Strain identifier

BacDive ID: 433

Type strain: Yes

Species: Alicyclobacillus shizuokensis

Strain Designation: 4A-336

Strain history: IAM 15226 <-- K. Goto 4-A336.

NCBI tax ID(s): 1220573 (strain), 392014 (species)

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General

@ref: 7313

BacDive-ID: 433

DSM-Number: 17981

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

description: Alicyclobacillus shizuokensis 4A-336 is an aerobe, spore-forming, thermophilic bacterium that was isolated from soil, crop field.

NCBI tax id

NCBI tax idMatching level
392014species
1220573strain

strain history

@refhistory
7313<- Keiichi Goto, 4-A336
67770IAM 15226 <-- K. Goto 4-A336.

doi: 10.13145/bacdive433.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Alicyclobacillaceae
  • genus: Alicyclobacillus
  • species: Alicyclobacillus shizuokensis
  • full scientific name: Alicyclobacillus shizuokensis Goto et al. 2007

@ref: 7313

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Alicyclobacillaceae

genus: Alicyclobacillus

species: Alicyclobacillus shizuokensis

full scientific name: Alicyclobacillus shizuokensis Goto et al. 2007

strain designation: 4A-336

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31943positive04-05 µm0.7-0.8 µmrod-shapedyes
69480positive100

pigmentation

  • @ref: 31943
  • production: no

Culture and growth conditions

culture medium

  • @ref: 7313
  • name: BACILLUS ACIDOCALDARIUS MEDIUM (DSMZ Medium 13)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/13
  • composition: Name: BACILLUS ACIDOCALDARIUS MEDIUM (DSMZ Medium 13) Composition: Agar 20.0 g/l Glucose 1.0 g/l Yeast extract 1.0 g/l KH2PO4 0.6 g/l MgSO4 x 7 H2O 0.5 g/l CaCl2 x 2 H2O 0.25 g/l (NH4)2SO4 0.2 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
7313positivegrowth50thermophilic
31943positivegrowth35-60
31943positiveoptimum45-50thermophilic
67770positivegrowth50thermophilic
69480thermophilic99.999

culture pH

@refabilitytypepHPH range
31943positivegrowth4.0-4.5acidophile
31943positiveoptimum4.25

Physiology and metabolism

oxygen tolerance

  • @ref: 31943
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31943yes
69481yes95
69480yes95.405

halophily

@refsaltgrowthtested relationconcentration
31943NaClpositivegrowth0-5 %
31943NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3194322599arabinose+carbon source
3194317057cellobiose+carbon source
3194328260galactose+carbon source
3194317306maltose+carbon source
3194329864mannitol+carbon source
3194328053melibiose+carbon source
3194317814salicin+carbon source
3194317992sucrose+carbon source
3194327082trehalose+carbon source
3194318222xylose+carbon source

enzymes

  • @ref: 31943
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7313soil, crop fieldShizuoka cityJapanJPNAsia
67770Soil of a crop field in Shizuoka CityShizuoka Pref.JapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5562.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_313;96_2685;97_3297;98_4150;99_5562&stattab=map
  • Last taxonomy: Alicyclobacillus shizuokensis
  • 16S sequence: AB264024
  • Sequence Identity:
  • Total samples: 348
  • soil counts: 122
  • aquatic counts: 17
  • animal counts: 176
  • plant counts: 33

Safety information

risk assessment

  • @ref: 7313
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7313
  • description: Alicyclobacillus shizuokensis gene for 16S ribosomal RNA, partial sequence
  • accession: AB264024
  • length: 1519
  • database: ena
  • NCBI tax ID: 392014

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alicyclobacillus shizuokensis NBRC 1031031220573.3wgspatric1220573
66792Alicyclobacillus shizuokensis NBRC 1031032731957577draftimg1220573
67770Alicyclobacillus shizuokensis NBRC 103103GCA_001552255contigncbi1220573

GC content

@refGC-contentmethod
731360.5
6777060.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes95no
motileyes86.064yes
gram-positiveyes83.563no
anaerobicno99.047yes
aerobicyes88.608yes
halophileno89.982no
spore-formingyes95.874yes
glucose-utilyes90.331no
flagellatedno67.997no
thermophileyes99.998yes
glucose-fermentno91.843no

External links

@ref: 7313

culture collection no.: DSM 17981, IAM 15226, JCM 21680, NBRC 103103

straininfo link

  • @ref: 70112
  • straininfo: 309423

literature

  • topic: Phylogeny
  • Pubmed-ID: 17551043
  • title: Proposal of six species of moderately thermophilic, acidophilic, endospore-forming bacteria: Alicyclobacillus contaminans sp. nov., Alicyclobacillus fastidiosus sp. nov., Alicyclobacillus kakegawensis sp. nov., Alicyclobacillus macrosporangiidus sp. nov., Alicyclobacillus sacchari sp. nov. and Alicyclobacillus shizuokensis sp. nov.
  • authors: Goto K, Mochida K, Kato Y, Asahara M, Fujita R, An SY, Kasai H, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64692-0
  • year: 2007
  • mesh: Aerobiosis, Bacterial Proteins/genetics, Bacterial Typing Techniques, Beverages/*microbiology, Carbohydrate Metabolism, Carboxylic Acids/metabolism, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Bacteria/*classification/cytology/*isolation & purification/physiology, Guaiacol/metabolism, Hydrogen-Ion Concentration, Microscopy, Phase-Contrast, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7313Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17981)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17981
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
31943Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2819928776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
70112Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309423.1StrainInfo: A central database for resolving microbial strain identifiers