Strain identifier

BacDive ID: 1259

Type strain: Yes

Species: Shouchella oshimensis

Strain Designation: K11

Strain history: CIP <- 2005, JCM <- I. Yumoto, Sapporo, Japan: strain K11

NCBI tax ID(s): 290588 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
7798<- CIP <- JCM <- I. Yomoto, strain K11
67770I. Yumoto K11.
121457CIP <- 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

    @refsynonym
    20215Shouchella plakortidis
    20215Shouchella lehensis
    20215Alkalihalobacillus lehensis
    20215Alkalihalobacillus oshimensis
    20215Alkalicoccobacillus plakortidis
    20215Bacillus lehensis
    20215Bacillus plakortidis
    20215Alkalihalobacillus plakortidis
    20215Bacillus 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31410positive2.75 µm0.8 µmrod-shapedno
69480yes93.283
69480positive100
121457positiverod-shapedyes

colony morphology

  • @ref: 121457
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7798HORIKOSHI ALKALINE (DSMZ Medium 940)yeshttps://mediadive.dsmz.de/medium/940Name: 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
37639MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121457CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121457CIP Medium 648yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=648

culture temp

@refgrowthtypetemperaturerange
7798positivegrowth30mesophilic
31410positivegrowth13-41
31410positiveoptimum30mesophilic
37639positivegrowth30mesophilic
67770positivegrowth27mesophilic
121457positivegrowth30-37mesophilic
121457nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
31410positivegrowth07-10alkaliphile
31410positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31410aerobe
121457obligate aerobe

spore formation

@refspore formationconfidence
31410yes
69481yes100
69480yes100
121457yes

halophily

@refsaltgrowthtested relationconcentration
31410NaClpositivegrowth0-20 %
31410NaClpositiveoptimum7 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
314105291gelatin+carbon source
3141017754glycerol+carbon source
3141017306maltose+carbon source
3141029864mannitol+carbon source
3141037684mannose+carbon source
3141028053melibiose+carbon source
3141016634raffinose+carbon source
3141033942ribose+carbon source
3141027082trehalose+carbon source
3141053424tween 20+carbon source
3141053423tween 40+carbon source
3141053425tween 60+carbon source
3141053426tween 80+carbon source
3141017151xylitol+carbon source
3141018222xylose+carbon source
12145717632nitrate-reduction
12145716301nitrite-reduction
12145717632nitrate-respiration

metabolite production

  • @ref: 121457
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31410catalase+1.11.1.6
31410cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
121457oxidase+
121457alcohol dehydrogenase-1.1.1.1
121457catalase+1.11.1.6
121457lysine decarboxylase-4.1.1.18
121457ornithine decarboxylase-4.1.1.17
121457urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121457--++-+---++++--+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7798soilHokkaidoJapanJPNAsia
67770SoilHokkaidoJapanJPNAsia
121457Environment, SoilHokkaidoJapanJPNAsia

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

@refbiosafety levelbiosafety level comment
77981Risk group (German classification)
1214571Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus oshimensis strain DSM 18940290588.4wgspatric290588
67770Shouchella oshimensis DSM 18940GCA_002019765scaffoldncbi290588

GC content

@refGC-contentmethod
779840.8
6777040.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes88.765yes
anaerobicno99.351yes
halophileyes93.151yes
spore-formingyes94.562no
glucose-utilyes90.332no
motileyes88.006no
flagellatedyes65.435yes
aerobicyes91.808yes
thermophileno99.204yes
glucose-fermentno88.88no

External links

@ref: 7798

culture collection no.: DSM 18940, CIP 108751, JCM 12663, NCIMB 14023

straininfo link

  • @ref: 70915
  • straininfo: 137998

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774684Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile.Yumoto I, Hirota K, Goto T, Nodasaka Y, Nakajima KInt J Syst Evol Microbiol10.1099/ijs.0.63488-02005Bacillus/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 MicrobiologyGenetics
Phylogeny17267957Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil.Ghosh A, Bhardwaj M, Satyanarayana T, Khurana M, Mayilraj S, Jain RKInt J Syst Evol Microbiol10.1099/ijs.0.64617-02007Alkalies/*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 MicrobiologyGenetics
Phylogeny31312953Genome-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 WJAntonie Van Leeuwenhoek10.1007/s10482-019-01299-z2019Bacillus/*classification/*genetics, Bacterial Proteins/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Genome, Bacterial, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7798Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18940)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18940
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31410Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2771928776041
37639Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6414
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70915Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137998.1StrainInfo: A central database for resolving microbial strain identifiers
121457Curators of the CIPCollection of Institut Pasteur (CIP 108751)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108751