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, Gram-positive, motile, rod-shaped

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/bacdive1132.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: 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

  • @ref: 118306
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

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

@refgrowthtypetemperature
3250positivegrowth30
35806positivegrowth30
118306positivegrowth22-45
118306nogrowth10
118306nogrowth55

culture pH

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

Physiology and metabolism

oxygen tolerance

  • @ref: 118306
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 125439
  • spore formation: yes
  • confidence: 94.7

halophily

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11830617632nitrate+reduction
11830616301nitrite+reduction
11830617632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837112936D-galactose-builds acid from
6837117754glycerol-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
68382beta-glucuronidase-3.2.1.31
68382alkaline phosphatase+3.1.3.1

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: nuccore
  • 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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes72.053no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.324yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes74.362yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes88.066no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.072yes
125438motile2+flagellatedAbility to perform flagellated movementyes80.52no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes94.7
125439BacteriaNetmotilityAbility to perform movementyes86.9
125439BacteriaNetgram_stainReaction to gram-stainingvariable86.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe87.7

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1