Strain identifier

BacDive ID: 1462

Type strain: Yes

Species: Gracilibacillus quinghaiensis

Strain history: CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM KN4, 2008 <- Xiao-Long Cui: strain YIM C229

NCBI tax ID(s): 470774 (species)

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General

@ref: 7144

BacDive-ID: 1462

DSM-Number: 17858

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

description: Gracilibacillus quinghaiensis DSM 17858 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from sediment.

NCBI tax id

  • NCBI tax id: 470774
  • Matching level: species

strain history

@refhistory
7144<- Xiao-Long Cui; YIM-C229
122096CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM KN4, 2008 <- Xiao-Long Cui: strain YIM C229

doi: 10.13145/bacdive1462.20230509.8.1

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 quinghaiensis
  • full scientific name: Gracilibacillus quinghaiensis Chen et al. 2008

@ref: 7144

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Gracilibacillus

species: Gracilibacillus quinghaiensis

full scientific name: Gracilibacillus quinghaiensis Chen et al. 2008

type strain: yes

Morphology

cell morphology

  • @ref: 122096
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7144BACTO 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
33888Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122096CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7144positivegrowth30mesophilic
33888positivegrowth30mesophilic
122096positivegrowth15-37
122096nogrowth5psychrophilic
122096nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122096
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 122096
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
122096NaClnogrowth0 %
122096NaClnogrowth2 %
122096NaClnogrowth4 %
122096NaClnogrowth6 %
122096NaClnogrowth8 %
122096NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate-reduction
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12209617108D-arabinose-degradation
12209615824D-fructose-degradation
12209617634D-glucose-degradation
12209616024D-mannose-degradation
12209665327D-xylose-degradation
12209617057cellobiose-degradation
12209617716lactose-degradation
12209617306maltose-degradation
12209617814salicin-degradation
12209617992sucrose-degradation
12209616947citrate-carbon source
1220964853esculin+hydrolysis
12209617234glucose-fermentation
12209617716lactose-fermentation
12209617632nitrate-reduction
12209616301nitrite-reduction
122096132112sodium thiosulfate-builds gas from
12209617632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12209635581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12209615688acetoin-
12209617234glucose-

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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
122096oxidase+
122096beta-galactosidase+3.2.1.23
122096alcohol dehydrogenase-1.1.1.1
122096gelatinase-
122096amylase-
122096caseinase+3.4.21.50
122096catalase+1.11.1.6
122096tween esterase+
122096gamma-glutamyltransferase+2.3.2.2
122096lecithinase-
122096lipase-
122096lysine decarboxylase-4.1.1.18
122096ornithine decarboxylase-4.1.1.17
122096phenylalanine ammonia-lyase-4.3.1.24
122096protease-
122096tryptophan deaminase-
122096urease-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
122096-+++---------+------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUNO2N2
122096--------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122096------------------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7144sedimentXiaochaidamu salt lake, Qaidam Basin, Qinghai ProvinceChinaCHNAsia
122096Environment, SedimentQinghaiChinaCHNAsia2002

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4990.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2444;97_2979;98_3731;99_4990&stattab=map
  • Last taxonomy: Gracilibacillus
  • 16S sequence: EU135723
  • Sequence Identity:
  • Total samples: 580
  • soil counts: 251
  • aquatic counts: 111
  • animal counts: 166
  • plant counts: 52

Safety information

risk assessment

  • @ref: 122096
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7144
  • description: Gracilibacillus quinghaiensis strain YIM-C229 16S ribosomal RNA gene, partial sequence
  • accession: EU135723
  • length: 1517
  • database: ena
  • NCBI tax ID: 470774

GC content

  • @ref: 7144
  • GC-content: 40.9

External links

@ref: 7144

culture collection no.: DSM 17858, CGMCC 1.6304, YIM C229, CIP 108074

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18571887Gracilibacillus quinghaiensis sp. nov., isolated from salt-lake sediment in the Qaidam Basin, north-west China.Chen YG, Cui XL, Zhang YQ, Li WJ, Wang YX, Xu LH, Peng Q, Wen ML, Jiang CLSyst Appl Microbiol10.1016/j.syapm.2008.05.0012008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Gram-Positive Endospore-Forming Rods/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium ChlorideGenetics
Phylogeny21984665Gracilibacillus bigeumensis sp. nov., a moderately halophilic bacterium from solar saltern soil.Kim P, Lee JC, Park DJ, Shin KS, Kim JY, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.034264-02011Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride, Soil/analysis, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitle
7144Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17858)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17858
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
33888Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5656
68368Automatically annotated from API 20E
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
122096Curators of the CIPCollection of Institut Pasteur (CIP 108074)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108074