Strain identifier

BacDive ID: 1069

Type strain: Yes

Species: Bacillus benzoevorans

Strain Designation: B1

Strain history: CIP <- 1991, F. Pichinoty, CNRS, Marseille, France: strain B1

NCBI tax ID(s): 1456 (species)

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General

@ref: 2134

BacDive-ID: 1069

DSM-Number: 5391

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

description: Bacillus benzoevorans B1 is a facultative anaerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1456
  • Matching level: species

strain history

@refhistory
2134<- F. Pichinoty; B1
355551991, F. Pichinoty, CNRS, Marseille, France: strain B1
116785CIP <- 1991, F. Pichinoty, CNRS, Marseille, France: strain B1

doi: 10.13145/bacdive1069.20240916.9.1

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 benzoevorans
  • full scientific name: Bacillus benzoevorans Pichinoty et al. 1987

@ref: 2134

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus benzoevorans

full scientific name: Bacillus benzoevorans Pichinoty et al. 1987

strain designation: B1

type strain: yes

Morphology

cell morphology

  • @ref: 116785
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 116785

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2134NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 5.0 g/l Yeast extract 4.0 g/l Meat extract 3.0 g/l Na-benzoate 2.0 g/l Distilled water
35555MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116785CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
2134positivegrowth30
35555positivegrowth30
116785positivegrowth22-37
116785nogrowth10
116785nogrowth45
116785nogrowth55

culture pH

  • @ref: 116785
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 116785
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
116785yes
69481yes100

halophily

@refsaltgrowthtested relationconcentration
116785NaClpositivegrowth0 %
116785NaClnogrowth2 %
116785NaClnogrowth4 %
116785NaClnogrowth6 %
116785NaClnogrowth8 %
116785NaClnogrowth10 %

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
68371turanose-builds acid from32528
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
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
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
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116785esculin-hydrolysis4853
116785hippurate-hydrolysis606565
116785nitrate+reduction17632
116785nitrite-reduction16301
116785nitrate+respiration17632

metabolite production

  • @ref: 116785
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11678515688acetoin+
11678517234glucose-

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
116785oxidase-
116785beta-galactosidase-3.2.1.23
116785alcohol dehydrogenase-1.1.1.1
116785gelatinase-
116785amylase-
116785DNase-
116785caseinase-3.4.21.50
116785catalase-1.11.1.6
116785tween esterase-
116785gamma-glutamyltransferase-2.3.2.2
116785lysine decarboxylase-4.1.1.18
116785ornithine decarboxylase-4.1.1.17
116785urease+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
116785--++-------+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116785-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116785--------------------------------------+----------+----+----+-+-+--++++-----+---++-+-----+-----+-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2134soilMarseilleFranceFRAEurope
116785Environment, SoilMarseilleFranceFRAEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
21341Risk group (German classification)
1167851Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus benzoevorans strain DSM5391 DNA for 16S ribosomal RNA, partial sequenceD783111433nuccore1456
20218B.benzeovorans 16S ribosomal RNAX606111430nuccore1456

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus benzoevorans DSM 5391GCA_014207535scaffoldncbi1456
66792Bacillus benzoevorans strain DSM 53911456.3wgspatric1456
66792Bacillus benzoevorans DSM 53912861430565draftimg1456

GC content

  • @ref: 2134
  • GC-content: 42.0

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes65.863no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.346yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes60.601no
69480spore-formingspore-formingAbility to form endo- or exosporesyes88.424no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno90.548yes
69480flagellatedmotile2+Ability to perform flagellated movementyes76.611no

External links

@ref: 2134

culture collection no.: DSM 5391, ATCC 49005, CCM 3364, LMD 79.7, NCIB 12555, CIP 103477, LMG 9582, NCIMB 12555

straininfo link

  • @ref: 70742
  • straininfo: 1098

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Metabolism6508078[Biochemical characterization of Bacillus benzoevorans sp. nov., a new filamentous, sheathed mesophilic species, degrading various aromatic acids and phenols].Pichinoty F, Asselineau J, Mandel MAnn Microbiol (Paris)1984Bacillus/classification/growth & development/*metabolism, Carboxylic Acids/*metabolism, Chemical Phenomena, Chemistry, Culture Media, Phenols/*metabolism, TemperaturePhylogeny
Phylogeny12656168Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are gamma-radiation resistant.Venkateswaran K, Kempf M, Chen F, Satomi M, Nicholson W, Kern RInt J Syst Evol Microbiol2003Bacillus/genetics/*isolation & purification/*radiation effects, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Disinfection, Fatty Acids/analysis, Gamma Rays, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Radiation Tolerance, Spacecraft, Spores, Bacterial/genetics/radiation effects, Ultraviolet Rays, United States, United States National Aeronautics and Space AdministrationGenetics10.1099/ijs.0.02311-0
Phylogeny27265352Bacillus oryzisoli sp. nov., isolated from rice rhizosphere.Zhang XX, Gao JS, Zhang L, Zhang CW, Ma XT, Zhang JInt J Syst Evol Microbiol2016Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome10.1099/ijsem.0.001215

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2134Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5391)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5391
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
35555Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15279
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
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
70742Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1098.1StrainInfo: A central database for resolving microbial strain identifiers
116785Curators of the CIPCollection of Institut Pasteur (CIP 103477)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103477