Strain identifier
BacDive ID: 1314
Type strain: 
Species: Shouchella clausii
Strain Designation: SC-N012
Strain history: <- M. Madhaiyan, Tamil Nadu Agric. Univ., Coimbatore, India; SC-N012
NCBI tax ID(s): 866786 (species)
version 9.3 (current version)
General
@ref: 16030
BacDive-ID: 1314
DSM-Number: 21911
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Shouchella clausii SC-N012 is a spore-forming, mesophilic bacterium that was isolated from soil from the rhizosphere of sugar cane Saccharum officinarum L..
NCBI tax id
- NCBI tax id: 866786
- Matching level: species
strain history
- @ref: 16030
- history: <- M. Madhaiyan, Tamil Nadu Agric. Univ., Coimbatore, India; SC-N012
doi: 10.13145/bacdive1314.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Shouchella
- species: Shouchella clausii
- full scientific name: Shouchella clausii (Nielsen et al. 1995) Joshi et al. 2022
synonyms
@ref synonym 20215 Bacillus clausii 20215 Alkalihalobacillus rhizosphaerae 20215 Bacillus rhizosphaerae 20215 Shouchella rhizosphaerae 20215 Alkalihalobacillus clausii
@ref: 16030
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Caryophanales
family: Bacillaceae
genus: Shouchella
species: Shouchella clausii
full scientific name: Shouchella clausii (Nielsen et al. 2015) Joshi et al. 2022
strain designation: SC-N012
type strain: no
Culture and growth conditions
culture medium
- @ref: 16030
- name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
- growth: yes
- link: https://mediadive.dsmz.de/medium/220
- composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water
culture temp
- @ref: 16030
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: microaerophile
- confidence: 94.1
spore formation
- @ref: 125438
- spore formation: yes
- confidence: 93.736
Isolation, sampling and environmental information
isolation
- @ref: 16030
- sample type: soil from the rhizosphere of sugar cane Saccharum officinarum L.
- host species: Saccharum officinarum
- geographic location: Coimbatore
- country: India
- origin.country: IND
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Rhizosphere |
taxonmaps
- @ref: 69479
- File name: preview.99_822.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_499;97_571;98_656;99_822&stattab=map
- Last taxonomy: Alkalihalobacillus clausii
- 16S sequence: FJ233848
- Sequence Identity:
- Total samples: 16321
- soil counts: 6394
- aquatic counts: 1580
- animal counts: 5862
- plant counts: 2485
Safety information
risk assessment
- @ref: 16030
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16030
- description: Bacillus rhizosphaerae strain SC-N012 16S ribosomal RNA gene, partial sequence
- accession: FJ233848
- length: 1433
- database: nuccore
- NCBI tax ID: 866786
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Shouchella rhizosphaerae SC-N012,DSM 21911,NCCB 100267 | GCA_900142675 | scaffold | ncbi | 866786 |
| 66792 | Bacillus rhizosphaerae strain SC-N012,DSM 21911,NCCB 100267 | 866786.3 | wgs | patric | 866786 |
GC content
- @ref: 16030
- GC-content: 43.0
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 79.937 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.04 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 79.387 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 93.736 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 89.769 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 81.218 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 54.4 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 58.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 78.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | microaerophile | 94.1 |
External links
@ref: 16030
culture collection no.: DSM 21911, NCCB 100267
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21671194 | Bacillus rhizosphaerae sp. nov., an novel diazotrophic bacterium isolated from sugarcane rhizosphere soil. | Madhaiyan M, Poonguzhali S, Lee JS, Lee KC, Hari K | Antonie Van Leeuwenhoek | 10.1007/s10482-011-9600-3 | 2011 | Bacillus/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, *Nitrogen Fixation, Phylogeny, *Rhizosphere, Saccharum/growth & development/*microbiology, *Soil Microbiology | Metabolism |
| Phylogeny | 31312953 | Genome-based reclassification of Bacillus plakortidis Borchert et al. 2007 and Bacillus lehensis Ghosh et al. 2007 as a later heterotypic synonym of Bacillus oshimensis Yumoto et al. 2005; Bacillus rhizosphaerae Madhaiyan et al. 2011 as a later heterotypic synonym of Bacillus clausii Nielsen et al. 1995. | Liu GH, Narsing Rao MP, Dong ZY, Wang JP, Che JM, Chen QQ, Sengonca C, Liu B, Li WJ | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01299-z | 2019 | Bacillus/*classification/*genetics, Bacterial Proteins/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Genome, Bacterial, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 16030 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21911) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21911 | |
| 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 | |
| 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 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |