Strain identifier
BacDive ID: 14073
Type strain: 
Species: Shewanella gaetbuli
Strain Designation: TF-27
Strain history: J.-H. Yoon TF-27.
NCBI tax ID(s): 220752 (species)
version 8.1 (current version)
General
@ref: 6443
BacDive-ID: 14073
DSM-Number: 16422
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Shewanella gaetbuli TF-27 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat.
NCBI tax id
- NCBI tax id: 220752
- Matching level: species
strain history
| @ref | history |
|---|---|
| 6443 | <- J.-H. Yoon; TF-27 |
| 67770 | J.-H. Yoon TF-27. |
doi: 10.13145/bacdive14073.20230509.8.1
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 gaetbuli
- full scientific name: Shewanella gaetbuli Yoon et al. 2004
@ref: 6443
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Shewanellaceae
genus: Shewanella
species: Shewanella gaetbuli
full scientific name: Shewanella gaetbuli Yoon et al. 2004
strain designation: TF-27
type strain: yes
Morphology
cell morphology
- @ref: 29946
- gram stain: negative
- cell length: 2.25 µm
- cell width: 0.6 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 29946
- production: yes
Culture and growth conditions
culture medium
- @ref: 6443
- 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 | growth | type | temperature | range |
|---|---|---|---|---|
| 6443 | positive | growth | 28 | mesophilic |
| 29946 | positive | growth | 25-35 | mesophilic |
| 29946 | positive | optimum | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29946 | positive | growth | 05-08 |
| 29946 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 29946
- oxygen tolerance: facultative anaerobe
spore formation
- @ref: 29946
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29946 | NaCl | positive | growth | <8 % |
| 29946 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67770
- observation: quinones: MK-7, Q-7, Q-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29946 | 33942 | ribose | + | carbon source |
| 29946 | 27082 | trehalose | + | carbon source |
| 29946 | 53426 | tween 80 | + | carbon source |
| 29946 | 4853 | esculin | + | hydrolysis |
enzymes
- @ref: 29946
- value: alkaline phosphatase
- activity: +
- ec: 3.1.3.1
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6443 | tidal flat | Mokpo City | Republic of Korea | KOR | Asia |
| 67770 | Tidal flat near Mokpo | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Tidal flat
taxonmaps
- @ref: 69479
- File name: preview.99_41960.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_126;97_1400;98_30494;99_41960&stattab=map
- Last taxonomy: Shewanella gaetbuli subclade
- 16S sequence: AY190533
- Sequence Identity:
- Total samples: 125
- aquatic counts: 116
- animal counts: 9
Safety information
risk assessment
- @ref: 6443
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 29946
- description: Shewanella gaetbuli 16S ribosomal RNA gene, partial sequence
- accession: AY190533
- length: 1497
- database: nuccore
- NCBI tax ID: 220752
Genome sequences
- @ref: 66792
- description: Shewanella gaetbuli DSM 16422
- accession: GCA_023284065
- assembly level: contig
- database: ncbi
- NCBI tax ID: 220752
GC content
| @ref | GC-content | method |
|---|---|---|
| 29946 | 42 | |
| 67770 | 42 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | yes | 80.852 | no |
| gram-positive | no | 98.88 | yes |
| anaerobic | no | 98.162 | yes |
| aerobic | no | 51.425 | yes |
| halophile | yes | 51.525 | no |
| spore-forming | no | 94.611 | yes |
| motile | yes | 85.544 | no |
| glucose-ferment | no | 68.036 | no |
| thermophile | no | 98.135 | yes |
| glucose-util | yes | 90.387 | no |
External links
@ref: 6443
culture collection no.: DSM 16422, JCM 11814, KCCM 41648, KCTC 22431
straininfo link
- @ref: 83242
- straininfo: 131434
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15023965 | Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea. | Yoon JH, Kang KH, Oh TK, Park YH | Int J Syst Evol Microbiol | 10.1099/ijs.0.02731-0 | 2004 | Biomass, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Phylogeny, Quinones/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Shewanella/*classification/isolation & purification/physiology, Ubiquinone/metabolism | Genetics |
| Phylogeny | 17158991 | Shewanella spongiae sp. nov., isolated from a marine sponge. | Yang SH, Kwon KK, Lee HS, Kim SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.64540-0 | 2006 | Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Marine Biology, Molecular Sequence Data, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Shewanella/*classification/genetics/isolation & purification/physiology | Genetics |
| Phylogeny | 23950150 | Shewanella aestuarii sp. nov., a marine bacterium isolated from a tidal flat. | Park HY, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.055178-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/genetics/isolation & purification | Genetics |
| Phylogeny | 25096326 | Psychrobium conchae gen. nov., sp. nov., a psychrophilic marine bacterium isolated from the Iheya North hydrothermal field. | Nogi Y, Abe M, Kawagucci S, Hirayama H | Int J Syst Evol Microbiol | 10.1099/ijs.0.066738-0 | 2014 | Animals, Bacterial Typing Techniques, Base Composition, Bivalvia/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Hydrothermal Vents, Japan, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
| Phylogeny | 28629494 | Shewanella intestini sp. nov., isolated from the intestine of abalone, Haliotis diversicolor. | Gai Y, Huang Z, Lai Q, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001878 | 2017 | Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastropoda/*microbiology, Intestines/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Shewanella/*classification/genetics/isolation & purification, Vitamin K 2/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6443 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16422) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16422 | |||
| 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 | |||
| 29946 | 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 | 26315 | 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) | |||
| 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 | |||
| 83242 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131434.1 | StrainInfo: A central database for resolving microbial strain identifiers |