Strain identifier

BacDive ID: 11423

Type strain: Yes

Species: Brevibacillus choshinensis

Strain Designation: HPD 52, HPD52

Strain history: CIP <- 1993, H. Takagi, Higeta Shoyu Co., Chiba, Japan: strain HPD52

NCBI tax ID(s): 54911 (species)

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General

@ref: 3294

BacDive-ID: 11423

DSM-Number: 8552

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

description: Brevibacillus choshinensis HPD 52 is an obligate aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 54911
  • Matching level: species

strain history

@refhistory
3294<- O. Shida
398601993, H. Takagi, Res. Lab., Higeta Shoyu Co., Japan: strain HPD52
67770O. Shida HPD52.
118257CIP <- 1993, H. Takagi, Higeta Shoyu Co., Chiba, Japan: strain HPD52

doi: 10.13145/bacdive11423.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Brevibacillus
  • species: Brevibacillus choshinensis
  • full scientific name: Brevibacillus choshinensis (Takagi et al. 1993) Shida et al. 1996

  • synonyms

    • @ref: 20215
    • synonym: Bacillus choshinensis

@ref: 3294

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Brevibacillus

species: Brevibacillus choshinensis

full scientific name: Brevibacillus choshinensis (Takagi et al. 1993) Shida et al. 1996

strain designation: HPD 52, HPD52

type strain: yes

Morphology

cell morphology

  • @ref: 118257
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3294BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
39860MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118257CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
3294positivegrowth30
39860positivegrowth30
59096positivegrowth30-37
67770positivegrowth30
118257positivegrowth18-37
118257nogrowth10
118257nogrowth45
118257nogrowth55

culture pH

  • @ref: 118257
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 118257
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
118257yes
69480yes91.734
69481yes100

compound production

  • @ref: 3294
  • compound: protein

halophily

@refsaltgrowthtested relationconcentration
118257NaClpositivegrowth0-2 %
118257NaClnogrowth4 %
118257NaClnogrowth6 %
118257NaClnogrowth8 %
118257NaClnogrowth10 %

observation

@refobservation
67770Production of A large amount of protein
67770quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-mannoside-builds acid from43943
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368L-arabinose-fermentation30849
68368amygdalin-fermentation27613
68368melibiose-fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol-fermentation16899
68368D-glucose-fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
118257citrate-carbon source16947
118257nitrate-reduction17632
118257nitrite-reduction16301
118257nitrate-respiration17632

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11825735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
118257oxidase+
118257gelatinase-
118257amylase-
118257caseinase-3.4.21.50
118257catalase-1.11.1.6
118257lecithinase-
118257urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    59096C14:01.314
    59096C16:07.916
    59096C14:0 ISO1.913.618
    59096C15:0 ANTEISO36.114.711
    59096C15:0 ISO31.614.621
    59096C16:0 iso3.515.626
    59096C16:1 ω11c1.415.757
    59096C17:0 anteiso6.216.722
    59096C17:0 iso10.216.629
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
59096----+----++----------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
59096-----------+++----++-++--+++++-++-----------------
118257----+/------------------------------------------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3294soil
59096SoilChibaJapanJPNAsia
67770Soil
118257Environment, SoilChibaJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1600.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_95;96_241;97_263;98_292;99_1600&stattab=map
  • Last taxonomy: Brevibacillus
  • 16S sequence: LC379069
  • Sequence Identity:
  • Total samples: 732
  • soil counts: 355
  • aquatic counts: 125
  • animal counts: 163
  • plant counts: 89

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32941Risk group (German classification)
1182571Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Brevibacillus choshinensis clone Bchosh-1R 16S ribosomal RNA gene, and 16S-23S internal transcribed spacer, partial sequenceAF478095257nuccore54911
20218Brevibacillus choshinensis gene for 16S rRNA, partial sequence, strain:DSM 8552TAB1127131486nuccore54911
20218Brevibacillus choshinensis DNA for 16S ribosomal RNAD784591419nuccore54911
20218Brevibacillus choshinensis gene for 16S rRNA, partial sequence, strain: NBRC 15518AB6808871461nuccore54911
67770Brevibacillus choshinensis gene for 16S rRNA, partial sequence, strain: JCM 8505LC3790691458nuccore54911

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevibacillus choshinensis strain DSM 855254911.3wgspatric54911
67770Brevibacillus choshinensis DSM 8552GCA_001420695scaffoldncbi54911

GC content

  • @ref: 3294
  • GC-content: 48.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes58.659no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.3yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes91.734no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes75.161no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno91.787yes
69480flagellatedmotile2+Ability to perform flagellated movementyes78.668no

External links

@ref: 3294

culture collection no.: DSM 8552, ATCC 51359, CIP 103838, IFO 15518, JCM 8505, NBRC 15518, CCUG 51061, NRRL B-23247, LMG 15968, CGMCC 1.3099, KCTC 3836, NCIMB 13345

straininfo link

@refstraininfo
806578295
80658312200

literature

  • topic: Genetics
  • Pubmed-ID: 26847894
  • title: Draft Genome Sequence of Brevibacillus choshinensis HPD52T (DSM 8552), a Bacterial Host for Efficient Expression of Heterologous Proteins.
  • authors: Wang JP, Liu B, Liu GH, Che JM, Chen Z, Chen M, Shi H
  • journal: Genome Announc
  • DOI: 10.1128/genomeA.01688-15
  • year: 2016
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3294Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8552)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8552
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
39860Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15680
59096Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51061)https://www.ccug.se/strain?id=51061
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
80657Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8295.1StrainInfo: A central database for resolving microbial strain identifiers
80658Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312200.1StrainInfo: A central database for resolving microbial strain identifiers
118257Curators of the CIPCollection of Institut Pasteur (CIP 103838)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103838