Strain identifier
BacDive ID: 130439
Type strain: 
Species: Garicola koreensis
Strain Designation: SJ5-4
Strain history: C. O. Jeon SJ5-4.
NCBI tax ID(s): 1262554 (species)
version 9.1 (current version)
General
@ref: 22146
BacDive-ID: 130439
DSM-Number: 28238
keywords: genome sequence, 16S sequence, Bacteria
description: Garicola koreensis SJ5-4 is a bacterium that was isolated from saeu-jeot .
NCBI tax id
- NCBI tax id: 1262554
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22146 | <- C. O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea; SJ5-4 <- S. H. Lee and C. O. Jeon |
| 67770 | C. O. Jeon SJ5-4. |
doi: 10.13145/bacdive130439.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Garicola
- species: Garicola koreensis
- full scientific name: Garicola koreensis Lo et al. 2015
@ref: 22146
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Garicola
species: Garicola koreensis
full scientific name: Garicola koreensis Lo et al. 2015
strain designation: SJ5-4
type strain: yes
Culture and growth conditions
culture medium
- @ref: 22146
- 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 |
|---|---|---|---|
| 22146 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
observation
- @ref: 67770
- observation: quinones: MK-7, MK-8, MK-9
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 22146 | saeu-jeot (Korean salted fermented shrimp) | Republic of Korea | KOR | Asia |
| 67770 | Seau-jeot, a traditional fermented seafood | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Vegetable (incl. Grains) |
| #Engineered | #Food production | #Fermented |
taxonmaps
- @ref: 69479
- File name: preview.99_171540.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_12501;97_44596;98_61626;99_171540&stattab=map
- Last taxonomy: Garicola koreensis subclade
- 16S sequence: JX152781
- Sequence Identity:
- Total samples: 160
- soil counts: 2
- aquatic counts: 7
- animal counts: 143
- plant counts: 8
Safety information
risk assessment
- @ref: 22146
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22146
- description: Garicola koreensis strain SJ5-4 16S ribosomal RNA gene, partial sequence
- accession: JX152781
- length: 1459
- database: nuccore
- NCBI tax ID: 1262554
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Garicola koreensis DSM 28238 | GCA_014195445 | contig | ncbi | 1262554 |
| 66792 | Garicola koreensis strain DSM 28238 | 1262554.3 | wgs | patric | 1262554 |
| 66792 | [Nesterenkonia] koreensis DSM 28238 | 2827611747 | draft | img | 1262554 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 22146 | 61.8 | fluorimetric |
| 67770 | 61.8 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 85.689 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 92.317 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 79.78 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 76.948 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 86.819 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 89.5 | no |
External links
@ref: 22146
culture collection no.: DSM 28238, JCm 18572, KACC 16909
straininfo link
- @ref: 88969
- straininfo: 397249
literature
- topic: Phylogeny
- Pubmed-ID: 25563923
- title: Garicola koreensis gen. nov., sp. nov., isolated from saeu-jeot, traditional Korean fermented shrimp.
- authors: Lo N, Lee SH, Jin HM, Jung JY, Schumann P, Jeon CO
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000056
- year: 2015
- mesh: Animals, Bacterial Typing Techniques, Base Composition, Crustacea/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistry
- topic2: Biotechnology
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22146 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28238 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28238) | |
| 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 | |
| 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. | 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 | |
| 88969 | 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-ID397249.1 |