Strain identifier

BacDive ID: 1132

Type strain: Yes

Species: Evansella clarkii

Strain Designation: PN 102, VP 395

Strain history: CIP <- 1997, DSMZ <- H. Outtrup, Novo Nordisk A/S: strain PN 102

NCBI tax ID(s): 79879 (species)

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General

@ref: 3250

BacDive-ID: 1132

DSM-Number: 8720

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

description: Evansella clarkii PN 102 is an obligate aerobe, spore-forming, mesophilic bacterium of the family Bacillaceae.

NCBI tax id

  • NCBI tax id: 79879
  • Matching level: species

strain history

@refhistory
3250<- H. Outtrup, Novo Nordisk A/S; VP 395
118306CIP <- 1997, DSMZ <- H. Outtrup, Novo Nordisk A/S: strain PN 102

doi: 10.13145/bacdive1132.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Evansella
  • species: Evansella clarkii
  • full scientific name: Evansella clarkii (Nielsen et al. 1995) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus clarkii

@ref: 3250

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Evansella

species: Evansella clarkii

full scientific name: Evansella clarkii (Nielsen et al. 1995) Gupta et al. 2020

strain designation: PN 102, VP 395

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.191
69480100positive
118306yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3250ALKALINE 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
35806MEDIUM 113 - for BacillusyesDistilled water make up to (900.000 ml);Columbia agar (39.000 g);Solution 1 - M00343 (100.000 ml)
118306CIP Medium 113yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=113

culture temp

@refgrowthtypetemperaturerange
3250positivegrowth30mesophilic
35806positivegrowth30mesophilic
118306positivegrowth22-45
118306nogrowth10psychrophilic
118306nogrowth55thermophilic

culture pH

  • @ref: 118306
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 118306
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.674

halophily

  • @ref: 118306
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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
68371glycogen+builds acid from28087
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
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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
118306nitrate+reduction17632
118306nitrite+reduction16301
118306nitrate-respiration17632

metabolite production

  • @ref: 118306
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11830615688acetoin+
11830617234glucose+

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
118306oxidase-
118306beta-galactosidase+3.2.1.23
118306alcohol dehydrogenase-1.1.1.1
118306gelatinase-
118306catalase+1.11.1.6
118306gamma-glutamyltransferase+2.3.2.2
118306lysine decarboxylase-4.1.1.18
118306ornithine decarboxylase-4.1.1.17
118306phenylalanine ammonia-lyase-4.3.1.24
118306urease-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
118306-+++-+---+++-+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118306----+-----+++--------++/-++++/-+---+---++---------+/---

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_6198.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2701;97_3317;98_4594;99_6198&stattab=map
  • Last taxonomy: Bacillales
  • 16S sequence: X76444
  • Sequence Identity:
  • Total samples: 657
  • soil counts: 122
  • aquatic counts: 68
  • animal counts: 416
  • plant counts: 51

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32501Risk group (German classification)
1183061Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Bacillus clarkii DSM 8720, 16S rRNA gene
  • accession: X76444
  • length: 1522
  • database: ena
  • NCBI tax ID: 79879

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Evansella clarkii DSM 8720GCA_002019695scaffoldncbi79879
66792[Bacillus] clarkii strain DSM 872079879.3wgspatric79879
66792Bacillus clarkii DSM 87202898074128draftimg79879

GC content

  • @ref: 3250
  • GC-content: 42.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes69.45no
gram-positiveyes88.058no
anaerobicno97.979no
halophileyes87.636no
spore-formingyes91.665no
glucose-utilyes89.919no
aerobicyes82.658no
thermophileno93.064no
motileyes86.453no
glucose-fermentno94.548no

External links

@ref: 3250

culture collection no.: DSM 8720, ATCC 700162, CIP 105301

straininfo link

  • @ref: 70803
  • straininfo: 10537

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17158996Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea.Lim JM, Jeon CO, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.64036-02006Bacillus/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Sodium Chloride, *SunlightGenetics
Phylogeny18175695Bacillus polygoni sp. nov., a moderately halophilic, non-motile obligate alkaliphile isolated from indigo balls.Aino K, Hirota K, Matsuno T, Morita N, Nodasaka Y, Fujiwara T, Matsuyama H, Yoshimune K, Yumoto IInt J Syst Evol Microbiol10.1099/ijs.0.65193-02008Bacillus/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Indigofera/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
22437739Relationship between rates of respiratory proton extrusion and ATP synthesis in obligately alkaliphilic Bacillus clarkii DSM 8720(T).Hirabayashi T, Goto T, Morimoto H, Yoshimune K, Matsuyama H, Yumoto IJ Bioenerg Biomembr10.1007/s10863-012-9430-72012Adenosine Triphosphate/*biosynthesis, Bacillus/*physiology, Electron Transport/physiology, Hydrogen-Ion Concentration, Membrane Potentials/physiology, Oxygen Consumption/*physiology, Proton-Motive Force/*physiology, *Protons
Metabolism26749514Contribution of intracellular negative ion capacity to Donnan effect across the membrane in alkaliphilic Bacillus spp.Goto T, Hirabayashi T, Morimoto H, Yamazaki K, Inoue N, Matsuyama H, Yumoto IJ Bioenerg Biomembr10.1007/s10863-015-9641-92016Adenosine Triphosphate/*metabolism, Bacillus/*metabolism, Bacterial Proteins/*metabolism, Cell Membrane/*metabolism, Electron Transport/physiology, Membrane Potentials/*physiology, Proton-Motive Force/*physiology
Phylogeny29111966Bacillus populi sp. nov. isolated from Populus euphratica rhizosphere soil of the Taklamakan desert.Liu B, Liu GH, Wang XY, Wang JP, Zhu YJ, Zhang HF, Sengonca CInt J Syst Evol Microbiol10.1099/ijsem.0.0024762017Bacillus/*classification/genetics/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, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3250Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8720)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8720
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
35806Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17305
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
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
70803Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10537.1StrainInfo: A central database for resolving microbial strain identifiers
118306Curators of the CIPCollection of Institut Pasteur (CIP 105301)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105301