Strain identifier

BacDive ID: 1460

Type strain: Yes

Species: Gracilibacillus halotolerans

Strain Designation: NN

Strain history: DSM 11805 <-- M. Wainø strain NN.

NCBI tax ID(s): 74386 (species)

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General

@ref: 4494

BacDive-ID: 1460

DSM-Number: 11805

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, halotolerant, chemoorganotroph, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, colony-forming, pigmented

description: Gracilibacillus halotolerans NN is an obligate aerobe, halotolerant, chemoorganotroph bacterium that forms circular colonies and has a creamy white pigmentation.

NCBI tax id

  • NCBI tax id: 74386
  • Matching level: species

strain history

@refhistory
4494<- K. Ingvorsen, NN
67770DSM 11805 <-- M. Wainø strain NN.

doi: 10.13145/bacdive1460.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Gracilibacillus
  • species: Gracilibacillus halotolerans
  • full scientific name: Gracilibacillus halotolerans Wainø et al. 1999

@ref: 4494

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Gracilibacillus

species: Gracilibacillus halotolerans

full scientific name: Gracilibacillus halotolerans Wainø et al. 1999

strain designation: NN

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23041positive2.0-5.0 µm0.4-0.6 µmrod-shapedyesperitrichous
69480yes95.443
69480positive100

colony morphology

  • @ref: 23041
  • colony size: 2.0 mm
  • colony color: creamy white
  • colony shape: circular
  • incubation period: 5 days
  • medium used: GSL-2 agar medium

pigmentation

  • @ref: 23041
  • production: yes
  • color: creamy white

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4494GRACILIBACILLUS MEDIUM (DSMZ Medium 802)yeshttps://mediadive.dsmz.de/medium/802Name: GRACILIBACILLUS MEDIUM (DSMZ Medium 802) Composition: NaCl 100.0 g/l KH2PO4 23.4 g/l MgSO4 x 7 H2O 20.0 g/l Tris-HCl 12.0 g/l Glucose 2.0 g/l KCl 2.0 g/l Yeast extract 2.0 g/l Trypticase peptone 2.0 g/l NaBr 0.1 g/l FeCl2 x 4 H2O 0.04 g/l MnCl2 x 4 H2O 0.04 g/l HCl 0.0064 g/l CoCl2 x 6 H2O 0.00049505 g/l ZnCl2 0.000138614 g/l NiCl2 x 6 H2O 0.000138614 g/l AlCl3 x 6 H2O 0.000118812 g/l Na2MoO4 x 2 H2O 7.9208e-05 g/l Na2WO4 x 2 H2O 1.18812e-05 g/l H3BO3 1.18812e-05 g/l CuCl2 x 2 H2O 3.9604e-06 g/l CaCl2 Distilled water
4494BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
23041GSL-2 agar mediumyes
23041Tris-mediumyescontaining (1-l distilled water) (pH 7.8): NaCl,1OOg; MgSO4.7H2O, 20g; KCl, 5g; (NH4)2SO4, 2g; NaBr, 0.1g; yeast extract (Difco), 2g; trypticase peptone (BBL),1g; Tris/HCl, 12g; trace metal solution (TMS 3), 2ml; KH2PO4 (50 g l-1), 10ml; CaCl2.2H2O, (100 g 1-l), 5ml and FeCl2/MnCl2 solution, 2ml

culture temp

@refgrowthtypetemperaturerange
4494positivegrowth30mesophilic
23041positivegrowth6.0-50.0
23041positiveoptimum47.0thermophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
23041positivegrowth5.0-10.0alkaliphile
23041positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 23041
  • oxygen tolerance: obligate aerobe

nutrition type

  • @ref: 23041
  • type: chemoorganotroph

spore formation

@refspore descriptiontype of sporespore formationconfidence
23041ellipsoid,terminal,in swollen sporangiaendosporeyes
69481yes100
69480yes99.999

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23041halotolerantNaClpositivegrowth0.0-20.0 %(w/v)
23041NaCloptimum0.0 %

murein

  • @ref: 23041
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2304117234glucose-fermentation
2304118222xylose-fermentation
2304127856acetamide-growth
2304130089acetate-growth
2304115347acetone-growth
2304117128adipate-growth
2304140813anisic acid-growth
2304135391aspartate-growth
2304128179benzamide-growth
2304116150benzoate-growth
2304117750betaine-growth
2304128885butanol-growth
2304117968butyrate-growth
2304125646octanoate-growth
2304162968cellulose-growth
2304116947citrate-growth
23041coconut oil-growth
23041crab shell chitin-growth
2304117924D-sorbitol-growth
2304116236ethanol-growth
2304116000ethanolamine-growth
2304115740formate-growth
2304133984fucose-growth
2304129806fumarate-growth
2304117859glutaric acid-growth
2304129805glycolate-growth
2304136655glyoxylate-growth
2304117120hexanoate-growth
2304116977L-alanine-growth
2304116467L-arginine-growth
2304117561L-cysteine-growth
2304129985L-glutamate-growth
2304118019L-lysine-growth
2304116643L-methionine-growth
2304115729L-ornithine-growth
2304117295L-phenylalanine-growth
2304117203L-proline-growth
2304117115L-serine-growth
2304116857L-threonine-growth
2304124996lactate-growth
2304117790methanol-growth
2304116830methylamine-growth
2304132544nicotinate-growth
23041oil of cedar wood-growth
2304144884pentanol-growth
2304138184picolinate-growth
2304128831propanol-growth
2304117272propionate-growth
2304115361pyruvate-growth
2304130031succinate-growth
2304145373sulfanilamide-growth
2304127897tryptophan-growth
2304131011valerate-growth
23041casein-hydrolysis
2304117634D-glucose+builds acid from
2304116899D-mannitol+builds acid from
2304165327D-xylose+builds acid from
2304128102amylose+growth
2304122599arabinose+growth
2304122651ascorbate+growth
2304117057cellobiose+growth
2304115824D-fructose+growth
2304112936D-galactose+growth
2304118024D-galacturonic acid+growth
230418391D-gluconate+growth
2304115748D-glucuronate+growth
2304116024D-mannose+growth
230416731melezitose+growth
2304128053melibiose+growth
2304116551D-trehalose+growth
2304165327D-xylose+growth
2304117234glucose+growth
2304117754glycerol+growth
2304128087glycogen+growth
2304115443inulin+growth
2304115589L-malate+growth
2304162345L-rhamnose+growth
2304117716lactose+growth
2304117306maltose+growth
2304129864mannitol+growth
23041506227N-acetylglucosamine+growth
23041309162-oxoglutarate+growth
2304116634raffinose+growth
2304128017starch+growth
2304117992sucrose+growth
2304118139trimethylamine+growth
2304153426tween 80+growth
230414853esculin+hydrolysis
230415291gelatin+hydrolysis
2304128017starch+hydrolysis
2304153426tween 80+hydrolysis
2304116199urea+hydrolysis
2304117632nitrate+reduction
23041yeast extract+required for growth

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2304128971ampicillinyesyes
2304117833gentamicinyesyes
230416104kanamycinyesyes
23041100147nalidixic acidyesyes
230417507neomycinyesyes
2304127902tetracyclineyesyes
2304128669bacitracinyesyes
230413393carbenicillinyesyes
2304117698chloramphenicolyesyes
2304148923erythromycinyesyes
2304128368novobiocinyesyes
2304117334penicillinyesyes
2304128077rifampicinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2304135581indoleno
2304115688acetoinno
2304116136hydrogen sulfideyes

metabolite tests

  • @ref: 23041
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
23041alkaline phosphatase+3.1.3.1
23041arginine dihydrolase-3.5.3.6
23041beta-galactosidase+3.2.1.23
23041catalase+1.11.1.6
23041chitinase-3.2.1.14
23041cytochrome oxidase+1.9.3.1
23041lecithinase-
23041lysine decarboxylase-4.1.1.18
23041ornithine decarboxylase-4.1.1.17
23041phenylalanine deaminase-4.3.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture composition
23041surface mudGreat Salt Lake,UtahUSAUSANorth Americaliquid GSL-2 mediumcontaining of (1-1 distilled water): NaCl, 100g; MgSO4.7H2O, 10g; KCl, 5g; NH4Cl, 2g; NaHCO3, 1g; citric acid, 0.5g; yeast extract (Difco), 2g; trypticase peptone (BBL), 2g; trace metal solution (TMS 3), 2ml; KH2PO4 (50 g l-1),10 ml; CaCl2.2H2O (20 g 1-l),10;FeCl2/MnCl2 solution [FeCl2.4H2O (20 gl-1) + MnCl2.4H2O (20 gl-1)], 2ml and Glucose (0.2% w/v)
4494Utah, Great Salt LakeUSAUSANorth America
67770Surface mud, the Great Salt LakeUTUSAUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Mud (Sludge)

Safety information

risk assessment

  • @ref: 4494
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gracilibacillus halotolerans isolate Gh10 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723657439ena74386
20218Gracilibacillus halotolerans isolate Gh19 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723658592ena74386
4494Gracilibacillus halotolerans 16S ribosomal RNA gene, complete sequenceAF0369221541ena74386

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gracilibacillus halotolerans DSM 11805GCA_014206945scaffoldncbi74386
66792Gracilibacillus halotolerans strain DSM 1180574386.3wgspatric74386
66792Gracilibacillus halotolerans DSM 118052829726240draftimg74386

GC content

@refGC-contentmethod
2304138
6777038high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes76.968no
gram-positiveyes93.082yes
anaerobicno99.138yes
aerobicyes88.302no
halophileyes83.057no
spore-formingyes94.27yes
glucose-utilyes89.305yes
thermophileno86.072no
motileyes88.207yes
glucose-fermentno88.197yes

External links

@ref: 4494

culture collection no.: DSM 11805, JCM 10718, ATCC 700849

straininfo link

  • @ref: 71107
  • straininfo: 44174

literature

  • topic: Phylogeny
  • Pubmed-ID: 10319508
  • title: Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov.
  • authors: Waino M, Tindall BJ, Schumann P, Ingvorsen K
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-2-821
  • year: 1999
  • mesh: Bacillus/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Gram-Positive Endospore-Forming Rods/chemistry/*classification/genetics/physiology, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Spores, Bacterial/physiology, Utah, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4494Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11805)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11805
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
23041Michael Waino,B. J. Tindall,Peter Schumann,Kjeld Ingvorsen10.1099/00207713-49-2-821Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov.IJSEM 49: 821-831 199910319508
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/
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
71107Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44174.1StrainInfo: A central database for resolving microbial strain identifiers