Strain identifier

BacDive ID: 756

Type strain: Yes

Species: Bacillus pumilus

Strain Designation: 272

Strain history: CIP <- 1952, R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA: strain 272 <- 1914, F. Löhnis <- Kràl Collection, Vienna, Austria

NCBI tax ID(s): 536229 (strain), 1408 (species)

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General

@ref: 2028

BacDive-ID: 756

DSM-Number: 27

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

description: Bacillus pumilus 272 is an obligate aerobe, spore-forming, mesophilic human pathogen of the family Bacillaceae.

NCBI tax id

NCBI tax idMatching level
1408species
536229strain

strain history

@refhistory
2028<- ATCC <- N.R. Smith, 272 <- F. Löhnis <- Král <- O. Gottheil
67770CCM 2144 <-- R. E. Gordon.
122057CIP <- 1952, R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA: strain 272 <- 1914, F. Löhnis <- Kràl Collection, Vienna, Austria

doi: 10.13145/bacdive756.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Bacillus
  • species: Bacillus pumilus
  • full scientific name: Bacillus pumilus Meyer and Gottheil 1901 (Approved Lists 1980)

@ref: 2028

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus pumilus

full scientific name: Bacillus pumilus Meyer and Gottheil 1901

strain designation: 272

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.053
69480100positive
122057yespositiverod-shaped

colony morphology

  • @ref: 122057

multimedia

  • @ref: 2028
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27.jpg
  • caption: DSM 27 Bacillus pumilus
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2028NUTRIENT 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
40218MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122057CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
2028positivegrowth30mesophilic
40218positivegrowth30mesophilic
67770positivegrowth30mesophilic
122057positivegrowth22-45
122057nogrowth5psychrophilic
122057nogrowth10psychrophilic

culture pH

  • @ref: 122057
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 122057
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 122057
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2290023652dextrin-growth
2290028260galactose+growth
2290024265gluconate+growth
2290028087glycogen-growth
2290030849L-arabinose+growth
22900506227N-acetyl-D-glucosamine+growth
2290026546rhamnose-growth
2290028017starch-growth
2290017632nitrate-reduction
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
1220574853esculin+hydrolysis
12205717632nitrate-reduction
12205716301nitrite-reduction
12205717632nitrate-respiration

metabolite production

  • @ref: 122057
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12205715688acetoin+
12205717234glucose+

enzymes

@refvalueactivityec
22900alpha-glucosidase-3.2.1.20
22900arginine dihydrolase-3.5.3.6
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
122057oxidase+
122057beta-galactosidase+3.2.1.23
122057alcohol dehydrogenase-1.1.1.1
122057gelatinase+
122057amylase-
122057DNase-
122057caseinase+3.4.21.50
122057catalase+1.11.1.6
122057tween esterase+
122057lecithinase-
122057lipase+
122057lysine decarboxylase-4.1.1.18
122057ornithine decarboxylase-4.1.1.17
122057urease-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
122057-+++-----++-----+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122057+--++-----+++----+---+-++++---++------+--+-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122057+++++--+-------+-+++++--------++-+---------------+++-+-----+--+-++-------+-----++-----+--++--------

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_885.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_17;97_607;98_698;99_885&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: AM237370
  • Sequence Identity:
  • Total samples: 20329
  • soil counts: 7187
  • aquatic counts: 3497
  • animal counts: 6743
  • plant counts: 2902

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
2028yes, in single cases1Risk group (German classification)
1220571Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus pumilus 16S ribosomal RNA gene, partial sequenceDQ1059671449ena1408
20218Bacillus pumilus strain 001T 16S ribosomal RNA gene, partial sequenceFJ477095650ena1408
20218Bacillus pumilus clone Bpumi-1F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478070416ena1408
20218Bacillus pumilus strain ATCC 7061 16S ribosomal RNA gene, partial sequenceAY8762891434ena1408
20218Bacillus pumilus strain ATCC 7061 16S ribosomal RNA gene, partial sequenceGQ911554803ena1408
20218Bacillus pumilus strain ATCC 7061 16S ribosomal RNA gene, partial sequenceJQ4248871456ena1408
20218Bacillus pumilus strain CIP 52.67 16S ribosomal RNA gene, partial sequenceAY8760451065ena1408
20218Bacillus pumilus partial 16S rRNA gene, isolate OS-70AM2373701459ena1408
20218Bacillus pumilus strain DSMZ27 16S ribosomal RNA gene, partial sequenceAY4562631481ena1408
20218Bacillus pumilus gene for 16S rRNA, partial sequenceAB006934274ena1408
20218Bacillus pumilus gene for 16S rRNA, partial sequenceAB2717531474ena1408
20218B.pumilus 16S ribosomal RNAX606371427ena1408
20218Bacillus pumilus strain NRRL NRS-272 16S ribosomal RNA gene, partial sequenceEU1385171167ena1408

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus pumilus NCTC10337GCA_900186955completencbi1408
66792Bacillus pumilus ATCC 7061536229.4wgspatric536229
66792Bacillus pumilus strain NCTC103371408.193completepatric1408
66792Bacillus pumilus NCTC 103372880148112completeimg1408
66792Bacillus pumilus ATCC 7061642791616draftimg536229
67770Bacillus pumilus ATCC 7061GCA_000172815contigncbi536229

GC content

@refGC-contentmethod
202841.9thermal denaturation, midpoint method (Tm)
202840.7Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes88.833no
flagellatedyes83.908no
gram-positiveyes87.555no
anaerobicno99.274no
aerobicyes89.887no
halophileyes73.882no
spore-formingyes96.357no
thermophileno96.428no
glucose-utilyes89.779no
glucose-fermentno88.36no

External links

@ref: 2028

culture collection no.: DSM 27, ATCC 7061, CCM 2144, IFO 12092, JCM 2508, NBRC 12092, NCIB 9369, NCTC 10337, NRS 272, BCRC 11706, CCUG 26015, CECT 29, CGMCC 1.3533, CIP 52.67, IAM 12469, IAM 14177, KCTC 3348, LMG 7132, NCIMB 9369, NRIC 1010, NRRL NRS-272, VKM B-508, VTT E-95572, NCDO 1766

straininfo link

  • @ref: 70430
  • straininfo: 92134

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology6319195A novel glycerophosphodiesterase from Bacillus pumilus.Kusser W, Fiedler FFEBS Lett10.1016/0014-5793(84)80100-31984Bacillus/*enzymology, Bacillus subtilis, Cell Wall, Kinetics, Phosphoric Diester Hydrolases/isolation & purification/*metabolism, Staphylococcus aureus, Substrate SpecificityPhylogeny
Phylogeny15941382Recurrent isolation of hydrogen peroxide-resistant spores of Bacillus pumilus from a spacecraft assembly facility.Kempf MJ, Chen F, Kern R, Venkateswaran KAstrobiology10.1089/ast.2005.5.3912005Bacillus/classification/drug effects/isolation & purification/*physiology, Drug Resistance, Bacterial, Extraterrestrial Environment, Hydrogen Peroxide/*pharmacology, Phylogeny, *Spacecraft, Spores, Bacterial/drug effects/physiologyPathogenicity
Pathogenicity19111835Sterilization of Bacillus pumilus spores using supercritical fluid carbon dioxide containing various modifier solutions.Shieh E, Paszczynski A, Wai CM, Lang Q, Crawford RLJ Microbiol Methods10.1016/j.mimet.2008.11.0052008Bacillus/*drug effects/physiology, Carbon Dioxide/*pharmacology, Formates/pharmacology, Hydrogen Peroxide/pharmacology, Octoxynol/pharmacology, Spores, Bacterial/drug effects, Sterilization/instrumentation/*methods, tert-Butylhydroperoxide/pharmacology
Enzymology22752169Protection of Bacillus pumilus spores by catalases.Checinska A, Burbank M, Paszczynski AJAppl Environ Microbiol10.1128/AEM.01211-122012Bacillus/*enzymology/isolation & purification/metabolism/*physiology, Catalase/isolation & purification/*metabolism, Electrophoresis, Polyacrylamide Gel, Environmental Microbiology, Hydrogen Peroxide/*toxicity, Mass Spectrometry, Microbial Viability/*drug effects, Oxygen/metabolism, Spores, Bacterial/*enzymology/metabolism/*physiology, United States, United States National Aeronautics and Space AdministrationMetabolism
Transcriptome23799069Candidate genes that may be responsible for the unusual resistances exhibited by Bacillus pumilus SAFR-032 spores.Tirumalai MR, Rastogi R, Zamani N, O'Bryant Williams E, Allen S, Diouf F, Kwende S, Weinstock GM, Venkateswaran KJ, Fox GEPLoS One10.1371/journal.pone.00660122013Bacillus/*genetics/physiology, Bacterial Proteins/genetics, Genes, Bacterial, Genetic Association Studies, Microbial Viability/*genetics/radiation effects, Molecular Sequence Annotation, Pseudogenes, Sequence Analysis, DNA, Spacecraft, Spores, Bacterial/genetics, Ultraviolet Rays
Genetics23812891An ICEBs1-like element may be associated with the extreme radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores.Tirumalai MR, Fox GEExtremophiles10.1007/s00792-013-0559-z2013Bacillus/*genetics, Evolution, Molecular, Genome, Bacterial, Radiation Tolerance/*genetics, Retroelements/genetics
Phylogeny24158533Bacillus xiamenensis sp. nov., isolated from intestinal tract contents of a flathead mullet (Mugil cephalus).Lai Q, Liu Y, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-013-0057-42013Animals, Bacillus/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, China, DNA, Bacterial/genetics/metabolism, Fatty Acids/chemistry/metabolism, Intestines/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Smegmamorpha/*microbiologyMetabolism
Phylogeny25171924Bacillus invictae sp. nov., isolated from a health product.Branquinho R, Sousa C, Osorio H, Meirinhos-Soares L, Lopes J, Carrico JA, Busse HJ, Abdulmawjood A, Klein G, Kampfer P, Pintado ME, Peixe LVInt J Syst Evol Microbiol10.1099/ijs.0.067850-02014Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Drug Contamination, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Enzymology25287558Improving the thermoactivity and thermostability of pectate lyase from Bacillus pumilus for ramie degumming.Liang C, Gui X, Zhou C, Xue Y, Ma Y, Tang SYAppl Microbiol Biotechnol10.1007/s00253-014-6091-y2014Amino Acid Sequence, Bacillus/*enzymology, Bacterial Proteins/*chemistry/genetics, Boehmeria/*chemistry, Cloning, Molecular, DNA Primers, DNA, Bacterial/genetics, Enzyme Stability, Escherichia coli/genetics, Half-Life, Hydrogen-Ion Concentration, Molecular Sequence Data, Pectins/chemistry, Plant Gums/*chemistry, Polysaccharide-Lyases/*chemistry, Sequence Alignment, Substrate Specificity, TemperatureGenetics
Phylogeny25977285Reclassification of Bacillus invictae as a later heterotypic synonym of Bacillus altitudinis.Liu Y, Lai Q, Du J, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.0003362015Bacillus/*classification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny26705002Bacillus zhangzhouensis sp. nov. and Bacillus australimaris sp. nov.Liu Y, Lai Q, Du J, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0008562015
Biotechnology28616451Dataset on potential large scale production of biosurfactant using Bacillus sp.Heryani H, Putra MDData Brief10.1016/j.dib.2017.05.0372017
Phylogeny29884123Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates.Tirumalai MR, Stepanov VG, Wunsche A, Montazari S, Gonzalez RO, Venkateswaran K, Fox GEBMC Microbiol10.1186/s12866-018-1191-y2018Bacillus/classification/*genetics, Bacillus pumilus/genetics, Bacterial Proteins/genetics, DNA Gyrase/genetics, Gene Order, *Genome, Bacterial, Molecular Sequence Annotation, Open Reading Frames, Phylogeny, Sequence Analysis, DNA/*methods, Spacecraft, Spores, Bacterial/classification/genetics/*isolation & purificationGenetics
Metabolism30728983Novel cyanide electro-biodegradation using Bacillus pumilus ATCC 7061 in aqueous solution.Ojaghi A, Shafaie Tonkaboni SZ, Shariati P, Doulati Ardejani FJ Environ Health Sci Eng10.1007/s40201-018-0289-32018
Metabolism36396722The release of petroleum hydrocarbons from a saline-sodic soil by the new biosurfactant-producing strain of Bacillus sp.Kalvandi S, Garousin H, Pourbabaee AA, Farahbakhsh MSci Rep10.1038/s41598-022-24321-32022*Petroleum/metabolism, Soil/chemistry, *Bacillus/metabolism, RNA, Ribosomal, 16S/genetics/metabolism, Phylogeny, Biodegradation, Environmental, *Soil Pollutants/metabolism, Surface-Active Agents/chemistry, Hydrocarbons/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2028Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27)https://www.dsmz.de/collection/catalogue/details/culture/DSM-27
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
22900A. G. O'DONNELL, J. R. NORRIS, R. C. W. BERKELEY, D. CLAUS, T. KANEKO, N. A. LOGAN, R. NOZAKI10.1099/00207713-30-2-448Characterization of Bacillus subtilis, Bacillus pumilus, Bacillus licheniformis, and Bacillus amyloliquefaciens by Pyrolysis Gas-Liquid Chromatography, Deoxyribonucleic Acid-Deoxyribonucleic Acid Hybridization, Biochemical Tests, and API SystemsIJSEM 30: 448-459 1980
40218Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13289
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
70430Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92134.1StrainInfo: A central database for resolving microbial strain identifiers
122057Curators of the CIPCollection of Institut Pasteur (CIP 52.67)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2052.67