Strain identifier

BacDive ID: 1538

Type strain: Yes

Species: Lysinibacillus boronitolerans

Strain Designation: 10a

Strain history: CIP <- 2007, JCM <- 2007, IAM <- I. Ahmed, Tokyo Univ., Tokyo, Japan: strain 10a

NCBI tax ID(s): 1294264 (strain), 309788 (species)

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General

@ref: 6786

BacDive-ID: 1538

DSM-Number: 17140

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

description: Lysinibacillus boronitolerans 10a is an obligate aerobe, moderately halophilic, spore-forming bacterium that forms circular colonies and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1294264strain
309788species

strain history

@refhistory
6786<- I. Ahmed; strain 10a
67770IAM 15262 <-- I. Ahmed et al. 10a.
116898CIP <- 2007, JCM <- 2007, IAM <- I. Ahmed, Tokyo Univ., Tokyo, Japan: strain 10a

doi: 10.13145/bacdive1538.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Lysinibacillus
  • species: Lysinibacillus boronitolerans
  • full scientific name: Lysinibacillus boronitolerans Ahmed et al. 2007

@ref: 6786

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Lysinibacillus

species: Lysinibacillus boronitolerans

full scientific name: Lysinibacillus boronitolerans Ahmed et al. 2007

strain designation: 10a

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23066positive3.0-5.0 µm0.8-1.5 µmrod-shapedyes
69480yes97.902
69480positive100
116898positiverod-shapedyes

colony morphology

  • @ref: 23066
  • colony size: 2.0-3.0 mm
  • colony shape: circular
  • incubation period: 2 days
  • medium used: nutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6786CASO 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
23066Marine agar (MA)yes
23066Nutrient agar (NA)yes
23066tryptone soy agaryes
37294MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116898CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6786positivegrowth30mesophilic
23066positivegrowth16.0-45.0
23066nogrowth>50.0thermophilic
23066positivegrowth16.0psychrophilic
23066positiveoptimum37.0mesophilic
37294positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
23066positivegrowth5.5-9.5alkaliphile
23066positiveoptimum7.0-8.0
23066nogrowth5.0

Physiology and metabolism

oxygen tolerance

  • @ref: 116898
  • oxygen tolerance: obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23066ellipsoidal or spherical,terminal,in a swollen sporangiumendosporeyes
69481yes100
69480yes100

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23066moderately halophilicNaClnogrowth>5.0 %(w/v)
23066NaClpositivegrowth0.0 %(w/v)

murein

@refmurein short keytype
6786A11.31A4alpha L-Lys-D-Asp
23066A11.31A4alpha L-Lys-D-Asp

observation

  • @ref: 67770
  • observation: quinones: MK-7, MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2306617992sucrose-builds acid from
230665291gelatin-hydrolysis
230668295beta-hydroxybutyrate-oxidation
2306617632nitrate-reduction
2306665327D-xylose+builds acid from
230664853esculin+builds acid from
23066506227N-acetylglucosamine+builds acid from
230664853esculin+hydrolysis
2306616199urea+hydrolysis
2306616651(S)-lactate+oxidation
2306615589L-malate+oxidation
23066172562-deoxyadenosine+oxidation
23066645522-hydroxybutyrate+oxidation
23066167632-oxobutanoate+oxidation
23066286442-oxopentanoate+oxidation
2306630089acetate+oxidation
2306616335adenosine+oxidation
2306616027amp+oxidation
23066495055beta-cyclodextrin+oxidation
2306673706bromosuccinate+oxidation
2306616383cis-aconitate+oxidation
2306616947citrate+oxidation
2306615570D-alanine+oxidation
230668391D-gluconate+oxidation
2306616988D-ribose+oxidation
2306616443D-tagatose+oxidation
2306617113erythritol+oxidation
2306616000ethanolamine+oxidation
2306615740formate+oxidation
2306628087glycogen+oxidation
2306673804glycyl L-aspartic acid+oxidation
2306617596inosine+oxidation
2306621217L-alaninamide+oxidation
2306616977L-alanine+oxidation
2306673786L-alanylglycine+oxidation
2306617196L-asparagine+oxidation
2306629985L-glutamate+oxidation
2306615971L-histidine+oxidation
2306615603L-leucine+oxidation
2306615729L-ornithine+oxidation
23066L-proline-4-nitroanilide+oxidation
2306617115L-serine+oxidation
2306616857L-threonine+oxidation
2306675144lactamide+oxidation
2306624996lactate+oxidation
2306651850methyl pyruvate+oxidation
2306675146monomethyl succinate+oxidation
2306673784glycyl-l-glutamate+oxidation
2306617272propionate+oxidation
2306615361pyruvate+oxidation
2306617748thymidine+oxidation
2306663528thymidine 5'-monophosphate+oxidation
2306616695uridine 5'-monophosphate+oxidation
2306616704uridine+oxidation
11689817632nitrate-reduction
11689816301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.
2306628077rifampicinyesno0.25 µg/mL
2306648923erythromycinyesno1 µg/mL
2306627902tetracyclineyesno2 µg/mL
2306617698chloramphenicolyesno8 µg/mL
2306617076streptomycinyesno8 µg/mL
2306637943colistinyesyes
2306671321fusidateyesyes
230666472lincomycinyesyes
230666909metronidazoleyesyes
2306659066oxolinateyesyes
230669332sulfamethoxazoleyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2306635581indoleno
2306616136hydrogen sulfideno
2306615688acetoinyes
11689835581indoleno

metabolite tests

  • @ref: 23066
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
23066acid phosphatase+3.1.3.2
23066alkaline phosphatase+3.1.3.1
23066alpha-chymotrypsin+3.4.21.1
23066arginine dihydrolase+3.5.3.6
23066catalase+1.11.1.6
23066cytochrome oxidase+1.9.3.1
23066esterase lipase (C 8)+
23066leucine arylamidase+3.4.11.1
23066lysine decarboxylase-4.1.1.18
23066naphthol-AS-BI-phosphohydrolase+
23066ornithine decarboxylase-4.1.1.17
23066tryptophan deaminase+4.1.99.1
23066valine 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
116898oxidase+
116898catalase+1.11.1.6
116898urease+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
116898-+++-+++-+++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6786soilUniversity of TokyoJapanJPNAsia
23066soilexperimental area of the University of Tokyo (Yayoi campus)JapanJPNAsia
67770Soil collected in the experimental area of the Univ. of Tokyo (Yayoi campus)JapanJPNAsia
116898Environment, SoilTokyoJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67861Risk group (German classification)
1168981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6786
  • description: Lysinibacillus boronitolerans gene for 16S ribosomal RNA, partial sequence, strain: 10a
  • accession: AB199591
  • length: 1484
  • database: ena
  • NCBI tax ID: 309788

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysinibacillus boronitolerans JCM 21713 = 10a = NBRC 1031081294264.5wgspatric1294264
66792Lysinibacillus boronitolerans JCM 21713 = 10a = NBRC 1031081294264.6wgspatric1294264
66792Lysinibacillus boronitolerans JCM 21713 = 10a = NBRC 103108 strain NBRC 1031081294264.9wgspatric1294264
66792Lysinibacillus boronitolerans 10a2728369705draftimg1294264
66792Lysinibacillus boronitolerans JCM 21713 = 10a = NBRC 1031082627853777draftimg1294264
67770Lysinibacillus boronitolerans JCM 21713 = 10a = NBRC 103108GCA_002200915contigncbi1294264
67770Lysinibacillus boronitolerans JCM 21713 = 10a = NBRC 103108GCA_001312025contigncbi1294264
67770Lysinibacillus boronitolerans JCM 21713 = 10a = NBRC 103108GCA_000772935contigncbi1294264

GC content

@refGC-contentmethod
678636.5
2306636.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.224yes
gram-positiveyes89.779yes
anaerobicno97.478no
aerobicyes91.275no
halophileno93.958yes
spore-formingyes96.493no
thermophileno99.781no
glucose-utilyes88.514no
flagellatedyes86.539no
glucose-fermentno87.855no

External links

@ref: 6786

culture collection no.: DSM 17140, ATCC BAA 1146, IAM 15262, JCM 21713, CIP 109652, NBRC 103108

straininfo link

  • @ref: 71183
  • straininfo: 308618

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17473269Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov.Ahmed I, Yokota A, Yamazoe A, Fujiwara TInt J Syst Evol Microbiol10.1099/ijs.0.63867-02007Bacillaceae/chemistry/*classification/genetics/metabolism, Bacterial Typing Techniques, Base Composition, Boron/metabolism, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureMetabolism
Phylogeny22140163Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov. with emended description of the genus Lysinibacillus.Jung MY, Kim JS, Paek WK, Styrak I, Park IS, Sin Y, Paek J, Park KA, Kim H, Kim HL, Chang YHInt J Syst Evol Microbiol10.1099/ijs.0.033837-02011Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/*analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6786Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17140)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17140
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
23066Iftikhar Ahmed,Akira Yokota,Atsushi Yamazoe,Toru Fujiwara10.1099/ijs.0.63867-0Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov.IJSEM 57: 1117-1125 200717473269
37294Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7419
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
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
71183Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308618.1StrainInfo: A central database for resolving microbial strain identifiers
116898Curators of the CIPCollection of Institut Pasteur (CIP 109652)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109652