Strain identifier

BacDive ID: 1394

Type strain: Yes

Species: Ureibacillus thermosphaericus

Strain Designation: p-11, HAMBI:1900

Strain history: CIP <- 1996, M. Andersson, Helsinki Univ., Helsinki, Finland: strain HAMBI:1900

NCBI tax ID(s): 51173 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3990

BacDive-ID: 1394

DSM-Number: 10633

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

description: Ureibacillus thermosphaericus p-11 is an aerobe, spore-forming, thermophilic bacterium that forms circular colonies and was isolated from landfill air.

NCBI tax id

  • NCBI tax id: 51173
  • Matching level: species

strain history

@refhistory
3990<- M. Salkinoja-Salonen, University of Helsinki
351711996, M. Andersson, Helsinki Univ., Finland: strain HAMBI:1900
123516CIP <- 1996, M. Andersson, Helsinki Univ., Helsinki, Finland: strain HAMBI:1900

doi: 10.13145/bacdive1394.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Ureibacillus
  • species: Ureibacillus thermosphaericus
  • full scientific name: Ureibacillus thermosphaericus (Andersson et al. 1996) Fortina et al. 2001
  • synonyms

    • @ref: 20215
    • synonym: Bacillus thermosphaericus

@ref: 3990

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Ureibacillus

species: Ureibacillus thermosphaericus

full scientific name: Ureibacillus thermosphaericus (Andersson et al. 1996) Fortina et al. 2001

strain designation: p-11, HAMBI:1900

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23024negative1.0-6.0 µm0.5-0.7 µmrod-shapedyes
123516positiverod-shapedyes

colony morphology

@refcolony colorcolony shapeincubation period
23024transparentcircular1-1.5 days
123516

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3990TRYPTICASE 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
35171MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123516CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3990positivegrowth55thermophilic
23024positivegrowth37.0-60.0
23024positivegrowth37.0mesophilic
23024nogrowth65.0thermophilic
35171positivegrowth37mesophilic
123516positivegrowth30-55
123516nogrowth10psychrophilic
123516nogrowth22psychrophilic

culture pH

@refabilitytypepHPH range
23024positivegrowth9.0alkaliphile
123516positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23024aerobe
123516obligate aerobe

spore formation

@refspore descriptiontype of sporespore formation
23024spherical,terminal or subterminal,in swollen sporangiaendosporeyes
123516yes

halophily

@refsaltgrowthtested relationconcentration
23024NaClpositivegrowth5.0 %
123516NaClpositivegrowth0-2 %
123516NaClnogrowth4 %
123516NaClnogrowth6 %
123516NaClnogrowth8 %
123516NaClnogrowth10 %

murein

  • @ref: 3990
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
23024casein-hydrolysis
23024gelatin-hydrolysis5291
23024starch-hydrolysis28017
23024nitrate-reduction17632
23024citrate+builds acid from16947
23024glucose+builds acid from17234
23024L-arabinose+builds acid from30849
23024maltose+builds acid from17306
23024mannose+builds acid from37684
23024rhamnose+builds acid from26546
23024ribose+builds acid from33942
23024sucrose+builds acid from17992
23024trehalose+builds acid from27082
23024xylose+builds acid from18222
23024urea+hydrolysis16199
123516citrate-carbon source16947
123516esculin-hydrolysis4853
123516hippurate+hydrolysis606565
123516nitrate-reduction17632
123516nitrite-reduction16301
123516nitrate-respiration17632

metabolite production

@refChebi-IDmetaboliteproduction
2302435581indoleno
2302415688acetoinno
12351635581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2302415688acetoin-
12351615688acetoin-
12351617234glucose-

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
123516oxidase+
123516beta-galactosidase+3.2.1.23
123516alcohol dehydrogenase-1.1.1.1
123516gelatinase-
123516amylase-
123516DNase-
123516caseinase-3.4.21.50
123516catalase+1.11.1.6
123516tween esterase-
123516gamma-glutamyltransferase-2.3.2.2
123516lecithinase-
123516lipase-
123516lysine decarboxylase-4.1.1.18
123516ornithine decarboxylase-4.1.1.17
123516protease-
123516urease-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
123516--+--+----+---------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
3990landfill airFinlandFINEurope
23024urban air and municipal landfill sites
123516Environment, Landfill airFinlandFINEuropePorvoo1987

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Landfill
#Environmental#Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_16631.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_8510;97_10240;98_12572;99_16631&stattab=map
  • Last taxonomy: Ureibacillus thermosphaericus subclade
  • 16S sequence: X90640
  • Sequence Identity:
  • Total samples: 19476
  • soil counts: 8797
  • aquatic counts: 2235
  • animal counts: 5636
  • plant counts: 2808

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
39901Risk group (German classification)
1235161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ureibacillus thermosphaericus gene for 16S rRNA, partial sequenceAB1015941540ena51173
20218Ureibacillus thermosphaericus isolate Uth41 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723669539ena51173
20218Ureibacillus thermosphaericus isolate Uth60 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723670372ena51173
20218Ureibacillus thermosphaericus isolate Uth61 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723671384ena51173
20218B.thermosphaericus DNA for 16S ribosomal RNA geneX906401488ena51173

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ureibacillus thermosphaericus DSM 10633GCA_012396605contigncbi51173
66792Ureibacillus thermosphaericus DSM 10633GCA_014202525scaffoldncbi51173
66792Ureibacillus thermosphaericus strain DSM 1063351173.7wgspatric51173
66792Ureibacillus thermosphaericus strain DSM 1063351173.6wgspatric51173
66792Ureibacillus thermosphaericus DSM 106332861563776draftimg51173

GC content

@refGC-contentmethod
399037high performance liquid chromatography (HPLC)
2302435.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes86.473no
gram-positiveyes82.52no
anaerobicno96.627no
aerobicyes87.959yes
halophileno79.512no
spore-formingyes96.394yes
glucose-utilyes67.307no
thermophileno92.866no
motileyes91.303yes
glucose-fermentno91.06no

External links

@ref: 3990

culture collection no.: DSM 10633, HAMBI 1900, CIP 104857, KCTC 13004

straininfo link

  • @ref: 71045
  • straininfo: 14023

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11321090Ureibacillus gen. nov., a new genus to accommodate Bacillus thermosphaericus (Andersson et al. 1995), emendation of Ureibacillus thermosphaericus and description of Ureibacillus terrenus sp. nov.Fortina MG, Pukall R, Schumann P, Mora D, Parini C, Manachini PL, Stackebrandt EInt J Syst Evol Microbiol10.1099/00207713-51-2-4472001Bacillus/*classification/cytology, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S, Sequence Homology, Nucleic Acid, *Soil Microbiology, Terminology as Topic, Vitamin K/analysisGenetics
Genetics11718544Phenotypic and genotypic characterization of esterase-producing Ureibacillus thermosphaericus isolated from an aerobic digestor of swine waste.Gagne A, Chicoine M, Morin A, Houde ACan J Microbiol10.1139/w01-0962001Aerobiosis, Animals, Base Sequence, Culture Media, *Environmental Microbiology, Esterases/biosynthesis/*metabolism, Genes, Bacterial, Genotype, *Gram-Negative Bacteria/chemistry/classification/physiology, Manure/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, RNA, Spores, Bacterial/genetics, SwinePhylogeny
Phylogeny16514046Ureibacillus suwonensis sp. nov., isolated from cotton waste composts.Kim BY, Lee SY, Weon HY, Kwon SW, Go SJ, Park YK, Schumann P, Fritze DInt J Syst Evol Microbiol10.1099/ijs.0.63703-02006Bacillus/*classification/genetics/isolation & purification/physiology, DNA, Bacterial, DNA, Ribosomal/chemistry, Gossypium, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyPhenotype
Phylogeny24491829Ureibacillus defluvii sp. nov., isolated from a thermophilic microbial fuel cell.Zhou S, Tang J, Qin D, Lu Q, Yang GInt J Syst Evol Microbiol10.1099/ijs.0.056655-02014Bacterial Typing Techniques, Base Composition, Bioelectric Energy Sources/*microbiology, Biofilms, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Planococcaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3990Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10633)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10633
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
23024M. G. Fortina,R. Pukall,P. Schumann,D. Mora,C. Parini,P. L. Manachini,E. Stackebrandt10.1099/00207713-51-2-447Ureibacillus gen. nov., a new genus to accommodate Bacillus thermosphaericus (Andersson et al. 1995), emendation of Ureibacillus thermosphaericus and description of Ureibacillus terrenus sp. nov.IJSEM 51: 447-455 200111321090
35171Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16812
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)
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
71045Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14023.1StrainInfo: A central database for resolving microbial strain identifiers
123516Curators of the CIPCollection of Institut Pasteur (CIP 104857)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104857