Strain identifier

BacDive ID: 1199

Type strain: No

Species: Halalkalibacterium halodurans

Strain Designation: No. 44, 44

Strain history: CIP <- 2011, DSMZ, Bacillus okuhidensis <- GTC <- Shuzo and Yamagata, Gifu, Japan: strain 44

NCBI tax ID(s): 86665 (species)

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General

@ref: 4948

BacDive-ID: 1199

DSM-Number: 13666

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, thermophilic, motile

description: Halalkalibacterium halodurans No. 44 is an obligate aerobe, spore-forming, thermophilic bacterium of the family Bacillaceae.

NCBI tax id

  • NCBI tax id: 86665
  • Matching level: species

strain history

@refhistory
4948<- Z. Li; GTC 854 <- Shuzo and Yamagata; No. 44
67770GTC 854 <-- S. Yamagata No. 44.
119802CIP <- 2011, DSMZ, Bacillus okuhidensis <- GTC <- Shuzo and Yamagata, Gifu, Japan: strain 44

doi: 10.13145/bacdive1199.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halalkalibacterium
  • species: Halalkalibacterium halodurans
  • full scientific name: Halalkalibacterium halodurans (Nielsen et al. 1995 ex Boyer et al. 1973) Joshi et al. 2022

  • synonyms

    @refsynonym
    20215Bacillus alcalophilus subsp. halodurans
    20215Bacillus okuhidensis
    20215Bacillus halodurans
    20215Alkalihalobacillus halodurans
    20215Alkalihalobacillus okuhidensis

@ref: 4948

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Halalkalibacterium

species: Halalkalibacterium halodurans

full scientific name: Alkalihalobacillus okuhidensis (Li et al. 2002) Patel and Gupta 2020

strain designation: No. 44, 44

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.69
69480100positive
119802yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4948BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215; with strain-specific modifications) Composition: Brain heart infusion 37.0 g/l MnSO4 0.01 g/l Distilled water
33150MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119802CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4948positivegrowth45thermophilic
33150positivegrowth45thermophilic
67770positivegrowth45thermophilic
119802positivegrowth22-55
119802nogrowth10psychrophilic

culture pH

  • @ref: 119802
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 119802
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
119802yes

halophily

  • @ref: 119802
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

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
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose+builds acid from28053
68371esculin+builds acid from4853
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
119802citrate-carbon source16947
119802esculin+hydrolysis4853
119802hippurate-hydrolysis606565
119802nitrate+reduction17632
119802nitrite-reduction16301

metabolite production

  • @ref: 119802
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11980215688acetoin-
11980217234glucose-

enzymes

@refvalueactivityec
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
119802oxidase+
119802beta-galactosidase+3.2.1.23
119802alcohol dehydrogenase-1.1.1.1
119802gelatinase+
119802amylase+
119802DNase+
119802caseinase+3.4.21.50
119802catalase+1.11.1.6
119802tween esterase+
119802gamma-glutamyltransferase-2.3.2.2
119802lysine decarboxylase-4.1.1.18
119802ornithine decarboxylase-4.1.1.17
119802urease-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
119802--+--+-----+++-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119802+/---+++---+/-+/-+/-+/-----+/----+/-+/-+/-++/-+/-+/-+/-++/-+/---+/-+/-+/----------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119802+++++-++++++++++++++++++-+-----+++-+-----+-------++--++----+++--+--------+-+----+-----+-+++-+++-+-+

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
4948Gifu, Okuhida Spa areaJapanJPNAsia
67770Gifu Pref.JapanJPNAsiaWater sample obtained from the Okuhida hot spa area
119802Okuhida hot spa areaJapanJPNAsiaEnvironment, Water

taxonmaps

  • @ref: 69479
  • File name: preview.99_4299.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2160;97_2613;98_3236;99_4299&stattab=map
  • Last taxonomy: Alkalihalobacillus halodurans
  • 16S sequence: LC379066
  • Sequence Identity:
  • Total samples: 6986
  • soil counts: 1545
  • aquatic counts: 1519
  • animal counts: 3493
  • plant counts: 429

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49481Risk group (German classification)
1198021Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus sp. GTC854 gene for 16S rRNA, partial sequenceAB0476841452ena136160
67770Alkalihalobacillus halodurans gene for 16S rRNA, partial sequence, strain: JCM 10945LC3790661472ena86665

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus okuhidensis strain DSM 13666136160.3wgspatric136160
66792Bacillus okuhidensis DSM 136662648501690draftimg136160
67770Halalkalibacterium halodurans DSM 13666GCA_001274915contigncbi86665

GC content

@refGC-contentmethod
494841
6777041high performance liquid chromatography (HPLC)
6777043.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes91.416no
gram-positiveyes80.993no
anaerobicno98.093no
halophileyes68.733no
spore-formingyes96.446no
thermophileno90.005no
glucose-utilyes90.426no
flagellatedyes85.718no
aerobicyes87.1no
glucose-fermentno91.595no

External links

@ref: 4948

culture collection no.: DSM 13666, CIP 107631, JCM 10945, GTC 854, KCTC 3795

straininfo link

  • @ref: 70855
  • straininfo: 49505

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12148629Bacillus okuhidensis sp. nov., isolated from the Okuhida spa area of Japan.Li Z, Kawamura Y, Shida O, Yamagata S, Deguchi T, Ezaki TInt J Syst Evol Microbiol10.1099/00207713-52-4-12052002Bacillus/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Ribosomal/analysis, Fresh Water/*microbiology, *Hot Temperature, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAStress
Phylogeny26612462Bacillus oceani sp. nov., isolated from seawater.Song L, Liu H, Wang J, Huang Y, Dai X, Han X, Zhou YInt J Syst Evol Microbiol10.1099/ijsem.0.0007932015
Phylogeny31436524Genome-based reclassification of Bacillus okuhidensis as a later heterotypic synonym of Bacillus halodurans.Liu GH, Narsing Rao MP, Dong ZY, Wang JP, Che JM, Chen QQ, Sengonca C, Liu B, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0036662019Bacillus/*classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Genome, Bacterial, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4948Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13666)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13666
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
33150Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5088
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/
68371Automatically annotated from API 50CH acid
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
70855Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49505.1StrainInfo: A central database for resolving microbial strain identifiers
119802Curators of the CIPCollection of Institut Pasteur (CIP 107631)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107631