Strain identifier

BacDive ID: 1461

Type strain: Yes

Species: Gracilibacillus boraciitolerans

Strain Designation: T-16x

Strain history: CIP <- 2007, DSMZ <- I. Ahmed, Tokyo Univ., Yayoi, Japan: strain T-16X

NCBI tax ID(s): 1298598 (strain), 307521 (species)

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General

@ref: 6857

BacDive-ID: 1461

DSM-Number: 17256

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

description: Gracilibacillus boraciitolerans T-16x is a facultative anaerobe, halotolerant, spore-forming bacterium that forms circular colonies and has a light pink to red pigmentation.

NCBI tax id

NCBI tax idMatching level
307521species
1298598strain

strain history

@refhistory
6857<- I. Ahmed, strain T-16X
67770IAM 15263 <-- I. Ahmed T-16X.
116840CIP <- 2007, DSMZ <- I. Ahmed, Tokyo Univ., Yayoi, Japan: strain T-16X

doi: 10.13145/bacdive1461.20230509.8.1

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 boraciitolerans
  • full scientific name: Gracilibacillus boraciitolerans Ahmed et al. 2007

@ref: 6857

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Gracilibacillus

species: Gracilibacillus boraciitolerans

full scientific name: Gracilibacillus boraciitolerans Ahmed et al. 2007

strain designation: T-16x

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
23040positive2.0-4.5 µm0.3-0.9 µmrod-shapedyesmonotrichous
116840positiverod-shapedno

colony morphology

  • @ref: 23040
  • colony size: 2.0-3.0 mm
  • colony color: Light pink to red
  • colony shape: circular
  • incubation period: 4 days
  • medium used: BUG agar medium (pH 7.5)

pigmentation

  • @ref: 23040
  • production: yes
  • color: light pink to red

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6857CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23040BUG agar medium (pH 7.5)yes
36593MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116840CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6857positivegrowth30mesophilic
23040positivegrowth16.0-37.0
23040nogrowth>45.0thermophilic
23040positiveoptimum25.0-28.0mesophilic
36593positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
23040positivegrowth6.0-10.0alkaliphile
23040positiveoptimum7.5-8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 116840
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 23040
  • spore description: spherical or ellipsoidal,terminal or subterminal,in non-swollen or slightly swollen sporangium
  • type of spore: endospore
  • spore formation: yes

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23040halotolerantNaClpositivegrowth11.0 %(w/v)
23040NaClpositivegrowth0.0-11.0 %(w/v)

murein

  • @ref: 23040
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23040168082-dehydro-D-gluconate-builds acid from
23040174265-dehydro-D-gluconate-builds acid from
2304027613amygdalin-builds acid from
2304018305arbutin-builds acid from
2304015963ribitol-builds acid from
2304017108D-arabinose-builds acid from
2304018333D-arabitol-builds acid from
2304028847D-fucose-builds acid from
2304012936D-galactose-builds acid from
2304062318D-lyxose-builds acid from
230406731melezitose-builds acid from
2304016634raffinose-builds acid from
2304017992sucrose-builds acid from
2304016443D-tagatose-builds acid from
2304032528turanose-builds acid from
2304016813galactitol-builds acid from
2304017113erythritol-builds acid from
2304028066gentiobiose-builds acid from
2304024265gluconate-builds acid from
2304017754glycerol-builds acid from
2304028087glycogen-builds acid from
2304017268myo-inositol-builds acid from
2304015443inulin-builds acid from
2304018403L-arabitol-builds acid from
2304018287L-fucose-builds acid from
2304062345L-rhamnose-builds acid from
2304017266L-sorbose-builds acid from
2304065328L-xylose-builds acid from
23040320061methyl alpha-D-glucopyranoside-builds acid from
2304043943methyl alpha-D-mannoside-builds acid from
23040506227N-acetylglucosamine-builds acid from
2304017814salicin-builds acid from
2304028017starch-builds acid from
2304017151xylitol-builds acid from
2304016947citrate-carbon source
2304027897tryptophan-energy source
230405291gelatin-hydrolysis
2304016199urea-hydrolysis
2304017632nitrate-reduction
2304017057cellobiose+builds acid from
2304015824D-fructose+builds acid from
2304017634D-glucose+builds acid from
2304017716lactose+builds acid from
2304017306maltose+builds acid from
2304016899D-mannitol+builds acid from
2304016024D-mannose+builds acid from
2304028053melibiose+builds acid from
2304016988D-ribose+builds acid from
2304017924D-sorbitol+builds acid from
2304016551D-trehalose+builds acid from
2304065327D-xylose+builds acid from
230404853esculin+builds acid from
2304030849L-arabinose+builds acid from
2304074863methyl beta-D-xylopyranoside+builds acid from
2304016651(S)-lactate+respiration
23040167632-oxobutanoate+respiration
23040739183-O-methyl-D-glucose+respiration
2304017925alpha-D-glucose+respiration
2304036219alpha-lactose+respiration
2304027613amygdalin+respiration
2304018305arbutin+respiration
2304017057cellobiose+respiration
2304015824D-fructose+respiration
2304012936D-galactose+respiration
230408391D-gluconate+respiration
2304015748D-glucuronate+respiration
2304016899D-mannitol+respiration
2304016024D-mannose+respiration
230406731melezitose+respiration
2304028053melibiose+respiration
2304027605D-psicose+respiration
2304016634raffinose+respiration
2304016988D-ribose+respiration
2304017924D-sorbitol+respiration
2304016551D-trehalose+respiration
2304065327D-xylose+respiration
2304023652dextrin+respiration
2304028066gentiobiose+respiration
2304017754glycerol+respiration
2304030849L-arabinose+respiration
230406359lactulose+respiration
2304017306maltose+respiration
2304061993maltotriose+respiration
2304055507methyl alpha-D-galactoside+respiration
23040320061methyl alpha-D-glucopyranoside+respiration
2304017540methyl beta-D-galactoside+respiration
23040320055methyl beta-D-glucopyranoside+respiration
2304018394palatinose+respiration
2304015361pyruvate+respiration
2304017814salicin+respiration
2304017992sucrose+respiration
2304032528turanose+respiration
11684017632nitrate-reduction
11684016301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistant
230402676amoxicillinyesyes
230406909metronidazoleyesyes
2304017334penicillinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2304035581indoleno
2304016136hydrogen sulfideno
2304015688acetoinyes
11684035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testcitrate test
2304015688acetoin+
2304035581indole-
2304016947citrate-

enzymes

@refvalueactivityec
23040acid phosphatase-3.1.3.2
23040alkaline phosphatase+3.1.3.1
23040alpha-chymotrypsin-3.4.21.1
23040alpha-fucosidase-3.2.1.51
23040alpha-galactosidase+3.2.1.22
23040alpha-glucosidase+3.2.1.20
23040alpha-mannosidase-3.2.1.24
23040arginine dihydrolase-3.5.3.6
23040beta-galactosidase+3.2.1.23
23040beta-glucoronidase-3.2.1.31
23040beta-glucosidase+3.2.1.21
23040catalase+1.11.1.6
23040cystine arylamidase-3.4.11.3
23040cytochrome oxidase+1.9.3.1
23040esterase (C 4)+
23040esterase lipase (C 8)+
23040leucine arylamidase+3.4.11.1
23040lipase (C 14)-
23040lysine decarboxylase-4.1.1.18
23040N-acetyl-beta-glucosaminidase-3.2.1.52
23040naphthol-AS-BI-phosphohydrolase-
23040ornithine decarboxylase-4.1.1.17
23040trypsin-3.4.21.4
23040tryptophan deaminase-4.1.99.1
23040valine arylamidase-
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
116840oxidase+
116840catalase+1.11.1.6
116840urease-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
116840-++-------++++-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
23040soil naturally containing boron mineralsHisarcik area in the Kutahya ProvinceTurkeyTURAsia
6857soilKutahya provinceTurkeyTURAsia
67770SoilTurkeyTURAsia
116840Environment, SoilKutahyaTurkeyTURAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

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: AB197126
  • Sequence Identity:
  • Total samples: 580
  • soil counts: 251
  • aquatic counts: 111
  • animal counts: 166
  • plant counts: 52

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68571Risk group (German classification)
1168401Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6857
  • description: Gracilibacillus boraciitolerans gene for 16S ribosomal RNA, partial sequence
  • accession: AB197126
  • length: 1500
  • database: ena
  • NCBI tax ID: 307521

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gracilibacillus boraciitolerans JCM 217141298598.3wgspatric1298598
66792Gracilibacillus boraciitolerans JCM 217142609459992draftimg1298598
67770Gracilibacillus boraciitolerans JCM 21714GCA_000521485contigncbi1298598

GC content

@refGC-contentmethod
685735.8
6777035.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.631yes
gram-positiveyes89.901yes
anaerobicno98.418no
aerobicyes88.813no
halophileyes89.515yes
spore-formingyes92.541no
thermophileno95.286no
glucose-utilyes87.171yes
flagellatedyes91.686yes
glucose-fermentno82.786no

External links

@ref: 6857

culture collection no.: DSM 17256, ATCC BAA 1190, CIP 109592, IAM 15263, JCM 21714

straininfo link

  • @ref: 71108
  • straininfo: 286034

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392209Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil.Ahmed I, Yokota A, Fujiwara TInt J Syst Evol Microbiol10.1099/ijs.0.64284-02007Bacillaceae/*classification/genetics/isolation & purification/physiology, Base Composition, Boron/metabolism/pharmacology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism/pharmacology, *Soil Microbiology, TurkeyMetabolism
Phylogeny21685255Gracilibacillus kekensis sp. nov., a moderate halophile isolated from Keke Salt Lake.Gao M, Liu ZZ, Zhou YG, Liu HC, Ma YC, Wang L, Chen SF, Ji XCInt J Syst Evol Microbiol10.1099/ijs.0.030858-02011Bacillaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, *Water MicrobiologyGenetics
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
Genetics24558242Draft Genome Sequence of the Boron-Tolerant and Moderately Halotolerant Bacterium Gracilibacillus boraciitolerans JCM 21714T.Ahmed I, Oshima K, Suda W, Kitamura K, Iida T, Ohmori Y, Fujiwara T, Hattori M, Ohkuma MGenome Announc10.1128/genomeA.00097-142014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6857Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17256)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17256
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
23040Iftikhar Ahmed,Akira Yokota,Toru Fujiwara10.1099/ijs.0.64284-0Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soilIJSEM 57: 796-802 200717392209
36593Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7353
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/
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
71108Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID286034.1StrainInfo: A central database for resolving microbial strain identifiers
116840Curators of the CIPCollection of Institut Pasteur (CIP 109592)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109592