Strain identifier
BacDive ID: 1259
Type strain:
Species: Shouchella oshimensis
Strain Designation: K11
Strain history: CIP <- 2005, JCM <- I. Yumoto, Sapporo, Japan: strain K11
NCBI tax ID(s): 290588 (species)
General
@ref: 7798
BacDive-ID: 1259
DSM-Number: 18940
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Shouchella oshimensis K11 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 290588
- Matching level: species
strain history
@ref | history |
---|---|
7798 | <- CIP <- JCM <- I. Yomoto, strain K11 |
67770 | I. Yumoto K11. |
121457 | CIP <- 2005, JCM <- I. Yumoto, Sapporo, Japan: strain K11 |
doi: 10.13145/bacdive1259.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Shouchella
- species: Shouchella oshimensis
- full scientific name: Shouchella oshimensis (Yumoto et al. 2005) Joshi et al. 2022
synonyms
@ref synonym 20215 Shouchella plakortidis 20215 Shouchella lehensis 20215 Alkalihalobacillus lehensis 20215 Alkalihalobacillus oshimensis 20215 Alkalicoccobacillus plakortidis 20215 Bacillus lehensis 20215 Bacillus plakortidis 20215 Alkalihalobacillus plakortidis 20215 Bacillus oshimensis
@ref: 7798
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Caryophanales
family: Bacillaceae
genus: Shouchella
species: Shouchella oshimensis
full scientific name: Shouchella oshimensis (Yumoto et al. 2005) Joshi et al. 2022
strain designation: K11
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31410 | positive | 2.75 µm | 0.8 µm | rod-shaped | no | |
69480 | yes | 93.283 | ||||
69480 | positive | 100 | ||||
121457 | positive | rod-shaped | yes |
colony morphology
- @ref: 121457
- hemolysis ability: 1
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7798 | HORIKOSHI ALKALINE (DSMZ Medium 940) | yes | https://mediadive.dsmz.de/medium/940 | Name: HORIKOSHI ALKALINE (DSMZ Medium 940) Composition: Agar 15.0 g/l D-Glucose 10.0 g/l Na2CO3 5.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water |
37639 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
121457 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
121457 | CIP Medium 648 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=648 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7798 | positive | growth | 30 | mesophilic |
31410 | positive | growth | 13-41 | |
31410 | positive | optimum | 30 | mesophilic |
37639 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 27 | mesophilic |
121457 | positive | growth | 30-37 | mesophilic |
121457 | no | growth | 55 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31410 | positive | growth | 07-10 | alkaliphile |
31410 | positive | optimum | 8.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31410 | aerobe |
121457 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31410 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
121457 | yes |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31410 | NaCl | positive | growth | 0-20 % |
31410 | NaCl | positive | optimum | 7 % |
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31410 | 5291 | gelatin | + | carbon source |
31410 | 17754 | glycerol | + | carbon source |
31410 | 17306 | maltose | + | carbon source |
31410 | 29864 | mannitol | + | carbon source |
31410 | 37684 | mannose | + | carbon source |
31410 | 28053 | melibiose | + | carbon source |
31410 | 16634 | raffinose | + | carbon source |
31410 | 33942 | ribose | + | carbon source |
31410 | 27082 | trehalose | + | carbon source |
31410 | 53424 | tween 20 | + | carbon source |
31410 | 53423 | tween 40 | + | carbon source |
31410 | 53425 | tween 60 | + | carbon source |
31410 | 53426 | tween 80 | + | carbon source |
31410 | 17151 | xylitol | + | carbon source |
31410 | 18222 | xylose | + | carbon source |
121457 | 17632 | nitrate | - | reduction |
121457 | 16301 | nitrite | - | reduction |
121457 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 121457
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31410 | catalase | + | 1.11.1.6 |
31410 | cytochrome oxidase | + | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
121457 | oxidase | + | |
121457 | alcohol dehydrogenase | - | 1.1.1.1 |
121457 | catalase | + | 1.11.1.6 |
121457 | lysine decarboxylase | - | 4.1.1.18 |
121457 | ornithine decarboxylase | - | 4.1.1.17 |
121457 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121457 | - | - | + | + | - | + | - | - | - | + | + | + | + | - | - | + | + | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7798 | soil | Hokkaido | Japan | JPN | Asia |
67770 | Soil | Hokkaido | Japan | JPN | Asia |
121457 | Environment, Soil | Hokkaido | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_4309.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1100;97_1288;98_3243;99_4309&stattab=map
- Last taxonomy: Alkalihalobacillus
- 16S sequence: AB188090
- Sequence Identity:
- Total samples: 5494
- soil counts: 2128
- aquatic counts: 620
- animal counts: 2142
- plant counts: 604
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7798 | 1 | Risk group (German classification) |
121457 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7798
- description: Bacillus oshimensis gene for 16S rRNA, partial sequence, strain:K11
- accession: AB188090
- length: 1467
- database: ena
- NCBI tax ID: 290588
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacillus oshimensis strain DSM 18940 | 290588.4 | wgs | patric | 290588 |
67770 | Shouchella oshimensis DSM 18940 | GCA_002019765 | scaffold | ncbi | 290588 |
GC content
@ref | GC-content | method |
---|---|---|
7798 | 40.8 | |
67770 | 40.8 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 88.765 | yes |
anaerobic | no | 99.351 | yes |
halophile | yes | 93.151 | yes |
spore-forming | yes | 94.562 | no |
glucose-util | yes | 90.332 | no |
motile | yes | 88.006 | no |
flagellated | yes | 65.435 | yes |
aerobic | yes | 91.808 | yes |
thermophile | no | 99.204 | yes |
glucose-ferment | no | 88.88 | no |
External links
@ref: 7798
culture collection no.: DSM 18940, CIP 108751, JCM 12663, NCIMB 14023
straininfo link
- @ref: 70915
- straininfo: 137998
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15774684 | Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile. | Yumoto I, Hirota K, Goto T, Nodasaka Y, Nakajima K | Int J Syst Evol Microbiol | 10.1099/ijs.0.63488-0 | 2005 | Bacillus/chemistry/*classification/genetics/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil Microbiology | Genetics |
Phylogeny | 17267957 | Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil. | Ghosh A, Bhardwaj M, Satyanarayana T, Khurana M, Mayilraj S, Jain RK | Int J Syst Evol Microbiol | 10.1099/ijs.0.64617-0 | 2007 | Alkalies/*pharmacology, Anti-Bacterial Agents/*pharmacology, Bacillus/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Drug Resistance, Bacterial, Genes, rRNA/genetics, Hydrogen-Ion Concentration, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology | Genetics |
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 | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7798 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18940) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18940 | |||
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 | |||
31410 | 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 | 27719 | 28776041 | |
37639 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6414 | ||||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
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 | |||
70915 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID137998.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121457 | Curators of the CIP | Collection of Institut Pasteur (CIP 108751) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108751 |