Strain identifier

BacDive ID: 133067

Type strain: Yes

Species: Bacillus capparidis

Strain history: <- W.-J. Li, Sun Yat-sen Univ., Guangzhou, People's Republic of China; EGI 6500252 <- H.-F. Wang, Xinjiang Inst. of Ecol. and Geography (XIEG), Chin. Acad. of Scs., Urumchi, China

NCBI tax ID(s): 1840411 (species)

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General

@ref: 24855

BacDive-ID: 133067

DSM-Number: 103394

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming

description: Bacillus capparidis DSM 103394 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized roots of the medicinal plant Capparis spinosa L..

NCBI tax id

  • NCBI tax id: 1840411
  • Matching level: species

strain history

  • @ref: 24855
  • history: <- W.-J. Li, Sun Yat-sen Univ., Guangzhou, People's Republic of China; EGI 6500252 <- H.-F. Wang, Xinjiang Inst. of Ecol. and Geography (XIEG), Chin. Acad. of Scs., Urumchi, China

doi: 10.13145/bacdive133067.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Bacillus
  • species: Bacillus capparidis
  • full scientific name: Bacillus capparidis Wang et al. 2017

@ref: 24855

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus capparidis

full scientific name: Bacillus capparidis Wang et al. 2017

type strain: yes

Morphology

cell morphology

  • @ref: 25175
  • gram stain: positive
  • cell length: 1.98-2.30 µm
  • cell width: 0.68 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 25175
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: ISP2 agar medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25175ISP2 agar mediumyes
24855CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
25175positivegrowth10.0-40.0
25175positiveoptimum25.0-30.0
24855positivegrowth30

culture pH

@refabilitytypepH
25175positivegrowth6.0-8.0
25175positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
25175aerobe
125439obligate aerobe97.2

spore formation

  • @ref: 25175
  • spore formation: no

halophily

@refsalttested relationconcentrationgrowth
25175NaCloptimum0.0-3.0 %
25175NaClgrowth0.0-10.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2517515588D-malate-respiration
25175168082-dehydro-D-gluconate-builds acid from
25175645522-hydroxybutyrate-respiration
25175167632-oxobutanoate-respiration
25175181014-hydroxyphenylacetic acid-respiration
25175581435-dehydro-D-gluconate-builds acid from
2517517128adipate-assimilation
2517522599arabinose-assimilation
25175casein-hydrolysis
2517562968cellulose-hydrolysis
2517516947citrate-assimilation
2517515963ribitol-builds acid from
2517517108D-arabinose-builds acid from
2517518333D-arabitol-builds acid from
2517528847D-fucose-builds acid from
2517512936D-galactose-builds acid from
2517530612D-glucarate-respiration
2517515748D-glucuronate-respiration
2517562318D-lyxose-builds acid from
2517516988D-ribose-builds acid from
2517516523D-serine-respiration
2517516443D-tagatose-builds acid from
2517565327D-xylose-builds acid from
2517527689decanoate-assimilation
25175370543-hydroxybutyrate-respiration
2517517113erythritol-builds acid from
2517516537galactarate-respiration
2517516813galactitol-builds acid from
2517517234glucose-fermentation
2517532323glucuronamide-respiration
2517517754glycerol-builds acid from
2517528087glycogen-builds acid from
2517517268myo-inositol-builds acid from
2517530849L-arabinose-builds acid from
2517518403L-arabitol-builds acid from
2517518287L-fucose-builds acid from
2517518183L-pyroglutamic acid-respiration
2517562345L-rhamnose-builds acid from
2517517266L-sorbose-builds acid from
2517565328L-xylose-builds acid from
2517517716lactose-builds acid from
2517543943methyl alpha-D-mannoside-builds acid from
2517574863methyl beta-D-xylopyranoside-builds acid from
2517551850methyl pyruvate-respiration
25175506227N-acetylglucosamine-assimilation
25175506227N-acetylglucosamine-respiration
25175506227N-acetylglucosamine-builds acid from
2517517632nitrate-reduction
2517518401phenylacetate-assimilation
2517517272propionate-respiration
2517528017starch-hydrolysis
2517528017starch-builds acid from
2517553424tween 20-hydrolysis
2517553423tween 40-hydrolysis
2517553425tween 60-hydrolysis
2517553426tween 80-hydrolysis
2517517151xylitol-builds acid from
2517517521(-)-quinic acid+respiration
2517516004(R)-lactate+respiration
2517516651(S)-lactate+respiration
2517515589L-malate+respiration
25175309162-oxoglutarate+respiration
25175739183-O-methyl-D-glucose+respiration
2517530089acetate+respiration
2517513705acetoacetate+respiration
2517527613amygdalin+builds acid from
2517518305arbutin+builds acid from
2517573706bromosuccinate+respiration
2517517057cellobiose+respiration
2517517057cellobiose+builds acid from
2517516947citrate+respiration
2517518333D-arabitol+respiration
2517529990D-aspartate+respiration
2517515824D-fructose+respiration
2517578697D-fructose 6-phosphate+respiration
2517528847D-fucose+respiration
2517515895D-galactonic acid lactone+respiration
2517512936D-galactose+respiration
2517518024D-galacturonic acid+respiration
251758391D-gluconate+respiration
2517517634D-glucose+respiration
2517517634D-glucose+builds acid from
2517514314D-glucose 6-phosphate+respiration
2517517716lactose+respiration
2517516899D-mannitol+respiration
2517516899D-mannitol+builds acid from
2517516024D-mannose+respiration
2517516024D-mannose+builds acid from
2517517924D-sorbitol+respiration
2517517924D-sorbitol+builds acid from
2517532528turanose+builds acid from
2517523652dextrin+respiration
251754853esculin+hydrolysis
251754853esculin+builds acid from
2517515740formate+respiration
2517528757fructose+builds acid from
2517516865gamma-aminobutyric acid+respiration
251755291gelatin+respiration
2517528066gentiobiose+respiration
2517528066gentiobiose+builds acid from
2517524265gluconate+builds acid from
2517517234glucose+assimilation
2517517754glycerol+respiration
2517570744glycine-proline+respiration
2517573804glycyl L-aspartic acid+respiration
2517517596inosine+respiration
2517517268myo-inositol+respiration
2517515443inulin+builds acid from
2517516977L-alanine+respiration
2517516467L-arginine+respiration
2517518287L-fucose+respiration
2517529985L-glutamate+respiration
2517515971L-histidine+respiration
2517562345L-rhamnose+respiration
2517517115L-serine+respiration
2517525115malate+assimilation
2517517306maltose+assimilation
2517517306maltose+respiration
2517517306maltose+builds acid from
2517529864mannitol+assimilation
2517537684mannose+assimilation
251756731melezitose+builds acid from
2517528053melibiose+respiration
2517528053melibiose+builds acid from
25175320061methyl alpha-D-glucopyranoside+builds acid from
2517537657methyl D-glucoside+respiration
2517563154N-acetyl-beta-D-mannosamine+respiration
2517528037N-acetylgalactosamine+respiration
2517535418n-acetylneuraminate+respiration
2517517309pectin+respiration
2517532032potassium gluconate+assimilation
2517516634raffinose+respiration
2517516634raffinose+builds acid from
2517517814salicin+respiration
2517517814salicin+builds acid from
2517517164stachyose+respiration
2517517992sucrose+respiration
2517517992sucrose+builds acid from
2517527082trehalose+respiration
2517527082trehalose+builds acid from
2517532528turanose+respiration

metabolite production

  • @ref: 25175
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

metabolite tests

  • @ref: 25175
  • Chebi-ID: 17234
  • metabolite: glucose
  • methylred-test: -

enzymes

@refvalueactivityec
25175catalase+1.11.1.6
25175cytochrome oxidase+1.9.3.1
25175urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25175C13:0 anteiso0.6
    25175C15:0 anteiso24
    25175C17:0 anteiso11
    25175C15:0 2OH2
    25175C15:0 iso30.4
    25175C15:0 iso 3OH1.5
  • type of FA analysis: whole cell analysis
  • incubation medium: tripticase soy agar (TSA;Difco)
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • method/protocol: Sasser 1990

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling dateenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
24855surface-sterilized roots of the medicinal plant Capparis spinosa L.Capparis spinosaXinjiang, Urumqi cityChinaCHNAsia
25175July 2014TWYE agaryeast 0.25 g, K2HPO4 0.5 g, agar 15.0 g, distilled water 1000 ml, pH 7.0–7.2) [7] supplemented with 3 % (w/v) NaCl14-42 days30

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

  • @ref: 24855
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
24855Bacillus capparidis strain EGI 6500252 16S ribosomal RNA gene, partial sequenceKX1194231514nuccore1840411
24855Bacillus capparidis strain EGI 6500252 16S ribosomal RNA gene, partial sequenceKY0031621546nuccore1840411

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus capparidis DSM 103394GCA_017832095contigncbi1840411
66792Bacillus capparidis strain DSM 1033941840411.3wgspatric1840411
66792Bacillus capparidis DSM 1033942901263064draftimg1840411

GC content

  • @ref: 24855
  • GC-content: 39.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes80.487yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.669yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes75.447yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.975yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.724yes
125438motile2+flagellatedAbility to perform flagellated movementyes85.562no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes79.7
125439BacteriaNetmotilityAbility to perform movementyes70.6
125439BacteriaNetgram_stainReaction to gram-stainingvariable83.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.2

External links

@ref: 24855

culture collection no.: DSM 103394, CGMCC 1.12820, KCTC 33514, EGI 6500252

straininfo link

  • @ref: 91332
  • straininfo: 405400

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902223
  • title: Bacillus capparidis sp. nov., an endophytic bacterium isolated from roots of Capparis spinosa L.
  • authors: Wang HF, Li QL, Zhang YG, Xiao M, Zhou XK, Guo JW, Duan YQ, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001616
  • year: 2017
  • mesh: Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Capparis/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24855Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103394Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103394)
25175H. F. L. Wang, Q. L.,Zhang, Y. G.,Xiao, M.,Zhou, X. K.,Guo, J. W.,Duan, Y. Q.,Li, W. J.Bacillus capparidis sp. nov., an endophytic bacterium isolated from roots of Capparis spinosa L10.1099/ijsem.0.001616IJSEM 67: 282-287 201727902223
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
91332Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405400.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG