Strain identifier

BacDive ID: 752

Type strain: No

Species: Bacillus pumilus

Strain Designation: E 601, E601

Strain history: CIP <- 1977, J. Blanchard, Specia Lab., Paris, France <- ATCC <- P.M. Borick <- V. Chandler

NCBI tax ID(s): 1408 (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: 232

BacDive-ID: 752

DSM-Number: 492

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, human pathogen

description: Bacillus pumilus E 601 is an anaerobe, mesophilic human pathogen of the family Bacillaceae.

NCBI tax id

  • NCBI tax id: 1408
  • Matching level: species

strain history

@refhistory
232<- Ethicon Inc., E 601
122056CIP <- 1977, J. Blanchard, Specia Lab., Paris, France <- ATCC <- P.M. Borick <- V. Chandler

doi: 10.13145/bacdive752.20230509.8.1

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: 232

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: E 601, E601

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.242
6948099.719positive
122056yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
232NUTRIENT 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
35031MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122056CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122056CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
232positivegrowth30mesophilic
35031positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
69480anaerobe97.557
122056obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no100
122056yes

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose+builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
122056nitrate-reduction17632
122056nitrite-reduction16301

metabolite production

  • @ref: 122056
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
122056oxidase+
122056catalase+1.11.1.6
122056urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    47925C16:01.916
    47925C15:0 ANTEISO38.514.711
    47925C15:0 ISO45.814.621
    47925C16:0 iso1.815.626
    47925C17:0 anteiso5.516.722
    47925C17:0 iso3.516.629
    47925C17:1 ISO I/C16:0 DMA0.816.481
    47925C17:1 ω10c ISO116.387
    47925C18:2 ω6,9c/C18:0 ANTE1.317.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122056-+++-+---++-----+-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122056+/---+++/----+/-+++----+-+/-+/-+/-+/-+++++/---++/-------++/--+-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122056+++++-+++-+---++++++++--------++-+++-----+-+---+-+++-+-----++------------+-----++-+---+--++++++---+

Isolation, sampling and environmental information

isolation

  • @ref: 232
  • country: USA
  • origin.country: USA
  • continent: North America

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: AY876287
  • 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
232yes, in single cases1Risk group (German classification)
1220561Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Bacillus pumilus strain ATCC 27142 16S ribosomal RNA gene, partial sequence
  • accession: AY876287
  • length: 1434
  • database: ena
  • NCBI tax ID: 1408

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus pumilus strain NCTC103271408.270wgspatric1408
66792Bacillus pumilus DSM 492GCA_029478105contigncbi1408

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno94.065no
gram-positiveyes92.776no
anaerobicyes70.355no
halophileno71.993no
spore-formingno96.751no
thermophileno95.552yes
glucose-utilyes90.947no
aerobicno94.423no
flagellatedno97.121no
glucose-fermentyes67.315no

External links

@ref: 232

culture collection no.: CCUG 24142, DSM 492, ATCC 27142, CIP 77.25, NCIB 10692, NCTC 10327, NCIMB 10692

straininfo link

  • @ref: 70426
  • straininfo: 1170

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
618680360Co-irradiation as an alternate method for sterilization of penicillin G, neomycin, novobiocin, and dihydrostreptomycin.Tsuji K, Rahn PD, Steindler KAJ Pharm Sci10.1002/jps.26007201061983Anti-Bacterial Agents/*radiation effects, Bacteria/radiation effects, Chromatography, High Pressure Liquid, *Cobalt Radioisotopes, Dihydrostreptomycin Sulfate/radiation effects, Drug Stability, Gamma Rays, Neomycin/radiation effects, Novobiocin/radiation effects, Penicillin G/radiation effects, Sterilization/*methods
7855057Gamma sterilization of a semi-solid poly(ortho ester) designed for controlled drug delivery--validation and radiation effects.Merkli A, Heller J, Tabatabay C, Gurny RPharm Res10.1023/a:10189645110531994Chemical Phenomena, Chemistry, Physical, Cobalt Radioisotopes, Gamma Rays, Magnetic Resonance Spectroscopy, Molecular Weight, Polyesters/chemical synthesis/chemistry/*radiation effects, Spectrophotometry, Infrared, Spores, Bacterial/radiation effects, *Sterilization, ViscosityPathogenicity
10469916Gamma irradiation for terminal sterilization of 17beta-estradiol loaded poly-(D,L-lactide-co-glycolide) microparticles.Mohr D, Wolff M, Kissel TJ Control Release10.1016/s0168-3659(99)00118-21999Bacillus/metabolism, *Drug Delivery Systems, Drug Stability, Estradiol/administration & dosage/chemistry/*radiation effects, *Gamma Rays, Lactic Acid/administration & dosage/*radiation effects, Polyglycolic Acid/administration & dosage/*radiation effects, Polylactic Acid-Polyglycolic Acid Copolymer, Polymers/administration & dosage/*radiation effects, SolubilityMetabolism
12452949Sterilization of plastic containers using electron beam irradiation directed through the opening.Cleghorn DA, Dunn J, Nablo SVJ Appl Microbiol10.1046/j.1365-2672.2002.01777.x2002Bacillus/radiation effects, *Electrons, Food Microbiology, *Food Packaging, *Plastics, Spores, Bacterial, Sterilization/*methodsBiotechnology
26825005Applicability of UV resistant Bacillus pumilus endospores as a human adenovirus surrogate for evaluating the effectiveness of virus inactivation in low-pressure UV treatment systems.Boczek LA, Rhodes ER, Cashdollar JL, Ryu J, Popovici J, Hoelle JM, Sivaganesan M, Hayes SL, Rodgers MR, Ryu HJ Microbiol Methods10.1016/j.mimet.2016.01.0122016Adenoviruses, Human/*radiation effects, Bacillus/*radiation effects, Cell Line, Disinfection/methods, Dose-Response Relationship, Radiation, Escherichia coli/radiation effects, Hot Temperature, Humans, Levivirus/radiation effects, Radiation Tolerance, Spores, Bacterial/drug effects/growth & development/*radiation effects, Ultraviolet Rays, Virus Inactivation/*radiation effects, Water Microbiology, Water Purification/methodsPathogenicityStress
31137345Detection of Heated Bacterial Spores with Fluid Thioglycollate and Soybean Casein Digest Broths Containing Variable Concentrations of Solids.Kallander KD, Romer JC, Sofos JN, Kreuzer KS, Singleton ERJ Food Prot10.4315/0362-028X-58.4.4211995

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
232Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 492)https://www.dsmz.de/collection/catalogue/details/culture/DSM-492
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
35031Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10938
47925Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24142)https://www.ccug.se/strain?id=24142
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
70426Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1170.1StrainInfo: A central database for resolving microbial strain identifiers
122056Curators of the CIPCollection of Institut Pasteur (CIP 77.25)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2077.25