Strain identifier
BacDive ID: 1257
Type strain: 
Species: Margalitia shackletonii
Strain Designation: B1724
Strain history: 2002, N.A. Logan, Glasgow, UK: strain B1724
NCBI tax ID(s): 157838 (species)
version 7.1 (current version)
General
@ref: 7755
BacDive-ID: 1257
DSM-Number: 18868
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-variable, motile, rod-shaped
description: Margalitia shackletonii B1724 is an aerobe, spore-forming, mesophilic bacterium that was isolated from volcanic soil.
NCBI tax id
- NCBI tax id: 157838
- Matching level: species
strain history
doi: 10.13145/bacdive1257.20221219.7.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Margalitia
- species: Margalitia shackletonii
- full scientific name: Margalitia shackletonii (Logan et al. 2004) Gupta et al. 2020
synonyms
- @ref: 20215
- synonym: Bacillus shackletonii
@ref: 7755
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Margalitia
species: Margalitia shackletonii
full scientific name: Margalitia shackletonii (Logan et al. 2004) Gupta et al. 2020
strain designation: B1724
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29918 | variable | 3.5 µm | 0.8 µm | rod-shaped | yes | |
| 69480 | yes | 80.68 | ||||
| 69480 | positive | 91.543 |
pigmentation
- @ref: 29918
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 7755 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
| 38229 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7755 | positive | growth | 30 | mesophilic |
| 29918 | positive | growth | 15-55 | |
| 29918 | positive | optimum | 37 | mesophilic |
| 38229 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29918 | positive | growth | 4.5-9.0 | alkaliphile |
| 29918 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29918
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29918 | yes | |
| 69480 | yes | 98.222 |
halophily
- @ref: 69480
- halophily level: non-halophilic
- confidence: 93.328
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29918 | 28260 | galactose | + | carbon source |
| 29918 | 17716 | lactose | + | carbon source |
| 29918 | 37684 | mannose | + | carbon source |
| 29918 | 33942 | ribose | + | carbon source |
| 29918 | 27082 | trehalose | + | carbon source |
| 29918 | 4853 | esculin | + | hydrolysis |
enzymes
- @ref: 29918
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 7755
- sample type: volcanic soil
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Environmental | #Terrestrial | #Volcanic |
| #Environmental | #Terrestrial | #Geologic |
taxonmaps
- @ref: 69479
- File name: preview.99_3213.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1672;97_2002;98_2462;99_3213&stattab=map
- Last taxonomy: Bacillus
- 16S sequence: AJ250318
- Sequence Identity:
- Total samples: 378
- soil counts: 166
- aquatic counts: 54
- animal counts: 127
- plant counts: 31
Safety information
risk assessment
- @ref: 7755
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7755
- description: Bacterium LMG 18435 16S rRNA gene, strain LMG 18435
- accession: AJ250318
- length: 1503
- database: ena
- NCBI tax ID: 157838
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Margalitia shackletonii LMG 18435 | GCA_001420715 | scaffold | ncbi | 157838 |
| 66792 | Margalitia shackletonii LMG 18435 | GCA_011008805 | contig | ncbi | 157838 |
| 66792 | Bacillus shackletonii strain LMG 18435 | 157838.3 | wgs | patric | 157838 |
| 66792 | Bacillus shackletonii strain LMG 18435 | 157838.12 | wgs | patric | 157838 |
| 66792 | Maritimibacter sp. HL-12 HL-12 | GCA_900177545 | scaffold | patric | 1162418 |
GC content
- @ref: 7755
- GC-content: 35.4
External links
@ref: 7755
culture collection no.: DSM 18868, CIP 107762, KCTC 13003, LMG 18435
straininfo link
| @ref | passport |
|---|---|
| 20218 | http://www.straininfo.net/strains/692107 |
| 20218 | http://www.straininfo.net/strains/377586 |
| 20218 | http://www.straininfo.net/strains/840260 |
| 20218 | http://www.straininfo.net/strains/45745 |
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15023945 | Bacillus shackletonii sp. nov., from volcanic soil on Candlemas Island, South Sandwich archipelago. | Logan NA, Lebbe L, Verhelst A, Goris J, Forsyth G, Rodriguez-Diaz M, Heyndrickx M, De Vos P | Int J Syst Evol Microbiol | 10.1099/ijs.0.02661-0 | 2004 | Antarctic Regions, Bacillus/*classification/genetics/growth & development/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Restriction Mapping, *Soil Microbiology, Volcanic Eruptions | Genetics |
| Phylogeny | 25603996 | Bacillus dabaoshanensis sp. nov., a Cr(VI)-tolerant bacterium isolated from heavy-metal-contaminated soil. | Cui X, Wang Y, Liu J, Chang M, Zhao Y, Zhou S, Zhuang L | Arch Microbiol | 10.1007/s00203-015-1082-7 | 2015 | Bacillus/*genetics/*growth & development/isolation & purification, Bacterial Typing Techniques, Base Composition/genetics, Cardiolipins/analysis, Chromium/*metabolism, DNA, Bacterial/genetics, Drug Resistance, Bacterial, Fatty Acids/analysis, Metals, Heavy, Microbial Sensitivity Tests, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/*chemistry, *Soil Microbiology, Soil Pollutants/chemistry/metabolism | Metabolism |
| Phylogeny | 26559004 | Bacillus ectoiniformans sp. nov., a halotolerant bacterium isolated from deep-sea sediments. | Zhu D, Zhang P, Niu L, Xie C, Li P, Sun J, Hang F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000763 | 2015 | ||
| Genetics | 26847895 | Draft Genome Sequence of Bacillus shackletonii LMG 18435T, Isolated from Volcanic Mossy Soil. | Wang JP, Liu B, Liu GH, Ge CB, Xiao RF, Zheng XF, Shi H | Genome Announc | 10.1128/genomeA.01689-15 | 2016 | Phylogeny | |
| Metabolism | 27084709 | Bacillus mesophilus sp. nov., an alginate-degrading bacterium isolated from a soil sample collected from an abandoned marine solar saltern. | Zhou YX, Liu GH, Liu B, Chen GJ, Du ZJ | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0692-7 | 2016 | Alginates/*metabolism, Bacillus/genetics/*isolation & purification/*metabolism, Cell Wall/metabolism, China, Fatty Acids/metabolism, Genotype, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Nucleic Acid Hybridization, Peptidoglycan/metabolism, Phenotype, Phosphatidylethanolamines/metabolism, Phylogeny, Sequence Analysis, DNA, Sodium Chloride, Soil/chemistry, *Soil Microbiology, Vitamin K 2/metabolism | Phylogeny |
| Phylogeny | 32375947 | Bacillus aquiflavi sp. nov., isolated from yellow water of strongly flavored Chinese baijiu. | Xie J, Cheng K, Zhao D, Yang G, Qiao Z, Qiu S, Yu X, Liu H, Li T, Feng H, Yao S, Zhai L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004185 | 2020 | Alcoholic Beverages/*microbiology, Bacillus/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 7755 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18868) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18868 | ||||
| 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 | ||
| 26289 | 10.1099/ijs.0.02661-0 | 15023945 | |||||
| 29918 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 26289 | ||
| 38229 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5233 | |||||
| 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 | ||
| 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) |