Strain identifier
BacDive ID: 23743
Type strain:
Species: Gracilibacillus orientalis
Strain Designation: XH-63
Strain history: CIP <- 2006, CECT <- 2005, A. Ventosa: strain XH-63
NCBI tax ID(s): 334253 (species)
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
@ref | history |
---|---|
20962 | <- CECT; CECT 7097 |
121437 | CIP <- 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
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
31654 | positive | 02-10 µm | 0.7-0.9 µm | rod-shaped | yes |
121437 | positive | rod-shaped | yes |
pigmentation
- @ref: 31654
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
20962 | MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b) | yes | https://mediadive.dsmz.de/medium/514b | Name: 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 |
36592 | MEDIUM 174 - for Salinicoccus hispanicus | yes | Sodium 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 | |
121437 | CIP Medium 174 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=174 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20962 | positive | growth | 37 | mesophilic |
31654 | positive | growth | 04-45 | |
31654 | positive | optimum | 37 | mesophilic |
36592 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31654 | positive | growth | 05-09 | alkaliphile |
31654 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 31654
- oxygen tolerance: aerobe
spore formation
- @ref: 31654
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31654 | NaCl | positive | growth | 01-20 % |
31654 | NaCl | positive | optimum | 10 % |
observation
- @ref: 31654
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31654 | 30089 | acetate | + | carbon source |
31654 | 16947 | citrate | + | carbon source |
31654 | 15740 | formate | + | carbon source |
31654 | 33984 | fucose | + | carbon source |
31654 | 17716 | lactose | + | carbon source |
31654 | 30911 | sorbitol | + | carbon source |
31654 | 31011 | valerate | + | carbon source |
121437 | 17632 | nitrate | - | reduction |
121437 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 121437
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31654 | catalase | + | 1.11.1.6 |
121437 | oxidase | - | |
121437 | catalase | + | 1.11.1.6 |
121437 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121437 | - | - | - | + | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
20962 | salt lake | Inner Mongolia near Xilin Hot | China | CHN | Asia |
121437 | Environment, Salt lake near Xilin Hot in Inner Mongolia | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
20962 | 1 | Risk group (German classification) |
121437 | 1 | Risk 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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16514034 | Gracilibacillus 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 A | Int J Syst Evol Microbiol | 10.1099/ijs.0.63971-0 | 2006 | Bacillaceae/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 Chloride | Phenotype |
Phylogeny | 18842841 | Gracilibacillus 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 CJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.65369-0 | 2008 | Bacillaceae/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 Microbiology | Genetics |
Phylogeny | 18842864 | Gracilibacillus 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 CL | Int J Syst Evol Microbiol | 10.1099/ijs.0.65698-0 | 2008 | Bacillaceae/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/chemistry | Genetics |
Phylogeny | 19542126 | Gracilibacillus 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 WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.006569-0 | 2009 | Bacillaceae/*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 Specificity | Genetics |
Phylogeny | 27572507 | Gracilibacillus 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 HJ | J Microbiol | 10.1007/s12275-016-6349-4 | 2016 | Bacillaceae/classification/genetics/*isolation & purification/metabolism, Base Composition, Brassica/metabolism/*microbiology, Fatty Acids/metabolism, Fermentation, Phylogeny, Sodium Chloride/*metabolism, Vegetables/metabolism/*microbiology | Metabolism |
Phylogeny | 32416748 | Gracilibacillus 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 Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004224 | 2020 | Bacillaceae/*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/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||||
20962 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28158 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28158) | ||||
31654 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27936 | 28776041 | ||
36592 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6980 | |||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 beta | https://microbeatlas.org/ | ||||
87780 | Reimer, 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 identifiers | 10.60712/SI-ID290973.1 | ||||
121437 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109259 | Collection of Institut Pasteur (CIP 109259) |