Strain identifier
BacDive ID: 23742
Type strain: 
Species: Amphibacillus marinus
Strain Designation: J1
Strain history: L. Zhang J1.
NCBI tax ID(s): 872970 (species)
version 8.1 (current version)
General
@ref: 20924
BacDive-ID: 23742
DSM-Number: 27991
keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Amphibacillus marinus J1 is a facultative aerobe, spore-forming, mesophilic bacterium that was isolated from deep sea mud.
NCBI tax id
- NCBI tax id: 872970
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20924 | <- JCM RIKEN BioResource Center, Tsukuba, Japan <- L. Zhang, Chinese Acad. Sci. (CAS), Beijing; J1 |
| 67770 | L. Zhang J1. |
doi: 10.13145/bacdive23742.20230509.8.1
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 marinus
- full scientific name: Amphibacillus marinus Ren et al. 2013
@ref: 20924
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Amphibacillus
species: Amphibacillus marinus
full scientific name: Amphibacillus marinus Ren et al. 2013
strain designation: J1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30846 | positive | 2.5 µm | 0.35 µm | rod-shaped | yes | |
| 69480 | yes | 96.506 | ||||
| 69480 | positive | 100 |
pigmentation
- @ref: 30846
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 20924 | TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) | yes | https://mediadive.dsmz.de/medium/545 | Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water |
| 20924 | 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20924 | positive | growth | 30 | mesophilic |
| 30846 | positive | growth | 07-55 | |
| 30846 | positive | optimum | 28 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30846 | positive | growth | 7.5-10 | alkaliphile |
| 30846 | positive | optimum | 9 |
Physiology and metabolism
oxygen tolerance
- @ref: 30846
- oxygen tolerance: facultative aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30846 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 99.629 |
halophily
- @ref: 30846
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-12 %
observation
- @ref: 30846
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30846 | 22599 | arabinose | + | carbon source |
| 30846 | 17057 | cellobiose | + | carbon source |
| 30846 | 28757 | fructose | + | carbon source |
| 30846 | 28260 | galactose | + | carbon source |
| 30846 | 17754 | glycerol | + | carbon source |
| 30846 | 17716 | lactose | + | carbon source |
| 30846 | 17306 | maltose | + | carbon source |
| 30846 | 29864 | mannitol | + | carbon source |
| 30846 | 26546 | rhamnose | + | carbon source |
| 30846 | 30911 | sorbitol | + | carbon source |
| 30846 | 27082 | trehalose | + | carbon source |
| 30846 | 18222 | xylose | + | carbon source |
enzymes
- @ref: 30846
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | continent |
|---|---|---|---|
| 20924 | deep sea mud | South China Sea | Asia |
| 67770 | Deep sea mud from South China Sea |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Mud (Sludge) |
taxonmaps
- @ref: 69479
- File name: preview.99_54166.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_230;97_30252;98_38710;99_54166&stattab=map
- Last taxonomy: Amphibacillus marinus subclade
- 16S sequence: GU213062
- Sequence Identity:
- Total samples: 88
- soil counts: 41
- aquatic counts: 11
- animal counts: 17
- plant counts: 19
Safety information
risk assessment
- @ref: 20924
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20924
- description: Amphibacillus marinus strain J1 16S ribosomal RNA gene, partial sequence
- accession: GU213062
- length: 1490
- database: ena
- NCBI tax ID: 872970
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Amphibacillus marinus strain CGMCC 1.10434 | 872970.3 | wgs | patric | 872970 |
| 66792 | Amphibacillus marinus CGMCC 1.10434 | 2617270769 | draft | img | 872970 |
| 67770 | Amphibacillus marinus CGMCC 1.10434 | GCA_900110345 | scaffold | ncbi | 872970 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20924 | 36.7 | thermal denaturation, midpoint method (Tm) |
| 30846 | 36.7 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 91.048 | yes |
| flagellated | yes | 61.284 | no |
| gram-positive | yes | 89.422 | yes |
| anaerobic | no | 94.289 | yes |
| halophile | yes | 79.925 | no |
| spore-forming | yes | 93.351 | yes |
| thermophile | no | 95.258 | yes |
| glucose-util | yes | 89.578 | no |
| aerobic | no | 92.347 | yes |
| glucose-ferment | no | 62.256 | no |
External links
@ref: 20924
culture collection no.: DSM 27991, CGMCC 1.10434, JCM 17099
straininfo link
- @ref: 87779
- straininfo: 406293
literature
- topic: Phylogeny
- Pubmed-ID: 22863987
- title: Amphibacillus marinus sp. nov., a member of the genus Amphibacillus isolated from marine mud.
- authors: Ren B, Yang N, Wang J, Ma XL, Wang Q, Xie F, Guo H, Liu ZH, Pugin B, Zhang LX
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.045807-0
- year: 2012
- mesh: Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, *Water Microbiology
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 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 | ||||
| 20924 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27991 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27991) | ||||
| 30846 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27176 | 28776041 | ||
| 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 | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | ||||
| 87779 | 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-ID406293.1 |