-EB3 | 425104.7 | complete | patric | 425104 |
66792 | Shewanella sediminis HAW-EB3 | 640753050 | complete | img | 425104 |
GC content
- @ref: 6724
- GC-content: 45
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 92.104 | no |
flagellated | yes | 90.708 | no |
gram-positive | no | 98.927 | yes |
anaerobic | no | 95.651 | yes |
aerobic | no | 81.265 | yes |
halophile | yes | 58.597 | no |
spore-forming | no | 94.016 | yes |
thermophile | no | 99.537 | yes |
glucose-util | yes | 90.272 | no |
glucose-ferment | no | 59.634 | no |
External links
@ref: 6724
culture collection no.: DSM 17055, CIP 109531, NCIMB 14036, CIP 108924
straininfo link
- @ref: 83243
- straininfo: 237174
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16014474 | Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment. | Zhao JS, Manno D, Beaulieu C, Paquet L, Hawari J | Int J Syst Evol Microbiol | 10.1099/ijs.0.63604-0 | 2005 | Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial, DNA, Ribosomal, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/chemistry/*classification/genetics/physiology, Sodium/*metabolism, Triazines/*metabolism | Genetics |
Phylogeny | 34904941 | Shewanella nanhaiensis sp. nov., a marine bacterium isolated from sediment of South China Sea, and emended descriptions of Shewanella woodyi, Shewanella hanedai and Shewanella canadensis. | Cao WR, Li X, Sun YY, Jiang MY, Xu XD, Li YJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005152 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Shewanella/classification/isolation & purification, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
6724 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17055) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17055 | ||||
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 | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
31456 | 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 | 28776041 | 27758 | ||
38368 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6608 | |||||
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) | ||||
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 | ||||
83243 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID237174.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
122537 | Curators of the CIP | Collection of Institut Pasteur (CIP 108924) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108924 |