Strain identifier
BacDive ID: 2244
Type strain: 
Species: Alkalibacterium thalassium
Strain Designation: T117-1-2
Strain history: <- M. Ishikawa and K. Yamasato, Faculty of Applied Bio-Science, Tokyo University of Agriculture, Setagaya-ku, Japan; T117-1-2
NCBI tax ID(s): 426701 (species)
version 8.1 (current version)
General
@ref: 7953
BacDive-ID: 2244
DSM-Number: 19181
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped
description: Alkalibacterium thalassium T117-1-2 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from decaying marine alga.
NCBI tax id
- NCBI tax id: 426701
- Matching level: species
strain history
- @ref: 7953
- history: <- M. Ishikawa and K. Yamasato, Faculty of Applied Bio-Science, Tokyo University of Agriculture, Setagaya-ku, Japan; T117-1-2
doi: 10.13145/bacdive2244.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Carnobacteriaceae
- genus: Alkalibacterium
- species: Alkalibacterium thalassium
- full scientific name: Alkalibacterium thalassium Ishikawa et al. 2009
@ref: 7953
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Carnobacteriaceae
genus: Alkalibacterium
species: Alkalibacterium thalassium
full scientific name: Alkalibacterium thalassium Ishikawa et al. 2009
strain designation: T117-1-2
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32511 | positive | 6.3 µm | 1 µm | rod-shaped | no | |
| 69480 | positive | 100 |
pigmentation
- @ref: 32511
- production: yes
Culture and growth conditions
culture medium
- @ref: 7953
- name: BOGORIELLA MEDIUM (DSMZ Medium 785)
- growth: yes
- link: https://mediadive.dsmz.de/medium/785
- composition: Name: BOGORIELLA MEDIUM (DSMZ Medium 785) Composition: NaCl 40.0 g/l Glucose 10.0 g/l Na2CO3 10.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7953 | positive | growth | 28 | mesophilic |
| 32511 | positive | growth | 10-42.5 | |
| 32511 | positive | optimum | 37 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32511 | positive | growth | 07-11 | alkaliphile |
| 32511 | positive | optimum | 9 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 7953 | microaerophile |
| 32511 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32511 | no | |
| 69480 | no | 99.834 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32511 | NaCl | positive | growth | 0-11 % |
| 32511 | NaCl | positive | optimum | 1.75 % |
murein
- @ref: 7953
- murein short key: A21.04
- type: A4ß L-Orn-D-Asp
observation
- @ref: 32511
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32511 | 30089 | acetate | + | carbon source |
| 32511 | 17057 | cellobiose | + | carbon source |
| 32511 | 16236 | ethanol | + | carbon source |
| 32511 | 28260 | galactose | + | carbon source |
| 32511 | 17234 | glucose | + | carbon source |
| 32511 | 24996 | lactate | + | carbon source |
| 32511 | 17716 | lactose | + | carbon source |
| 32511 | 16634 | raffinose | + | carbon source |
| 32511 | 17814 | salicin | + | carbon source |
| 32511 | 17992 | sucrose | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 7953
- sample type: decaying marine alga
- geographic location: Rayong province, seashore of Ko Samet, Samet Island
- country: Thailand
- origin.country: THA
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Host | #Algae |
taxonmaps
- @ref: 69479
- File name: preview.99_14937.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_27;96_47;97_49;98_11305;99_14937&stattab=map
- Last taxonomy: Alkalibacterium
- 16S sequence: AB294165
- Sequence Identity:
- Total samples: 171
- soil counts: 4
- aquatic counts: 81
- animal counts: 78
- plant counts: 8
Safety information
risk assessment
- @ref: 7953
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Alkalibacterium thalassium gene for 16S rRNA, partial sequence, strain: NBRC 103241 | AB681985 | 1478 | ena | 426701 |
| 7953 | Alkalibacterium thalassium gene for 16S rRNA, partial sequence, strain: T117-1-2 | AB294165 | 1487 | ena | 426701 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Alkalibacterium thalassium DSM 19181 | GCA_900101165 | scaffold | ncbi | 426701 |
| 66792 | Alkalibacterium thalassium strain DSM 19181 | 426701.4 | wgs | patric | 426701 |
| 66792 | Alkalibacterium thalassium DSM 19181 | 2619619006 | draft | img | 426701 |
GC content
- @ref: 7953
- GC-content: 41.7
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 83 | no |
| flagellated | no | 96.464 | no |
| gram-positive | yes | 93.627 | yes |
| anaerobic | no | 95.101 | yes |
| aerobic | no | 84.563 | no |
| halophile | yes | 92.722 | no |
| spore-forming | no | 92.157 | no |
| glucose-ferment | yes | 73.028 | no |
| thermophile | no | 99.453 | yes |
| glucose-util | yes | 91.273 | yes |
| motile | no | 93.053 | yes |
External links
@ref: 7953
culture collection no.: DSM 19181, NBRC 103241, NRIC 0718
straininfo link
- @ref: 71803
- straininfo: 407577
literature
- topic: Phylogeny
- Pubmed-ID: 19406822
- title: Alkalibacterium thalassium sp. nov., Alkalibacterium pelagium sp. nov., Alkalibacterium putridalgicola sp. nov. and Alkalibacterium kapii sp. nov., slightly halophilic and alkaliphilic marine lactic acid bacteria isolated from marine organisms and salted foods collected in Japan and Thailand.
- authors: Ishikawa M, Tanasupawat S, Nakajima K, Kanamori H, Ishizaki S, Kodama K, Okamoto-Kainuma A, Koizumi Y, Yamamoto Y, Yamasato K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65602-0
- year: 2009
- mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/isolation & purification, Eukaryota/microbiology, Fatty Acids/analysis, Fermentation, Fishes/*microbiology, Gram-Positive Asporogenous Rods/*classification/genetics/isolation & purification/*physiology, Hydrogen-Ion Concentration, Japan, Lactic Acid/*metabolism, *Marine Biology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species Specificity, Thailand
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 7953 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19181) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19181 | ||||
| 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 | ||
| 32511 | 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 | 28731 | ||
| 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) | ||||
| 71803 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407577.1 | StrainInfo: A central database for resolving microbial strain identifiers |