Strain identifier

BacDive ID: 1241

Type strain: Yes

Species: Halalkalibacter hemicellulosilyticus

Strain Designation: C-11

Strain history: CIP <- 2005, JCM <- 1994, K. Horikoshi, Japan Ag. Marine-Earth Science Technol., Yokosuka, Japan: strain C-11

NCBI tax ID(s): 1236971 (strain), 127886 (species)

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General

@ref: 6497

BacDive-ID: 1241

DSM-Number: 16731

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

description: Halalkalibacter hemicellulosilyticus C-11 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1236971strain
127886species

strain history

@refhistory
6497<- Y. Nogi <- Y. Ikura, K. Horikoshi; C-11
67770K. Horikoshi C-11.
119871CIP <- 2005, JCM <- 1994, K. Horikoshi, Japan Ag. Marine-Earth Science Technol., Yokosuka, Japan: strain C-11

doi: 10.13145/bacdive1241.20230509.8.1

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 hemicellulosilyticus
  • full scientific name: Halalkalibacter hemicellulosilyticus (Nogi et al. 2005) Joshi et al. 2022

  • synonyms

    @refsynonym
    20215Alkalihalobacillus hemicellulosilyticus
    20215Alkalihalobacillus haemicellulosilyticus
    20215Bacillus hemicellulosilyticus

@ref: 6497

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Halalkalibacter

species: Halalkalibacter hemicellulosilyticus

full scientific name: Alkalihalobacillus hemicellulosilyticus (Nogi et al. 2005) Patel and Gupta 2020

strain designation: C-11

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31483variable4 µm0.4 µmrod-shapedyes
69480yes97.196
69480positive100
119871positiverod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6497CASO 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
40093MEDIUM 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)
119871CIP Medium 291yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=291

culture temp

@refgrowthtypetemperaturerange
6497positivegrowth30mesophilic
31483positivegrowth10-40
31483positiveoptimum37mesophilic
40093positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31483positivegrowth08-11alkaliphile
31483positiveoptimum10

Physiology and metabolism

oxygen tolerance

  • @ref: 31483
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31483yes
69481yes100
69480yes100

compound production

  • @ref: 67770
  • compound: Hemicellulase

halophily

@refsaltgrowthtested relationconcentration
31483NaClpositivegrowth0-13 %
31483NaClpositiveoptimum7.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3148317057cellobiose+carbon source
3148328757fructose+carbon source
3148317234glucose+carbon source
3148317716lactose+carbon source
3148317306maltose+carbon source
3148329864mannitol+carbon source
3148337684mannose+carbon source
3148328053melibiose+carbon source
3148316634raffinose+carbon source
3148317814salicin+carbon source
3148330911sorbitol+carbon source
3148317992sucrose+carbon source
3148327082trehalose+carbon source
3148353424tween 20+carbon source
3148353423tween 40+carbon source
3148353425tween 60+carbon source
11987117632nitrate+reduction
11987116301nitrite-reduction

metabolite production

  • @ref: 119871
  • 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
119871oxidase-
119871alcohol dehydrogenase-1.1.1.1
119871catalase+1.11.1.6
119871lysine decarboxylase-4.1.1.18
119871ornithine decarboxylase-4.1.1.17
119871urease+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
119871-------------+-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6497soilSaitamaJapanJPNAsia
67770Soil
119871Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1056.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_608;97_711;98_830;99_1056&stattab=map
  • Last taxonomy: Alkalihalobacillus hemicellulosilyticus subclade
  • 16S sequence: AB043846
  • Sequence Identity:
  • Total samples: 798
  • soil counts: 257
  • aquatic counts: 149
  • animal counts: 362
  • plant counts: 30

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64971Risk group (German classification)
1198711Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6497
  • description: Bacillus hemicellulosilyticus gene for 16S rRNA
  • accession: AB043846
  • length: 1535
  • database: ena
  • NCBI tax ID: 127886

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus hemicellulosilyticus JCM 91521236971.4wgspatric1236971
66792Bacillus hemicellulosilyticus JCM 91521236971.3wgspatric1236971
66792Bacillus hemicellulosilyticus JCM 91522609459771draftimg1236971
67770Halalkalibacter hemicellulosilyticusJCM 9152GCA_000513115contigncbi1236971
67770Halalkalibacter hemicellulosilyticusJCM 9152GCA_001315065contigncbi1236971

GC content

@refGC-contentmethod
649736.8
6777033.6
6777036.8high performance liquid chromatography (HPLC)
6777038.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.805no
gram-positiveyes81.746yes
anaerobicno98.614yes
aerobicyes90.108yes
halophileyes54.466no
spore-formingyes94.946yes
glucose-utilyes89.689yes
flagellatedyes88.615no
thermophileno99.476no
glucose-fermentno90.803no

External links

@ref: 6497

culture collection no.: DSM 16731, JCM 9152, CIP 109021, FERM 3071

straininfo link

  • @ref: 70897
  • straininfo: 65679

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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6497Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16731)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16731
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
31483Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2778128776041
40093Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6716
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
70897Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID65679.1StrainInfo: A central database for resolving microbial strain identifiers
119871Curators of the CIPCollection of Institut Pasteur (CIP 109021)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109021