Strain identifier

BacDive ID: 1240

Type strain: Yes

Species: Halalkalibacter wakoensis

Strain Designation: N-1

Strain history: CIP <- 2005, JCM <- 1994, K. Horikoshi, Japan Ag. Marine-Earth Science Technol., Yokosuka, Japan: strain N-1

NCBI tax ID(s): 1236970 (strain), 127891 (species)

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General

@ref: 1109

BacDive-ID: 1240

DSM-Number: 2521

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

description: Halalkalibacter wakoensis N-1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1236970strain
127891species

strain history

@refhistory
1109<- ATCC <- Rikagaku Kenkyusho, N-1
67770K. Horikoshi N-1.
123903CIP <- 2005, JCM <- 1994, K. Horikoshi, Japan Ag. Marine-Earth Science Technol., Yokosuka, Japan: strain N-1

doi: 10.13145/bacdive1240.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halalkalibacter
  • species: Halalkalibacter wakoensis
  • full scientific name: Halalkalibacter wakoensis (Nogi et al. 2005) Joshi et al. 2022

  • synonyms

    @refsynonym
    20215Alkalihalobacillus wakoensis
    20215Bacillus wakoensis

@ref: 1109

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Halalkalibacter

species: Halalkalibacter wakoensis

full scientific name: Halalkalibacter wakoensis (Nogi etal. 2005) Joshi et al. 2022

strain designation: N-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31483positive1.75 µm0.65 µmrod-shapedyes
69480yes97.208
69480positive100
123903positiverod-shapedyes

pigmentation

  • @ref: 31483
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1109ALKALINE NUTRIENT AGAR (DSMZ Medium 31)yeshttps://mediadive.dsmz.de/medium/31Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water
40094MEDIUM 291 - for Bacillus hortiyesDistilled water make up to (900.000 ml);Magnesium sulphate heptahydrate (0.200 g);Agar (15.000 g);Glucose (10.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.000 g);Polypeptone (5.000 g);Sodium carbonate solution - M00442 (100.000 ml)
123903CIP Medium 291yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=291

culture temp

@refgrowthtypetemperaturerange
1109positivegrowth30mesophilic
31483positivegrowth10-40
31483positiveoptimum37mesophilic
40094positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31483positivegrowth08-10alkaliphile
31483positiveoptimum9.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31483
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31483yes
69481yes100
69480yes100

compound production

  • @ref: 1109
  • compound: cellulase, alkaline

halophily

@refsaltgrowthtested relationconcentration
31483NaClpositivegrowth0-10 %
31483NaClpositiveoptimum5 %

observation

@refobservation
31483aggregates in clumps
67770quinones: MK-6, MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3148317057cellobiose+carbon source
3148328757fructose+carbon source
3148317234glucose+carbon source
3148317306maltose+carbon source
3148329864mannitol+carbon source
3148337684mannose+carbon source
3148317814salicin+carbon source
3148330911sorbitol+carbon source
3148317992sucrose+carbon source
3148327082trehalose+carbon source
3148318222xylose+carbon source
3148317632nitrate+reduction
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837112936D-galactose-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12390317632nitrate+reduction
12390316301nitrite-reduction

metabolite production

  • @ref: 123903
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31483catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
67770cellulase3.2.1.4
123903oxidase-
123903alcohol dehydrogenase-1.1.1.1
123903catalase+1.11.1.6
123903lysine decarboxylase-4.1.1.18
123903ornithine decarboxylase-4.1.1.17
123903urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123903-++--+----+----++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123903---+/--+/---+/--+/-+/------+/--------+/-+/-+/---+/------------------+/-

Isolation, sampling and environmental information

isolation

@refsample type
1109soil
67770Soil
123903Environment, Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
11091Risk group (German classification)
1239031Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus sp. N1 partial 16S rRNA geneAJ786654649ena288813
20218Bacillus sp. N1 16S ribosomal RNA gene, partial sequenceDQ3769391322ena288813
20218Bacillus wakoensis 16S ribosomal RNA gene, partial sequenceFJ876429600ena127891
20218Bacillus sp. N1(2009) 16S ribosomal RNA gene, partial sequenceGU0864131514ena690148
20218Bacillus sp. N1(2011) 16S ribosomal RNA gene, partial sequenceHQ4518841420ena995018
20218Bacillus sp. N1(2012) 16S ribosomal RNA gene, partial sequenceJX2729221155ena1229622
20218Bacillus sp. N1(2013) 16S ribosomal RNA gene, partial sequenceKF0517771449ena1348145
31483Bacillus wakoensis gene for 16S rRNAAB0438511524nuccore127891

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus wakoensis JCM 91401236970.3wgspatric1236970
66792Bacillus wakoensis JCM 91401236970.4wgspatric1236970
66792Bacillus wakoensis JCM 91402609459807draftimg1236970
67770Halalkalibacter wakoensis JCM 9140GCA_000513095contigncbi1236970
67770Halalkalibacter wakoensis JCM 9140GCA_001315045contigncbi1236970

GC content

@refGC-contentmethod
110937.2
3148338.1
6777038.1high performance liquid chromatography (HPLC)
6777038.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.433yes
gram-positiveyes91.503no
anaerobicno97.88no
aerobicyes85.448no
halophileyes66.052no
spore-formingyes93.36yes
glucose-utilyes89.212yes
flagellatedyes87.519no
thermophileno99.251no
glucose-fermentno93.151no

External links

@ref: 1109

culture collection no.: DSM 2521, ATCC 21832, FERM P-1138, JCM 9140, CIP 109022, FERM 1138

straininfo link

  • @ref: 70896
  • straininfo: 44645

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280488Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species.Nogi Y, Takami H, Horikoshi KInt J Syst Evol Microbiol10.1099/ijs.0.63649-02005Bacillus/*classification/genetics/isolation & purification, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, *Industrial Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/geneticsGenetics
Genetics24482522Draft Genome Sequences of Three Alkaliphilic Bacillus Strains, Bacillus wakoensis JCM 9140T, Bacillus akibai JCM 9157T, and Bacillus hemicellulosilyticus JCM 9152T.Yuki M, Oshima K, Suda W, Oshida Y, Kitamura K, Iida T, Hattori M, Ohkuma MGenome Announc10.1128/genomeA.01258-132014
Phylogeny30912738Bacillus urbisdiaboli sp. nov., isolated from soil sampled in Xinjiang.Liu B, Liu GH, Wang XY, Wang JP, Chen Z, Chen MC, Zhang HF, Singonca CInt J Syst Evol Microbiol10.1099/ijsem.0.0033632019Bacillus/*classification/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, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
1109Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2521)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2521
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
31483Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127781
40094Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6718
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
70896Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44645.1StrainInfo: A central database for resolving microbial strain identifiers
123903Curators of the CIPCollection of Institut Pasteur (CIP 109022)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109022