Strain identifier

BacDive ID: 790

Type strain: Yes

Species: Peribacillus simplex

Strain Designation: NRS-960

Strain history: CIP <- 2001, CCUG <- 1991, L.K. Nakamura, NRRL, Peoria, USA: strain NRS-960

NCBI tax ID(s): 1478 (species)

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General

@ref: 519

BacDive-ID: 790

DSM-Number: 1321

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, motile

description: Peribacillus simplex NRS-960 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 1478
  • Matching level: species

strain history

@refhistory
519<- R.E. Gordon, NRS 960 (Bacillus megaterium) <- J.R. Porter <- O.F. Edwards <- H.J. Cohn
67770DSM 1321 <-- R. E. Gordon NRS 960 <-- J. R. Porter <-- O. F. Edwards <-- H. J. Cohn.
122621CIP <- 2001, CCUG <- 1991, L.K. Nakamura, NRRL, Peoria, USA: strain NRS-960

doi: 10.13145/bacdive790.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Peribacillus
  • species: Peribacillus simplex
  • full scientific name: Peribacillus simplex (Priest et al. 1989 ex Meyer and Gottheil 1901) Patel and Gupta 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus simplex

@ref: 519

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Peribacillus

species: Peribacillus simplex

full scientific name: Peribacillus simplex (Priest et al. 1989) Patel and Gupta 2020

strain designation: NRS-960

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.172
69480100positive
122621nopositiverod-shaped

colony morphology

@refcolony color
22903white
122621

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22903MacConkey agaryes
519NUTRIENT 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
34193MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122621CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
519positivegrowth30mesophilic
34193positivegrowth30mesophilic
67770positivegrowth30mesophilic
122621positivegrowth10-37
122621nogrowth45thermophilic
122621nogrowth55thermophilic

culture pH

  • @ref: 122621
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 122621
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
122621NaClpositivegrowth0-2 %
122621NaClnogrowth4 %
122621NaClnogrowth6 %
122621NaClnogrowth8 %
122621NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2290328757fructose-builds acid from
2290328260galactose-builds acid from
229035291gelatin-hydrolysis
2290317234glucose+builds acid from
2290317754glycerol+builds acid from
2290317716lactose-builds acid from
2290317306maltose+builds acid from
2290329864mannitol+builds acid from
2290337684mannose+builds acid from
2290316634raffinose-builds acid from
2290330911sorbitol+builds acid from
2290317992sucrose-builds acid from
2290327082trehalose+builds acid from
2290318222xylose+builds acid from
2290317632nitrate+reduction
22904casein+hydrolysis
2290417634D-glucose+builds acid from
2290416899D-mannitol+builds acid from
2290416024D-mannose-builds acid from
2290416988D-ribose+builds acid from
229045291gelatin+hydrolysis
2290430849L-arabinose-builds acid from
2290417716lactose-builds acid from
2290428017starch+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+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
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-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
12262116947citrate-carbon source
1226214853esculin-hydrolysis
122621606565hippurate+hydrolysis
12262117632nitrate+reduction
12262116301nitrite-reduction
12262117632nitrate-respiration

metabolite production

  • @ref: 122621
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12262115688acetoin-
12262117234glucose-

enzymes

@refvalueactivityec
22903acid phosphatase+3.1.3.2
22903alkaline phosphatase+3.1.3.1
22903alpha-chymotrypsin+3.4.21.1
22903alpha-glucosidase+3.2.1.20
22903beta-galactosidase-3.2.1.23
22903beta-glucosidase-3.2.1.21
22903cystine arylamidase-3.4.11.3
22903gelatinase-
22903N-acetyl-beta-glucosaminidase-3.2.1.52
22903trypsin-3.4.21.4
22903valine arylamidase-
22904gelatinase+
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
122621oxidase+
122621beta-galactosidase-3.2.1.23
122621alcohol dehydrogenase-1.1.1.1
122621gelatinase+/-
122621amylase-
122621DNase-
122621caseinase-3.4.21.50
122621catalase+1.11.1.6
122621tween esterase-
122621gamma-glutamyltransferase+2.3.2.2
122621lecithinase-
122621lipase-
122621lysine decarboxylase-4.1.1.18
122621ornithine decarboxylase-4.1.1.17
122621urease-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
122621--++----------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122621-----------+------+--------------------+--++-++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122621++-+-----++----+--++-+-+-------+++--+------+++--++-+-++-+--++++-+-++++--++-+-+-+++-++-+-+++++++--+-

Isolation, sampling and environmental information

isolation

@refsample type
67770Soil
122621Environment, Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_583.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_370;97_418;98_477;99_583&stattab=map
  • Last taxonomy: Peribacillus
  • 16S sequence: AJ439078
  • Sequence Identity:
  • Total samples: 10636
  • soil counts: 6241
  • aquatic counts: 1051
  • animal counts: 2464
  • plant counts: 880

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
5191Risk group (German classification)
1226211Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus simplex clone Bsim-1 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478071410ena1478
20218Bacillus simplex 16S rRNA gene, strain DSM 1321TAJ4390781522ena1478
20218Bacillus simplex DNA for 16S ribosomal RNA, partial sequenceD784781433ena1478
20218B.simplex 16S ribosomal RNAX606381429ena1478
20218Bacillus simplex partial 16S rRNA gene, type strain LMG 11160TAJ6287431503ena1478
20218Bacillus simplex gene for 16S rRNA, partial sequence, strain: NBRC 15720AB3637381476ena1478

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Peribacillus simplex NBRC 15720 = DSM 1321GCA_002243645completencbi1349754
66792Peribacillus simplex NBRC 15720 = DSM 1321 DE0084GCA_007679575scaffoldncbi1349754
66792Bacillus simplex NBRC 157201349754.4wgspatric1349754
66792Bacillus simplex NBRC 15720 = DSM 13211349754.5completepatric1349754
66792Bacillus simplex NBRC 15720 = DSM 1321 strain DE00841349754.9wgspatric1349754
66792Bacillus simplex DSM 13212823415468completeimg1349754
66792Bacillus simplex NBRC 157202731957667draftimg1349754
67770Peribacillus simplex NBRC 15720 = DSM 1321GCA_001591785contigncbi1349754

GC content

@refGC-contentmethod
51940.1
6777040-41thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes78.342no
gram-positiveyes91.011no
anaerobicno98.806no
aerobicyes89.356no
halophileno87.915no
spore-formingyes95.622no
glucose-utilyes89.813no
thermophileno99.318yes
motileyes87.312no
glucose-fermentno89.757no

External links

@ref: 519

culture collection no.: DSM 1321, ATCC 49097, NRS 960, JCM 12307, BCRC 15909, CCM 7148, CCUG 28889, CGMCC 1.3471, CIP 106934, IFO 15720, KCTC 3450, LMG 11160, NBRC 15720, NRRL NRS-960, VTT E-97781

straininfo link

  • @ref: 70464
  • straininfo: 1178

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18218958Bacillus butanolivorans sp. nov., a species with industrial application for the remediation of n-butanol.Kuisiene N, Raugalas J, Sproer C, Kroppenstedt RM, Chitavichius DInt J Syst Evol Microbiol10.1099/ijs.0.65332-02008Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Butanols/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Fatty Acids/analysis, Genes, rRNA, Industrial Microbiology/methods, Molecular Sequence Data, Nucleic Acid Hybridization, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny21441377Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root.Zhang YZ, Chen WF, Li M, Sui XH, Liu HC, Zhang XX, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.028936-02011Bacillus/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Endophytes, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/*microbiology, Species Specificity, Vitamin K 2/analysisGenetics
Phylogeny24903955Bacillus huizhouensis sp. nov., isolated from a paddy field soil.Li J, Yang G, Wu M, Zhao Y, Zhou SAntonie Van Leeuwenhoek10.1007/s10482-014-0208-22014Aerobiosis, Anaerobiosis, Bacillus/*classification/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Oryza, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny25256951Bacillus cihuensis sp. nov., isolated from rhizosphere soil of a plant in the Cihu area of Taiwan.Liu B, Liu GH, Sengonca C, Schumann P, Wang MK, Tang JY, Chen MCAntonie Van Leeuwenhoek10.1007/s10482-014-0284-32014Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Taiwan, TemperatureGenetics
Phylogeny26303844Bacillus gossypii sp. nov., isolated from the stem of Gossypium hirsutum.Kampfer P, Busse HJ, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0005552015Alabama, Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gossypium/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Stems/*microbiology, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27117173Bacillus loiseleuriae sp. nov., isolated from rhizosphere soil from a loiseleuria plant.Liu B, Liu GH, Zhu YJ, Wang JP, Che JM, Chen QQ, Chen ZInt J Syst Evol Microbiol10.1099/ijsem.0.0011072016Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Ericaceae/*microbiology, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Genetics27340061Draft Genome Sequence of Bacillus simplex DSM 1321 for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.Liu GH, Liu B, Wang JP, Che JM, Chen QQ, Chen ZGenome Announc10.1128/genomeA.00574-162016Phylogeny
Phylogeny32248281Reclassification of Brevibacterium frigoritolerans DSM 8801(T) as Bacillus frigoritolerans comb. nov. Based on Genome Analysis.Liu GH, Liu B, Wang JP, Che JM, Li PFCurr Microbiol10.1007/s00284-020-01964-x2020Bacillus/classification/*genetics, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Genome, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Whole Genome SequencingGenetics
Phylogeny35812926Peribacillus castrilensis sp. nov.: A Plant-Growth-Promoting and Biocontrol Species Isolated From a River Otter in Castril, Granada, Southern Spain.Rodriguez M, Reina JC, Sampedro I, Llamas I, Martinez-Checa FFront Plant Sci10.3389/fpls.2022.8967282022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
519Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1321)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1321
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
22903Isao Yumoto, Kikue Hirota, Shingo Yamaga, Yoshinobu Nodasaka, Tsuneshirou Kawasaki, Hidetoshi Matsuyama, Kenji Nakajima10.1099/ijs.0.03014-0Bacillus asahii sp. nov., a novel bacterium isolated from soil with the ability to deodorize the bad smell generated from short-chain fatty acidsIJSEM 54: 1997-2001 200415545424
22904Yun Zeng Zhang, Wen Feng Chen, Mao Li, Xin Hua Sui, Hong-Can Liu, Xiao Xia Zhang, Wen Xin Chen10.1099/ijs.0.028936-0Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean rootIJSEM 62: 359-363 201221441377
34193Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19119
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/
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
70464Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1178.1StrainInfo: A central database for resolving microbial strain identifiers
122621Curators of the CIPCollection of Institut Pasteur (CIP 106934)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106934