Strain identifier

BacDive ID: 140355

Type strain: Yes

Species: Cytobacillus praedii

Strain Designation: FJAT-25547

Strain history: <- G. Liu, Fujian Academy of Agricultural Sciences, Fuzhou, China; FJAT-25547

NCBI tax ID(s): 1742358 (species)

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General

@ref: 42962

BacDive-ID: 140355

DSM-Number: 101002

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

description: Cytobacillus praedii FJAT-25547 is an aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from paddy soil.

NCBI tax id

  • NCBI tax id: 1742358
  • Matching level: species

strain history

  • @ref: 42962
  • history: <- G. Liu, Fujian Academy of Agricultural Sciences, Fuzhou, China; FJAT-25547

doi: 10.13145/bacdive140355.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Cytobacillus
  • species: Cytobacillus praedii
  • full scientific name: Cytobacillus praedii (Liu et al. 2017) Patel and Gupta 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus praedii

@ref: 42962

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Cytobacillus

species: Cytobacillus praedii

full scientific name: Cytobacillus praedii (Liu et al. 2017) Patel and Gupta 2020

strain designation: FJAT-25547

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43457positive2.1-4.3 µm0.7-1.1 µmrod-shapedyes
69480yes98.03
69480positive100

colony morphology

  • @ref: 43457
  • colony size: 2-3 mm
  • colony color: light white to yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Luria Bertani agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43457LB (Luria-Bertani) MEDIUMyes
42962CASO 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

@refgrowthtypetemperaturerange
43457positivegrowth15-40
43457positiveoptimum30mesophilic
42962positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43457positivegrowth5-12alkaliphile
43457positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 43457
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43457ellipsoidal at subterminal positionsendosporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
43457NaClpositivegrowth0-10 %(w/v)
43457NaClpositiveoptimum4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4345716947citrate-assimilation
43457581435-dehydro-D-gluconate-builds acid from
4345717057cellobiose-builds acid from
4345717108D-arabinose-builds acid from
4345728847D-fucose-builds acid from
4345765327D-xylose-builds acid from
4345728757fructose-builds acid from
4345717306maltose-builds acid from
4345729864mannitol-builds acid from
4345733954tagatose-builds acid from
4345727613amygdalin-carbon source
4345722599arabinose-carbon source
4345717234glucose-carbon source
4345717268myo-inositol-carbon source
4345737684mannose-carbon source
434576731melezitose-carbon source
4345726546rhamnose-carbon source
4345727922sorbose-carbon source
4345717992sucrose-carbon source
4345716199urea-hydrolysis
4345727613amygdalin-nitrogen source
4345722599arabinose-nitrogen source
4345717234glucose-nitrogen source
4345717268myo-inositol-nitrogen source
4345737684mannose-nitrogen source
434576731melezitose-nitrogen source
4345726546rhamnose-nitrogen source
4345727922sorbose-nitrogen source
4345717992sucrose-nitrogen source
434574853esculin+builds acid from
4345717234glucose+builds acid from
4345717754glycerol+builds acid from
43457506227N-acetylglucosamine+builds acid from
4345733942ribose+builds acid from
434575291gelatin+hydrolysis
4345717632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
4345715688acetoinno
4345716136hydrogen sulfideno
4345735581indoleno

metabolite tests

  • @ref: 43457
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
43457alkaline phosphatase+3.1.3.1
43457esterase+
43457esterase Lipase (C 8)+
43457alpha-glucosidase+3.2.1.20
43457beta-galactosidase-3.2.1.23
43457naphthol-AS-BI-phosphohydrolase-
43457lipase (C 14)-
43457leucine arylamidase-3.4.11.1
43457valine arylamidase-
43457cystine arylamidase-3.4.11.3
43457trypsin-3.4.21.4
43457alpha-chymotrypsin-3.4.21.1
43457acid phosphatase-3.1.3.2
43457alpha-galactosidase-3.2.1.22
43457beta-glucuronidase-3.2.1.31
43457beta-glucosidase-3.2.1.21
43457N-acetyl-beta-glucosaminidase-3.2.1.52
43457alpha-mannosidase-3.2.1.24
43457alpha-fucosidase-3.2.1.51
43457catalase+1.11.1.6
43457cytochrome oxidase-1.9.3.1
43457arginine dihydrolase-3.5.3.6
43457lysine decarboxylase-4.1.1.18
43457ornithine decarboxylase-4.1.1.17
43457tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
42962paddy soilSichuan province, Yanting Prefecture, Linshan Township (31° 16' N 105° 27' E)ChinaCHNAsia31.2667105.45
43457purplish paddy soilLinshan Township, Yanting Prefecture, Sichuan ProvinceChinaCHNAsia31.266105.45

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Condition#Anoxic (anaerobic)
#Condition#Humid

taxonmaps

  • @ref: 69479
  • File name: preview.99_386.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_264;97_291;98_324;99_386&stattab=map
  • Last taxonomy: Bacillaceae
  • 16S sequence: KY582959
  • Sequence Identity:
  • Total samples: 541
  • soil counts: 273
  • aquatic counts: 80
  • animal counts: 120
  • plant counts: 68

Safety information

risk assessment

  • @ref: 42962
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42962
  • description: Bacillus praedii strain FJAT-25547 16S ribosomal RNA gene, partial sequence
  • accession: KY582959
  • length: 1420
  • database: ena
  • NCBI tax ID: 1742358

Genome sequences

  • @ref: 66792
  • description: Cytobacillus praedii FJAT-25547
  • accession: GCA_001439605
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1742358

GC content

@refGC-contentmethod
4345739.1
4296239.1sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes87.972no
gram-positiveyes91.394yes
anaerobicno97.977yes
aerobicyes87.795yes
halophileno78.992no
spore-formingyes95.637no
glucose-utilyes83.509yes
motileyes93.316yes
thermophileno98.264yes
glucose-fermentno93.966no

External links

@ref: 42962

culture collection no.: DSM 101002, CCTCC AB 2015208

straininfo link

  • @ref: 96653
  • straininfo: 406154

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28820088Bacillus praedii sp. nov., isolated from purplish paddy soil.Liu B, Liu GH, Sengonca C, Schumann P, Wang JP, Zhu YJ, Liu QY, Wang MKInt J Syst Evol Microbiol10.1099/ijsem.0.0020302017Bacillus/*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, Oryza, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny32382951Bacillus dafuensis sp. Nov., Isolated from a Forest Soil in China.Zheng X, Liu G, Wang Z, Wang J, Zhang H, Liu BCurr Microbiol10.1007/s00284-020-02014-22020*Bacillus/genetics, Bacterial Typing Techniques, Cell Wall, China, DNA, Bacterial/genetics, Diaminopimelic Acid, Forests, Peptidoglycan, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil MicrobiologyTranscriptome

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
42962Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101002Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101002)
43457Bo Liu, Guo-Hong Liu, Cetin Sengonca, Peter Schumann, Jie-Ping Wang, Yu-Jing Zhu, Qin-Ying Liu, Ming-Kuang WangBacillus praedii sp. nov., isolated from purplish paddy soil10.1099/ijsem.0.002030IJSEM 67: 2823-2828 201728820088
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96653Reimer, 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-ID406154.1