Strain identifier

BacDive ID: 158260

Type strain: Yes

Species: Cytobacillus solani

Strain Designation: 5L6

Strain history: <- Y. Liu, China Natl. Res. Inst. of Food and Fermentation Ind., Beijing, China; 5L6 <- Y. Cao

NCBI tax ID(s): 1637975 (species)

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General

@ref: 64919

BacDive-ID: 158260

DSM-Number: 104513

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

description: Cytobacillus solani 5L6 is an aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from maize seeds.

NCBI tax id

  • NCBI tax id: 1637975
  • Matching level: species

strain history

  • @ref: 64919
  • history: <- Y. Liu, China Natl. Res. Inst. of Food and Fermentation Ind., Beijing, China; 5L6 <- Y. Cao

doi: 10.13145/bacdive158260.20230509.8.1

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 solani
  • full scientific name: Cytobacillus solani (Liu et al. 2015) Patel and Gupta 2020

  • synonyms

    @refsynonym
    20215Cytobacillus ciccensis
    20215Bacillus ciccensis
    20215Bacillus solani

@ref: 64919

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Cytobacillus

species: Cytobacillus ciccensis

full scientific name: Cytobacillus ciccensis (Liu et al. 2017) Gupta et al. 2020

strain designation: 5L6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65267positive3-4 µm0.6-0.8 µmrod-shapedyesperitrichous
69480yes97.865
69480positive100

colony morphology

  • @ref: 65267
  • colony color: creamy
  • colony shape: circular
  • medium used: tryptic soy agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64919NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
65267tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
64919positivegrowth30mesophilic
65267positivegrowth4-45
65267positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
65267positivegrowth6-11alkaliphile
65267positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 65267
  • oxygen tolerance: aerobe

spore formation

@reftype of sporespore formationconfidence
65267endosporeyes
69480yes100
69481yes100

halophily

@refsaltgrowthtested relationconcentration
65267NaClpositivegrowth0-9 %(w/v)
65267NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 65267
  • observation: The cell-wall peptidoglycan contained ornithine, serine, aspartic acid, glutamic acid and alanine.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
652673557154-nitrophenyl beta-D-galactopyranoside-hydrolysis
6526727613amygdalin-builds acid from
6526722599arabinose-assimilation
6526718305arbutin-builds acid from
6526727689decanoate-assimilation
65267casein-hydrolysis
6526717057cellobiose+builds acid from
6526717057cellobiose+carbon source
6526716947citrate-assimilation
6526715963ribitol-builds acid from
6526717108D-arabinose-builds acid from
6526718333D-arabitol-builds acid from
6526715824D-fructose-builds acid from
6526728847D-fucose-builds acid from
6526712936D-galactose-builds acid from
6526717634D-glucose+builds acid from
6526717634D-glucose+carbon source
6526762318D-lyxose-builds acid from
6526716899D-mannitol-builds acid from
6526716024D-mannose-builds acid from
6526716988D-ribose+builds acid from
6526717924D-sorbitol+builds acid from
6526716443D-tagatose-builds acid from
6526765327D-xylose-builds acid from
6526716813galactitol-builds acid from
6526717113erythritol-builds acid from
652674853esculin+builds acid from
652674853esculin+carbon source
652674853esculin+hydrolysis
6526728066gentiobiose-builds acid from
6526717234glucose-builds acid from
6526717754glycerol+builds acid from
6526717754glycerol+carbon source
6526728087glycogen-builds acid from
6526717268myo-inositol-builds acid from
6526717268myo-inositol+builds acid from
6526715443inulin-builds acid from
6526730849L-arabinose-builds acid from
6526718403L-arabitol-builds acid from
6526718287L-fucose-builds acid from
6526762345L-rhamnose-builds acid from
6526717266L-sorbose-builds acid from
6526765328L-xylose-builds acid from
6526717716lactose-builds acid from
6526725115malate-assimilation
6526717306maltose-assimilation
6526717306maltose+builds acid from
6526717306maltose+carbon source
6526729864mannitol-assimilation
6526729864mannitol+builds acid from
6526737684mannose-assimilation
652676731melezitose-builds acid from
6526728053melibiose-builds acid from
65267320061methyl alpha-D-glucopyranoside-builds acid from
6526743943methyl alpha-D-mannoside-builds acid from
6526774863methyl beta-D-xylopyranoside-builds acid from
65267506227N-acetylglucosamine+builds acid from
65267506227N-acetylglucosamine+carbon source
6526717632nitrate+reduction
6526718401phenylacetate-assimilation
65267potassium 2-dehydro-D-gluconate-builds acid from
6526732032potassium gluconate-builds acid from
6526716634raffinose-builds acid from
6526717814salicin+builds acid from
6526717814salicin+carbon source
6526728017starch-builds acid from
6526717992sucrose-builds acid from
6526717992sucrose+builds acid from
6526717992sucrose+carbon source
6526727082trehalose-builds acid from
6526732528turanose-builds acid from
6526753424tween 20-hydrolysis
6526753426tween 80-hydrolysis
6526717151xylitol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6526715688acetoinno
6526716136hydrogen sulfideno
6526735581indoleno

metabolite tests

  • @ref: 65267
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
65267catalase+1.11.1.6
65267gelatinase+
65267cytochrome oxidase-1.9.3.1
65267arginine dihydrolase-3.5.3.6
65267lysine decarboxylase-4.1.1.18
65267ornithine decarboxylase-4.1.1.17
65267urease-3.5.1.5
65267tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
64919maize seedsGansu Province (39° 04' 57.94'' N, 100° 12' 49.40'' E), Zhangye City, scientific research base of the Beijing Academy of Agriculture and Forestry Sciences (BAAFS)ChinaCHNAsia39.0828100.214
65267isolated from seeds of hybrid maize (Zea mays L., Jingke 968)scientific research base of the Beijing Academy of Agriculture and Forestry Sciences (BAAFS) in Gansu ProvinceChinaCHNAsia39.0827100.2142014-09LB agar2 days30The hybrid maize seed suspension (about 100 g) was prepared according to the procedure described by Qiu et al. [10]. Strains 5L6 T and 6L6 were isolated on LB agar which had been inoculated with a suspension of maize seeds and incubated at 30°C for 48 h.

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Plant#Fruit (Seed)
#Host#Plants#Herbaceous plants (Grass,Crops)

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: KP965576
  • Sequence Identity:
  • Total samples: 541
  • soil counts: 273
  • aquatic counts: 80
  • animal counts: 120
  • plant counts: 68

Safety information

risk assessment

  • @ref: 64919
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64919
  • description: Bacillus ciccensis strain 5L6 16S ribosomal RNA gene, partial sequence
  • accession: KP965576
  • length: 1512
  • database: ena
  • NCBI tax ID: 1670641

Genome sequences

  • @ref: 66792
  • description: Cytobacillus solani 5L6
  • accession: GCA_006704205
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1637975

GC content

  • @ref: 64919
  • GC-content: 37.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.809yes
flagellatedyes90.422yes
gram-positiveyes91.021yes
anaerobicno97.875no
aerobicyes84.932no
halophileno80.174yes
spore-formingyes96.358no
thermophileno98.809yes
glucose-utilyes86.746yes
glucose-fermentno93.628no

External links

@ref: 64919

culture collection no.: DSM 104513, CICC 23855, KCTC 33663

straininfo link

  • @ref: 111079
  • straininfo: 403524

literature

  • topic: Phylogeny
  • Pubmed-ID: 28984568
  • title: Bacillus ciccensis sp. nov., isolated from maize (Zea mays L.) seeds.
  • authors: Liu Y, Li N, Eom MK, Schumann P, Zhang X, Cao Y, Ge Y, Xiao M, Zhao J, Cheng C, Kim SG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002341
  • year: 2017
  • mesh: Bacillus/*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, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology
  • 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
64919Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104513Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104513)
65267Yang Liu, Nannan Li, Mi Kyung Eom, Peter Schumann, Xin Zhang, Yanhua Cao, Yuanyuan Ge, Ming Xiao, Jiuran Zhao, Chi Cheng, Song-Gun KimBacillus ciccensis sp. nov., isolated from maize (Zea mays L.) seeds10.1099/ijsem.0.002341IJSEM 67: 4606-4611 201728984568
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
111079Reimer, 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-ID403524.1