Strain identifier

BacDive ID: 1449

Type strain: Yes

Species: Parageobacillus toebii

Strain Designation: R-35642, SK-1

Strain history: CIP <- 2004, KRIBB: strain SK-1

NCBI tax ID(s): 1223503 (strain), 153151 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5397

BacDive-ID: 1449

DSM-Number: 14590

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

description: Parageobacillus toebii R-35642 is an aerobe, spore-forming, thermophilic bacterium that was isolated from hay compost in farmyard.

NCBI tax id

NCBI tax idMatching level
153151species
1223503strain

strain history

@refhistory
5397<- S. Moon-Hee; SK-1
123555CIP <- 2004, KRIBB: strain SK-1

doi: 10.13145/bacdive1449.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Parageobacillus
  • species: Parageobacillus toebii
  • full scientific name: Parageobacillus toebii (Sung et al. 2002) Aliyu et al. 2019

  • synonyms

    @refsynonym
    20215Parageobacillus toebii
    20215Geobacillus toebii

@ref: 5397

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Parageobacillus

species: Parageobacillus toebii

full scientific name: Parageobacillus toebii (Sung et al. 2002) Aliyu et al. 2019

strain designation: R-35642, SK-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23037positive2.0-3.5 µm0.5-0.9 µmrod-shapedyes
69480yes91.71
69480positive100
123555positiverod-shapedyes

colony morphology

  • @ref: 123555

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5397CASO 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
33935MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123555CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerangeconfidence
5397positivegrowth55thermophilic
23037positivegrowth45.0-70.0thermophilic
23037nogrowth80.0hyperthermophilic
23037positiveoptimum60.0thermophilic
23037thermophilic
33935positivegrowth55thermophilic
69480thermophilic99.287
123555positivegrowth37-55
123555nogrowth10psychrophilic
123555nogrowth22psychrophilic
123555nogrowth30mesophilic

culture pH

@refabilitytypepHPH range
23037positivegrowth6.0-9.0alkaliphile
23037positiveoptimum7.5
23037nogrowth<6.0
23037nogrowth>9.0
123555positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23037aerobe
123555facultative anaerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23037ellipsoidal,subterminal to terminal,in swollen sporangiasporeyes
69481yes100
69480yes99.448
123555yes

halophily

@refsaltgrowthtested relationconcentration
23037NaClnogrowth5.0 %
23037NaClpositivegrowth0.0-5.0 %(w/v)
123555NaClpositivegrowth0-2 %
123555NaClnogrowth4 %
123555NaClnogrowth6 %
123555NaClnogrowth8 %
123555NaClnogrowth10 %

murein

  • @ref: 23037
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2303715963ribitol-builds acid from
2303717057cellobiose-builds acid from
2303728260galactose-builds acid from
2303717754glycerol-builds acid from
2303730849L-arabinose-builds acid from
2303717716lactose-builds acid from
2303729864mannitol-builds acid from
2303726546rhamnose-builds acid from
2303733942ribose-builds acid from
2303730911sorbitol-builds acid from
2303718222xylose-builds acid from
2303717234glucose-fermentation
230374853esculin-hydrolysis
230375291gelatin-hydrolysis
2303728017starch-hydrolysis
2303717634D-glucose+builds acid from
2303717268myo-inositol+builds acid from
23037casein+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12355516947citrate-carbon source
1235554853esculin-hydrolysis
123555606565hippurate-hydrolysis
12355517632nitrate+reduction
12355516301nitrite+reduction
12355517632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
2303715688acetoinyes
12355535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2303715688acetoin+
2303717234glucose-
12355515688acetoin-
12355517234glucose+

enzymes

@refvalueactivityec
23037catalase+1.11.1.6
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
123555oxidase-
123555beta-galactosidase+3.2.1.23
123555alcohol dehydrogenase-1.1.1.1
123555gelatinase-
123555amylase-
123555DNase+
123555caseinase-3.4.21.50
123555catalase+1.11.1.6
123555tween esterase-
123555gamma-glutamyltransferase+2.3.2.2
123555lecithinase-
123555lipase-
123555lysine decarboxylase-4.1.1.18
123555ornithine decarboxylase-4.1.1.17
123555urease-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
123555-+++------+-+--+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123555---------++++----+---------+-+/-++-+/-+/-+/----+/-------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123555+++++-+++++++-++++-+++++++++++-+++++++-++++++++++++-+-+++--++----------++++----+++++--++++++-+-+++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
5397hay compost in farmyardKorea, KongjuRepublic of KoreaKORAsia
23037farmland compostsolid modified basal medium (MBM)containing 5 g polypeptone, 1 g yeast extract, 6 g K2HPO4, 2 g KH2PO4, 0 .5 g MgSO4.7H2 and 0.5 g L-tyrosine l- 1 deionized water3 days60.0
123555Environment, Hay compost sample taken from a farm-yard in KongjuKongjuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Biodegradation#Composting
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5637.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_79;96_455;97_521;98_599;99_5637&stattab=map
  • Last taxonomy: Bacillaceae
  • 16S sequence: AF326278
  • Sequence Identity:
  • Total samples: 780
  • soil counts: 124
  • aquatic counts: 68
  • animal counts: 558
  • plant counts: 30

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53971Risk group (German classification)
1235551Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Geobacillus toebii strain DSM 14590 16S-23S ribosomal RNA intergenic spacer and tRNA-Ile gene, partial sequence; tRNA-Ala gene, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU157956400ena1223503
5397Geobacillus toebii 16S ribosomal RNA gene, complete sequenceAF3262781511ena153151
5397Geobacillus toebii partial 16S rRNA gene, strain R-35642FN4286901504ena1223503

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parageobacillus toebii NBRC 107807 DSM 14590GCA_003688615completencbi1223503
66792Parageobacillus toebii NBRC 107807 DSM 14590GCA_014196095scaffoldncbi1223503
66792Parageobacillus toebii NBRC 107807 strain DSM 145901223503.6wgspatric1223503
66792Parageobacillus toebii NBRC 107807 strain DSM 145901223503.9wgspatric1223503
66792Parageobacillus toebii DSM 145902773858069draftimg1223503
66792Parageobacillus toebii DSM 145902829804122draftimg1223503

GC content

  • @ref: 5397
  • GC-content: 43.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.162no
motileyes90.162no
flagellatedyes84.705no
flagellatedyes84.705no
gram-positiveyes92.474yes
gram-positiveyes92.474yes
anaerobicno97.593yes
anaerobicno97.593yes
aerobicyes89.584yes
aerobicyes89.584yes
halophileno88.775no
halophileno88.775no
spore-formingyes96.029no
spore-formingyes96.029no
glucose-utilyes90.181no
glucose-utilyes90.181no
thermophileyes99.634yes
thermophileyes99.634yes
glucose-fermentno91.822yes
glucose-fermentno91.822yes

External links

@ref: 5397

culture collection no.: DSM 14590, KCTC 0306BP, LMG 23037, CIP 108270

straininfo link

  • @ref: 71099
  • straininfo: 100656

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508894Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost.Sung MH, Kim H, Bae JW, Rhee SK, Jeon CO, Kim K, Kim JJ, Hong SP, Lee SG, Yoon JH, Park YH, Baek DHInt J Syst Evol Microbiol10.1099/00207713-52-6-22512002Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/metabolism, Hot Temperature, Korea, Molecular Sequence Data, Phenotype, Phylogeny, Poaceae/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicStress
Genetics32554784Methylome and Complete Genome Sequence of Parageobacillus toebii DSM 14590(T), a Thermophilic Bacterium.Hatmaker EA, O'Dell KB, Riley LA, Payne IC, Guss AMMicrobiol Resour Announc10.1128/MRA.00589-202020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5397Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14590)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14590
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
23037M. H. Sung,H. Kim,J. W. Bae,S. K. Rhee,C. O. Jeon,K. Kim,J. J. Kim,S. P. Hong,S. G. Lee,J. H. Yoon,Y. H. Park,D. H. Baek10.1099/00207713-52-6-2251Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost.IJSEM 52: 2251-2255 200212508894
33935Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5874
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)
68371Automatically annotated from API 50CH acid
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
71099Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100656.1StrainInfo: A central database for resolving microbial strain identifiers
123555Curators of the CIPCollection of Institut Pasteur (CIP 108270)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108270