Strain identifier

BacDive ID: 1127

Type strain: Yes

Species: Shouchella clausii

Strain Designation: PN 23, C 360

Strain history: CIP <- 1996, DSM <- NCIMB <- Novo Industri.: strain C 360 = PN 23

NCBI tax ID(s): 79880 (species)

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General

@ref: 3246

BacDive-ID: 1127

DSM-Number: 8716

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, motile

description: Shouchella clausii PN 23 is an aerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 79880
  • Matching level: species

strain history

@refhistory
3246<- NCIMB <- Novo Industri; C 360
118307CIP <- 1996, DSM <- NCIMB <- Novo Industri.: strain C 360 = PN 23

doi: 10.13145/bacdive1127.20230509.8.1

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 clausii
  • full scientific name: Shouchella clausii (Nielsen et al. 1995) Joshi et al. 2022

  • synonyms

    @refsynonym
    20215Alkalihalobacillus clausii
    20215Bacillus clausii
    20215Shouchella rhizosphaerae
    20215Alkalihalobacillus rhizosphaerae
    20215Bacillus rhizosphaerae

@ref: 3246

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: PN 23, C 360

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.366
69480100positive
118307yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3246ALKALINE NUTRIENT AGAR (DSMZ Medium 31)yeshttps://mediadive.dsmz.de/medium/31Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31; with strain-specific modifications) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaCl 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water
35723MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118307CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3246positivegrowth30mesophilic
35723positivegrowth30mesophilic
57609positivegrowth30-37mesophilic
118307positivegrowth10-45
118307nogrowth55thermophilic

culture pH

  • @ref: 118307
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57609aerobe
118307obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.718
118307yes

halophily

@refsaltgrowthtested relationconcentration
118307NaClpositivegrowth0-8 %
118307NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118307citrate-carbon source16947
118307nitrate+reduction17632
118307nitrite-reduction16301
118307nitrate-respiration17632

metabolite production

  • @ref: 118307
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 118307
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
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
118307oxidase+
118307alcohol dehydrogenase-1.1.1.1
118307gelatinase+
118307amylase-
118307DNase+
118307caseinase+3.4.21.50
118307catalase+1.11.1.6
118307lecithinase-
118307lysine decarboxylase-4.1.1.18
118307ornithine decarboxylase-4.1.1.17
118307urease-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
118307-+++------++-+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118307------------------------+-----------+/----------+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3246garden soilSlagelseDenmarkDNKEurope
57609Garden soil
118307Environment, Garden soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32461Risk group (German classification)
1183071Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Bacillus clausii DSM 8716, 16S rRNA gene
  • accession: X76440
  • length: 1505
  • database: ena
  • NCBI tax ID: 79880

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shouchella clausii DSM 8716GCA_002250115completencbi79880
66792Bacillus clausii strain DSM 871679880.14completepatric79880
66792Bacillus clausii DSM 87162811995369completeimg79880

GC content

  • @ref: 3246
  • GC-content: 42.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes69.434no
gram-positiveyes90.766no
anaerobicno99.297yes
aerobicyes92.416yes
halophileyes87.186no
spore-formingyes93.22no
glucose-utilyes87.692no
thermophileno97.801yes
motileyes90.401no
glucose-fermentno87.356no

External links

@ref: 3246

culture collection no.: DSM 8716, ATCC 700160, CIP 104718, NCIB 10309, CCUG 47262, NCIMB 10309, LMG 17945

straininfo link

  • @ref: 70798
  • straininfo: 14017

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics12654668Chromosomal aadD2 encodes an aminoglycoside nucleotidyltransferase in Bacillus clausii.Bozdogan B, Galopin S, Gerbaud G, Courvalin P, Leclercq RAntimicrob Agents Chemother10.1128/AAC.47.4.1343-1346.20032003Amino Acid Sequence, Bacillus/*drug effects/enzymology/genetics, Base Sequence, *Chromosomes, Bacterial, Drug Resistance, Bacterial, Molecular Sequence Data, Nucleotidyltransferases/*genetics, Promoter Regions, GeneticEnzymology
Pathogenicity14711653Characterization of a new erm-related macrolide resistance gene present in probiotic strains of Bacillus clausii.Bozdogan B, Galopin S, Leclercq RAppl Environ Microbiol10.1128/AEM.70.1.280-284.20042004Amino Acid Sequence, Bacillus/*drug effects/genetics, Bacillus subtilis/genetics, Base Sequence, Cloning, Molecular, Conjugation, Genetic, Drug Resistance, Bacterial/*genetics, Enterococcus/genetics, Humans, Macrolides/*pharmacology, Methyltransferases/*genetics, Microbial Sensitivity Tests, Molecular Sequence Data, *ProbioticsEnzymology
Biotechnology17105550Tolerance to challenges miming gastrointestinal transit by spores and vegetative cells of Bacillus clausii.Cenci G, Trotta F, Caldini GJ Appl Microbiol10.1111/j.1365-2672.2006.03042.x2006Animals, Bacillus/*physiology, Bile Acids and Salts/pharmacology, *Food Microbiology, Gastrointestinal Tract/*microbiology, Gastrointestinal Transit, Humans, Hydrogen-Ion Concentration, Microbiological Techniques, *Probiotics, Spores, Bacterial/physiologyPathogenicity
Phylogeny21671194Bacillus rhizosphaerae sp. nov., an novel diazotrophic bacterium isolated from sugarcane rhizosphere soil.Madhaiyan M, Poonguzhali S, Lee JS, Lee KC, Hari KAntonie Van Leeuwenhoek10.1007/s10482-011-9600-32011Bacillus/*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 MicrobiologyMetabolism
Phylogeny25008165Bacillus shacheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.Lei Z, Qiu P, Ye R, Tian J, Liu Y, Wang L, Tang SK, Li WJ, Tian YJ Gen Appl MicrobiolDN/JST.JSTAGE/jgam/60.1012014Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Enzymology28793235(R,R)-Butane-2,3-diol dehydrogenase from Bacillus clausii DSM 8716(T): Cloning and expression of the bdhA-gene, and initial characterization of enzyme.Muschallik L, Molinnus D, Bongaerts J, Pohl M, Wagner T, Schoning MJ, Siegert P, Selmer TJ Biotechnol10.1016/j.jbiotec.2017.07.0202017Acetoin/metabolism, Acetoin Dehydrogenase/genetics/metabolism, Alcohol Oxidoreductases/genetics/*metabolism, Bacillus clausii/enzymology/*genetics, Bacterial Proteins/genetics/*metabolism, Cloning, Molecular, Diacetyl/metabolism, Escherichia coli/genetics, Kinetics, Recombinant Proteins/genetics/*metabolism, StereoisomerismMetabolism
30263701Probiotic characterization of Bacillus subtilis P223 isolated from kimchi.Jeon HL, Lee NK, Yang SJ, Kim WS, Paik HDFood Sci Biotechnol10.1007/s10068-017-0148-52017
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
33297479Effect of Physical and Chemical Treatments on Viability, Sub-Lethal Injury, and Release of Cellular Components from Bacillus clausii and Bacillus coagulans Spores and Cells.Bevilacqua A, Petruzzi L, Sinigaglia M, Speranza B, Campaniello D, Ciuffreda E, Corbo MRFoods10.3390/foods91218142020
Enzymology35497574Synthesis of alpha-hydroxy ketones and vicinal (R,R)-diols by Bacillus clausii DSM 8716(T) butanediol dehydrogenase.Muschallik L, Molinnus D, Jablonski M, Kipp CR, Bongaerts J, Pohl M, Wagner T, Schoning MJ, Selmer T, Siegert PRSC Adv10.1039/d0ra02066d2020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3246Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8716)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8716
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35723Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16658
57609Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47262)https://www.ccug.se/strain?id=47262
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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
70798Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14017.1StrainInfo: A central database for resolving microbial strain identifiers
118307Curators of the CIPCollection of Institut Pasteur (CIP 104718)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104718