Strain identifier
BacDive ID: 5254
Type strain: 
Species: Tetragenococcus halophilus subsp. halophilus
Strain history: IAM 1693 <-- K. Sakaguchi d-6 ("Pediococcus soyae").
NCBI tax ID(s): 1513897 (subspecies)
version 8.1 (current version)
General
@ref: 8729
BacDive-ID: 5254
DSM-Number: 20338
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Tetragenococcus halophilus subsp. halophilus DSM 20338 is a spore-forming, mesophilic bacterium that was isolated from Soy sauce brewing mashes.
NCBI tax id
- NCBI tax id: 1513897
- Matching level: subspecies
strain history
| @ref | history |
|---|---|
| 8729 | <- NCDO <- IFO <- T. Hasegawa (Pediococcus soyae) |
| 67770 | IAM 1693 <-- K. Sakaguchi d-6 ("Pediococcus soyae"). |
doi: 10.13145/bacdive5254.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Enterococcaceae
- genus: Tetragenococcus
- species: Tetragenococcus halophilus subsp. halophilus
- full scientific name: Tetragenococcus halophilus subsp. halophilus (Mees 1934) Justé et al. 2012
@ref: 8729
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Enterococcaceae
genus: Tetragenococcus
species: Tetragenococcus halophilus subsp. halophilus
full scientific name: Tetragenococcus halophilus subsp. halophilus (Mees 1934) Justé et al. 2012
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 94.266 | |
| 69480 | 99.999 | positive |
Culture and growth conditions
culture medium
- @ref: 8729
- name: PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227)
- growth: yes
- link: https://mediadive.dsmz.de/medium/227
- composition: Name: PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227) Composition: NaCl 65.0 g/l Glucose 20.0 g/l Meat extract 10.0 g/l Casein peptone 10.0 g/l Yeast extract 5.0 g/l Na-acetate 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8729 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 92 |
| 69480 | no | 99.94 |
murein
- @ref: 8729
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Soy sauce brewing mashes
taxonmaps
- @ref: 69479
- File name: preview.99_261.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_184;97_200;98_223;99_261&stattab=map
- Last taxonomy: Tetragenococcus halophilus
- 16S sequence: AB911555
- Sequence Identity:
- Total samples: 23236
- soil counts: 861
- aquatic counts: 1678
- animal counts: 20165
- plant counts: 532
Safety information
risk assessment
- @ref: 8729
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: NBRC 12172 | AB680249 | 1484 | ena | 945021 |
| 67770 | Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: JCM 20259 | AB911555 | 1522 | ena | 51669 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Tetragenococcus halophilus NBRC 12172 | GCA_000283615 | complete | ncbi | 945021 |
| 66792 | Tetragenococcus halophilus NBRC 12172 | 945021.8 | complete | patric | 945021 |
| 66792 | Tetragenococcus halophilus NBRC 12172 | 2511231116 | complete | img | 945021 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 67770 | 35.9 | |
| 67770 | 34.2 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 92 | no |
| motile | no | 94.53 | no |
| flagellated | no | 97.323 | no |
| gram-positive | yes | 91.663 | no |
| anaerobic | no | 89.366 | no |
| aerobic | no | 96.655 | no |
| halophile | yes | 92.609 | no |
| spore-forming | no | 92.484 | no |
| thermophile | no | 97.273 | yes |
| glucose-util | yes | 89.721 | no |
| glucose-ferment | yes | 87.81 | no |
External links
@ref: 8729
culture collection no.: DSM 20338, IFO 12172, NBRC 12172, NCDO 1872, NCIB 9735, JCM 20259, IAM 1693, NCIMB 9735, NISL 7117
straininfo link
- @ref: 74744
- straininfo: 1239
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8729 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20338) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20338 | |||
| 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 | |
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 74744 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1239.1 | StrainInfo: A central database for resolving microbial strain identifiers |