Strain identifier

BacDive ID: 23743

Type strain: Yes

Species: Gracilibacillus orientalis

Strain Designation: XH-63

Strain history: CIP <- 2006, CECT <- 2005, A. Ventosa: strain XH-63

NCBI tax ID(s): 334253 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 20962

BacDive-ID: 23743

DSM-Number: 28158

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

description: Gracilibacillus orientalis XH-63 is an aerobe, spore-forming, mesophilic bacterium that was isolated from salt lake.

NCBI tax id

  • NCBI tax id: 334253
  • Matching level: species

strain history

@refhistory
20962<- CECT; CECT 7097
121437CIP <- 2006, CECT <- 2005, A. Ventosa: strain XH-63

doi: 10.13145/bacdive23743.20230509.8.1

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 orientalis
  • full scientific name: Gracilibacillus orientalis Carrasco et al. 2006

@ref: 20962

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Gracilibacillus

species: Gracilibacillus orientalis

full scientific name: Gracilibacillus orientalis Carrasco et al. 2006

strain designation: XH-63

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31654positive02-10 µm0.7-0.9 µmrod-shapedyes
121437positiverod-shapedyes

pigmentation

  • @ref: 31654
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20962MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)yeshttps://mediadive.dsmz.de/medium/514bName: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 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
36592MEDIUM 174 - for Salinicoccus hispanicusyesSodium hydrogen carbonate (0.060 g);Distilled water make up to (1000.000 ml);Sodium chloride (81.000 g);Potassium chloride (2.000 g);Magnesium chloride hexahydrate(7.000 g);Magnesium sulphate heptahydrate (9.600 g);Calcium chloride dihydrate (0.360 g);Glu
121437CIP Medium 174yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=174

culture temp

@refgrowthtypetemperaturerange
20962positivegrowth37mesophilic
31654positivegrowth04-45
31654positiveoptimum37mesophilic
36592positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31654positivegrowth05-09alkaliphile
31654positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31654
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31654
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31654NaClpositivegrowth01-20 %
31654NaClpositiveoptimum10 %

observation

  • @ref: 31654
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3165430089acetate+carbon source
3165416947citrate+carbon source
3165415740formate+carbon source
3165433984fucose+carbon source
3165417716lactose+carbon source
3165430911sorbitol+carbon source
3165431011valerate+carbon source
12143717632nitrate-reduction
12143716301nitrite-reduction

metabolite production

  • @ref: 121437
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31654catalase+1.11.1.6
121437oxidase-
121437catalase+1.11.1.6
121437urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121437---+-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20962salt lakeInner Mongolia near Xilin HotChinaCHNAsia
121437Environment, Salt lake near Xilin Hot in Inner MongoliaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_108119.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2444;97_7991;98_13791;99_108119&stattab=map
  • Last taxonomy: Gracilibacillus orientalis
  • 16S sequence: AM040716
  • Sequence Identity:
  • Total samples: 14
  • soil counts: 5
  • aquatic counts: 6
  • animal counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
209621Risk group (German classification)
1214371Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20962
  • description: Gracilibacillus orientalis partial 16S rRNA gene, type strain XH-63T
  • accession: AM040716
  • length: 1453
  • database: ena
  • NCBI tax ID: 334253

GC content

  • @ref: 31654
  • GC-content: 36.1-37.1

External links

@ref: 20962

culture collection no.: DSM 28158, AS 1.4250, CCM 7326, CECT 7097, CIP 109259

straininfo link

  • @ref: 87780
  • straininfo: 290973

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16514034Gracilibacillus orientalis sp. nov., a novel moderately halophilic bacterium isolated from a salt lake in Inner Mongolia, China.Carrasco IJ, Marquez MC, Yanfen X, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.63971-02006Bacillaceae/chemistry/*classification/genetics/*isolation & purification, China, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium ChloridePhenotype
Phylogeny18842841Gracilibacillus lacisalsi sp. nov., a halophilic Gram-positive bacterium from a salt lake in China.Jeon CO, Lim JM, Jang HH, Park DJ, Xu LH, Jiang CL, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65369-02008Bacillaceae/chemistry/*classification/*genetics/isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Phenotype, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, *Water MicrobiologyGenetics
Phylogeny18842864Gracilibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from saline soil.Chen YG, Cui XL, Zhang YQ, Li WJ, Wang YX, Xu LH, Peng Q, Wen ML, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.65698-02008Bacillaceae/chemistry/*classification/*genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny19542126Gracilibacillus saliphilus sp. nov., a moderately halophilic bacterium isolated from a salt lake.Tang SK, Wang Y, Lou K, Mao PH, Jin X, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.006569-02009Bacillaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny27572507Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.Oh YJ, Lee HW, Lim SK, Kwon MS, Lee J, Jang JY, Park HW, Nam YD, Seo MJ, Choi HJJ Microbiol10.1007/s12275-016-6349-42016Bacillaceae/classification/genetics/*isolation & purification/metabolism, Base Composition, Brassica/metabolism/*microbiology, Fatty Acids/metabolism, Fermentation, Phylogeny, Sodium Chloride/*metabolism, Vegetables/metabolism/*microbiologyMetabolism
Phylogeny32416748Gracilibacillus salitolerans sp. nov., a moderate halophile isolated from saline soil in Northwest China.Gan L, Li X, Chen J, Zhang S, Zhang R, Peng B, Tian YInt J Syst Evol Microbiol10.1099/ijsem.0.0042242020Bacillaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Sodium Chloride, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20962Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28158Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28158)
31654Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172793628776041
36592Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6980
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
87780Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID290973.1
121437Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109259Collection of Institut Pasteur (CIP 109259)