Strain identifier
BacDive ID: 139432
Type strain: 
Species: Bacillus gaemokensis
Strain Designation: BL3-6
Strain history: CIP <- 2016, JCM <- 2008, Y.H. Chang, KRIBB, Daejon, Korea: strain BL3-6
NCBI tax ID(s): 574375 (species)
version 9.1 (current version)
General
@ref: 41617
BacDive-ID: 139432
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, motile, rod-shaped
description: Bacillus gaemokensis BL3-6 is an aerobe, spore-forming, motile bacterium of the family Bacillaceae.
NCBI tax id
- NCBI tax id: 574375
- Matching level: species
strain history
| @ref | history |
|---|---|
| 67770 | Y.-H. Chang BL3-6. |
| 67771 | <- YH Chang, KRIBB |
| 41617 | CIP <- 2016, JCM <- 2008, Y.H. Chang, KRIBB, Daejon, Korea: strain BL3-6 |
doi: 10.13145/bacdive139432.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Bacillus
- species: Bacillus gaemokensis
- full scientific name: Bacillus gaemokensis Jung et al. 2021
@ref: 41617
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Caryophanales
family: Bacillaceae
genus: Bacillus
species: Bacillus gaemokensis
strain designation: BL3-6
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | flagellum arrangement | gram stain |
|---|---|---|---|---|
| 67771 | rod-shaped | yes | peritrichous | |
| 67771 | positive | |||
| 41617 | rod-shaped | no | positive |
Culture and growth conditions
culture medium
| @ref | name | growth | composition | link |
|---|---|---|---|---|
| 41617 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
| 41617 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 41617 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
| 67771 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | type of spore | spore formation | confidence |
|---|---|---|---|
| 67771 | endospore | yes | |
| 69481 | yes | 100 |
observation
| @ref | observation |
|---|---|
| 67770 | quinones: MK-7 |
| 67771 | quinones: MK-7 |
Isolation, sampling and environmental information
isolation
| @ref | geographic location | country | origin.country | continent | sample type |
|---|---|---|---|---|---|
| 41617 | Yellow Sea | Republic of Korea | KOR | Asia | |
| 67770 | Gaemock Harbor in the Yellow Sea coastal region of Tae-An | Republic of Korea | KOR | Asia | Oil-contaminated tidal flat sediment |
| 67771 | Taeahn | Republic of Korea | KOR | Asia | From tidal flat sediment |
| 41617 | Gaemock Harbor, Yellow Sea, coastal region of Tae-An | Republic of Korea | KOR | Asia | Environment, Oil contaminated tidal flat sediment |
Safety information
risk assessment
- @ref: 41617
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
- @ref: 67771
- description: Bacillus gaemokensis strain BL3-6 16S ribosomal RNA gene, partial sequence
- accession: FJ416489
- length: 1351
- database: nuccore
- NCBI tax ID: 574375
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bacillus gaemokensis strain JCM 15801 | 574375.6 | wgs | patric | 574375 |
| 66792 | Bacillus gaemokensis strain KCTC 13318 | 574375.8 | wgs | patric | 574375 |
| 66792 | Bacillus gaemokensis KCTC 13318 | 2724679201 | draft | img | 574375 |
| 66792 | Bacillus gaemokensis JCM 15801 | 2585428004 | draft | img | 574375 |
| 67770 | Bacillus gaemokensis JCM 15801 | GCA_000712615 | contig | ncbi | 574375 |
| 67771 | Bacillus gaemokensis KCTC 13318 | GCA_001590835 | scaffold | ncbi | 574375 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 67770 | 39.4 | thermal denaturation, midpoint method (Tm) |
| 67771 | 39.4 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 74.203 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.007 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 87.538 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 63.469 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 93.214 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 64.015 | yes |
External links
@ref: 41617
culture collection no.: CIP 111018, JCM 15801, KCTC 13318
straininfo link
- @ref: 95934
- straininfo: 413055
literature
- topic: Phylogeny
- Pubmed-ID: 21221948
- title: Bacillus gaemokensis sp. nov., isolated from foreshore tidal flat sediment from the Yellow Sea.
- authors: Jung MY, Paek WK, Park IS, Han JR, Sin Y, Paek J, Rhee MS, Kim H, Song HS, Chang YH
- journal: J Microbiol
- DOI: 10.1007/s12275-010-0148-0
- year: 2011
- mesh: Bacillus/chemistry/*classification/genetics/*isolation & purification, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Galactose/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology
- topic2: Genetics
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 | |
| 41617 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111018 | Collection of Institut Pasteur (CIP 111018) | |
| 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/ | ||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 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 | |
| 95934 | 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-ID413055.1 |