Strain identifier

BacDive ID: 1459

Type strain: Yes

Species: Gracilibacillus dipsosauri

Strain Designation: DD1

Strain history: CIP <- 1997, NCIMB <- 1994, C.E. Deutch

NCBI tax ID(s): 178340 (species)

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General

@ref: 4217

BacDive-ID: 1459

DSM-Number: 11125

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

description: Gracilibacillus dipsosauri DD1 is an obligate aerobe, chemoorganotroph, spore-forming bacterium that forms circular colonies and was isolated from salt glands of nasal cavity of Dipsosaurus dorsalis .

NCBI tax id

  • NCBI tax id: 178340
  • Matching level: species

strain history

@refhistory
4217<- NCFB
118943CIP <- 1997, NCIMB <- 1994, C.E. Deutch

doi: 10.13145/bacdive1459.20230509.8.1

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 dipsosauri
  • full scientific name: Gracilibacillus dipsosauri (Lawson et al. 1996) Wainø et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Bacillus dipsosauri

@ref: 4217

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Gracilibacillus

species: Gracilibacillus dipsosauri

full scientific name: Gracilibacillus dipsosauri (Lawson et al. 1996) Wainø et al. 1999

strain designation: DD1

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
23041positiveyes
69480yes97.635
69480positive100
118943positiveyesrod-shaped

colony morphology

@refcolony shape
23041circular
118943

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4217TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535; with strain-specific modifications) Composition: Soil extract 500.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
4217NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
36591MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118943CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4217positivegrowth30mesophilic
36591positivegrowth30mesophilic
118943positivegrowth22-45
118943nogrowth10psychrophilic
118943nogrowth55thermophilic

culture pH

  • @ref: 118943
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 118943
  • oxygen tolerance: obligate aerobe

nutrition type

  • @ref: 23041
  • type: chemoorganotroph

spore formation

@refspore descriptiontype of sporespore formationconfidence
23041terminal,in swollen sporangiaendosporeyes
69481yes100
69480yes100
118943yes

halophily

@refsaltgrowthtested relationconcentration
118943NaClpositivegrowth2-10 %
118943NaClnogrowth0 %

murein

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
23041casein-hydrolysis
23041glucose+growth17234
23041mannitol+growth29864
23041sucrose+growth17992
23041esculin+hydrolysis4853
23041gelatin+hydrolysis5291
23041starch+hydrolysis28017
23041nitrate+reduction17632
23041yeast extract+required for growth
118943citrate-carbon source16947
118943esculin+hydrolysis4853
118943nitrate+reduction17632
118943nitrite-reduction16301
118943nitrate-respiration17632

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2304128971ampicillinyesyes
2304117698chloramphenicolyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2304135581indoleno
2304115688acetoinno
11894335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2304115688acetoin-
11894315688acetoin-
11894317234glucose-

enzymes

@refvalueactivityec
23041arginine dihydrolase-3.5.3.6
23041beta-galactosidase+3.2.1.23
23041catalase+1.11.1.6
23041cytochrome oxidase+1.9.3.1
23041lysine decarboxylase-4.1.1.18
23041ornithine decarboxylase-4.1.1.17
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
118943oxidase-
118943beta-galactosidase+3.2.1.23
118943alcohol dehydrogenase-1.1.1.1
118943gelatinase-
118943amylase+
118943DNase-
118943caseinase-3.4.21.50
118943catalase+1.11.1.6
118943tween esterase-
118943gamma-glutamyltransferase-2.3.2.2
118943lysine decarboxylase-4.1.1.18
118943ornithine decarboxylase-4.1.1.17
118943urease-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
118943-+++--------++--+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118943---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
4217salt glands of nasal cavity of Dipsosaurus dorsalis (desert iguana)Dipsosaurus dorsalisUSAUSANorth America
118943Nasal salts glands of a desert iguana1994

isolation source categories

Cat1Cat2
#Host#Reptilia
#Host Body-Site#Oral cavity and airways
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_14475.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2444;97_7991;98_10968;99_14475&stattab=map
  • Last taxonomy: Gracilibacillus dipsosauri
  • 16S sequence: X82436
  • Sequence Identity:
  • Total samples: 3582
  • soil counts: 2215
  • aquatic counts: 371
  • animal counts: 588
  • plant counts: 408

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42171Risk group (German classification)
1189431Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gracilibacillus dipsosauri 16S rRNA geneX824361459ena178340
20218Gracilibacillus dipsosauri gene for 16S rRNA, partial sequenceAB1015911514ena178340
20218Gracilibacillus dipsosauri isolate Gd3 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723654789ena178340
20218Gracilibacillus dipsosauri isolate Gd5 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723655659ena178340
20218Gracilibacillus dipsosauri isolate Gd6 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723656507ena178340

Genome sequences

  • @ref: 66792
  • description: Gracilibacillus dipsosauri DD1
  • accession: GCA_003176895
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 178340

GC content

  • @ref: 4217
  • GC-content: 39.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes90.82no
gram-positiveyes89.131yes
anaerobicno98.825no
halophileyes84.283no
spore-formingyes95.588no
glucose-utilyes88.453yes
aerobicyes90.96no
thermophileno99.088no
motileyes93.274yes
glucose-fermentno83.334no

External links

@ref: 4217

culture collection no.: DSM 11125, NCFB 3027, CIP 105095

straininfo link

  • @ref: 71106
  • straininfo: 11850

literature

  • topic: Phylogeny
  • Pubmed-ID: 19671721
  • title: Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline-alkaline soil.
  • authors: Huo YY, Xu XW, Cui HL, Wu M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.016808-0
  • year: 2009
  • mesh: Base Composition, DNA, Bacterial/genetics, Gram-Positive Endospore-Forming Bacteria/classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Spores, Bacterial/classification/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4217Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11125)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11125
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
36591Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17075
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
71106Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11850.1StrainInfo: A central database for resolving microbial strain identifiers
118943Curators of the CIPCollection of Institut Pasteur (CIP 105095)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105095