Strain identifier
BacDive ID: 1408
Type strain: 
Species: Amphibacillus cookii
Strain Designation: JW/BP-GSL-QD
Strain history: <- J. Wiegel, Univ. of Georgia, Athens, USA; JW/BP-GSL-QD <- B. Pugin
NCBI tax ID(s): 767787 (species)
version 8.1 (current version)
General
@ref: 17354
BacDive-ID: 1408
DSM-Number: 23721
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, halophilic, spore-forming, mesophilic, Gram-variable, motile, rod-shaped, colony-forming
description: Amphibacillus cookii JW/BP-GSL-QD is a facultative anaerobe, halophilic, spore-forming bacterium that forms circular colonies and was isolated from sediment-water mixture with salt crust.
NCBI tax id
- NCBI tax id: 767787
- Matching level: species
strain history
- @ref: 17354
- history: <- J. Wiegel, Univ. of Georgia, Athens, USA; JW/BP-GSL-QD <- B. Pugin
doi: 10.13145/bacdive1408.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Amphibacillus
- species: Amphibacillus cookii
- full scientific name: Amphibacillus cookii Pugin et al. 2012
@ref: 17354
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Amphibacillus
species: Amphibacillus cookii
full scientific name: Amphibacillus cookii Pugin et al. 2012
strain designation: JW/BP-GSL-QD
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 23034 | variable | 2.0-7.0 µm | 0.5-0.6 µm | rod-shaped | yes | |
| 69480 | yes | 96.329 | ||||
| 69480 | positive | 100 |
colony morphology
- @ref: 23034
- colony size: 0.8-2.0 mm
- colony color: white
- colony shape: circular
- incubation period: 1 day
- medium used: 2 % (w/v) agar shake-roll tubes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 23034 | 2 %(w/v) agar shake-roll tubes | yes | ||
| 17354 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
| 17354 | AMPHIBACILLUS MEDIUM (DSMZ Medium 529) | yes | https://mediadive.dsmz.de/medium/529 | Name: AMPHIBACILLUS MEDIUM (DSMZ Medium 529) Composition: Agar 15.0 g/l Glucose 10.0 g/l Na2CO3 anhydrous 5.3 g/l NaHCO3 4.2 g/l Yeast extract 3.0 g/l NH4NO3 2.0 g/l K2HPO4 1.0 g/l Polypeptone 0.3 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.1 g/l MnSO4 x 7 H2O 0.005 g/l FeSO4 x 7 H2O 0.005 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17354 | positive | growth | 37 | mesophilic |
| 23034 | positive | growth | 14.5-47.0 | |
| 23034 | no | growth | <12.5 | psychrophilic |
| 23034 | no | growth | >49.0 | thermophilic |
| 23034 | positive | optimum | 39.0 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 23034 | positive | growth | 6.5-10.3 | alkaliphile |
| 23034 | positive | optimum | 8.0 | |
| 23034 | no | growth | <6.3 | |
| 23034 | no | growth | >10.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 17354 | facultative anaerobe |
| 23034 | facultative aerobe |
spore formation
| @ref | spore description | type of spore | spore formation | confidence |
|---|---|---|---|---|
| 23034 | terminal,circular,1.2-1.3 µm in diameter | spore | yes | |
| 69481 | yes | 100 | ||
| 69480 | yes | 100 |
halophily
- @ref: 23034
- halophily level: halophilic
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23034 | 17234 | glucose | - | fermentation |
| 23034 | tryptone | + | growth | |
| 23034 | yeast extract | + | growth |
metabolite production
- @ref: 23034
- Chebi-ID: 15688
- metabolite: acetoin
- production: no
metabolite tests
| @ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
|---|---|---|---|---|
| 23034 | 15688 | acetoin | - | |
| 23034 | 17234 | glucose | - |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 23034 | catalase | - | 1.11.1.6 |
| 23034 | cytochrome oxidase | - | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture temperature |
|---|---|---|---|---|---|---|---|---|---|---|
| 17354 | sediment-water mixture with salt crust | Utah, Antelope Island marina, Great Salt Lake, southern arm | USA | USA | North America | 40.7811 | -111.947 | |||
| 23034 | mixed water and sediment sample containing a salt crust | carbonate-buffered medium | containing (l-1): 0.2 g KH2PO4 , 0.1 g MgCl2.6H2O, 0.5 g NH4Cl, 0.2 g KCl, 100 g NaCl, 68 g Na2CO3 , 38 g NaHCO3 , 0.7 g cysteine/HCl, 5 g yeast extract, 5 g tryptone, 5 g sucrose, 1 ml trace element solution and 10 ml vitamin solution | 37 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_40876.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_230;97_252;98_281;99_40876&stattab=map
- Last taxonomy: Amphibacillus
- 16S sequence: HM057160
- Sequence Identity:
- Total samples: 23
- soil counts: 9
- aquatic counts: 3
- animal counts: 11
Safety information
risk assessment
- @ref: 17354
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17354
- description: Amphibacillus cookii strain JW/BP-GSL-QD 16S ribosomal RNA gene, partial sequence
- accession: HM057160
- length: 1394
- database: ena
- NCBI tax ID: 767787
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Amphibacillus cookii DSM 23721 | GCA_016908375 | contig | ncbi | 767787 |
| 66792 | Amphibacillus cookii strain DSM 23721 | 767787.3 | wgs | patric | 767787 |
| 66792 | Amphibacillus cookii DSM 23721 | 2901114716 | draft | img | 767787 |
GC content
- @ref: 17354
- GC-content: 35.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 86.712 | yes |
| flagellated | yes | 61.988 | no |
| gram-positive | yes | 78.992 | yes |
| anaerobic | no | 89.285 | no |
| halophile | yes | 82.484 | no |
| spore-forming | yes | 91.969 | no |
| glucose-util | yes | 91.079 | no |
| aerobic | no | 94.059 | yes |
| thermophile | no | 94.464 | no |
| glucose-ferment | no | 62.423 | yes |
External links
@ref: 17354
culture collection no.: DSM 23721, ATCC BAA 2118, NBRC 11149
straininfo link
- @ref: 71059
- straininfo: 399503
literature
- topic: Phylogeny
- Pubmed-ID: 22038999
- title: Amphibacillus cookii sp. nov., a facultatively aerobic, spore-forming, moderately halophilic, alkalithermotolerant bacterium.
- authors: Pugin B, Blamey JM, Baxter BK, Wiegel J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.034629-0
- year: 2011
- mesh: Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, *Phylogeny, Sequence Analysis, DNA, Spores, Bacterial/growth & development, Temperature, Utah
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17354 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23721) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23721 | |||
| 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 | |||
| 23034 | Benoît Pugin,Jenny M. Blamey,Bonnie K. Baxter,Juergen Wiegel | 10.1099/ijs.0.034629-0 | Amphibacillus cookii sp. nov., a facultatively aerobic, spore-forming, moderately halophilic, alkalithermotolerant bacterium | IJSEM 62: 2090-2096 2012 | 22038999 | |
| 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) | |||
| 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 | |||
| 71059 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399503.1 | StrainInfo: A central database for resolving microbial strain identifiers |