Strain identifier

BacDive ID: 11545

Type strain: Yes

Species: Paenibacillus chibensis

Strain Designation: B-142

Strain history: CIP <- 1997, O. Shida, Res. Lab., Higeta Shoyu Co, Chiba, Japan: strain HSCC 442 <- NRRL: strain B-142 <- FDA

NCBI tax ID(s): 59846 (species)

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

@ref: 4462

BacDive-ID: 11545

DSM-Number: 11731

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, motile

description: Paenibacillus chibensis B-142 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 59846
  • Matching level: species

strain history

@refhistory
4462<- O. Shida, Higeta Shoyu; HSCC 442 <- NRRL <- FDA; PCI 221
67770HSCC 442 <-- NRRL B-142 <-- FDA strain PCI 221.
118231CIP <- 1997, O. Shida, Res. Lab., Higeta Shoyu Co, Chiba, Japan: strain HSCC 442 <- NRRL: strain B-142 <- FDA

doi: 10.13145/bacdive11545.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus chibensis
  • full scientific name: Paenibacillus chibensis Shida et al. 1997

@ref: 4462

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus chibensis

full scientific name: Paenibacillus chibensis Shida et al. 1997

strain designation: B-142

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.823
69480100positive
118231yespositiverod-shaped

colony morphology

  • @ref: 118231

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4462NUTRIENT 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
35797MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118231CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4462positivegrowth30mesophilic
35797positivegrowth30mesophilic
67770positivegrowth30mesophilic
118231positivegrowth22-45
118231nogrowth10psychrophilic
118231nogrowth55thermophilic

culture pH

  • @ref: 118231
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 118231
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
118231yes

halophily

@refsaltgrowthtested relationconcentration
118231NaClpositivegrowth0-4 %
118231NaClnogrowth6 %
118231NaClnogrowth8 %
118231NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
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
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
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
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-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
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118231esculin+hydrolysis4853
118231hippurate-hydrolysis606565
118231nitrate+reduction17632
118231nitrite-reduction16301
118231nitrate+respiration17632

metabolite production

  • @ref: 118231
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11823115688acetoin-
11823117234glucose+

enzymes

@refvalueactivityec
118231oxidase+
118231beta-galactosidase+3.2.1.23
118231alcohol dehydrogenase-1.1.1.1
118231gelatinase-
118231amylase+
118231DNase-
118231caseinase-3.4.21.50
118231catalase+1.11.1.6
118231tween esterase-
118231gamma-glutamyltransferase-2.3.2.2
118231lecithinase-
118231lipase-
118231lysine decarboxylase-4.1.1.18
118231ornithine decarboxylase-4.1.1.17
118231urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118231--++-+----++++-+++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118231---+/-++--+++++-+/---+---+/-+++/-++++++++/--+++-++---+/---+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118231+++++-++++++++-+-++++++------------+------------------------+-------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4462soilUSAUSANorth America
67770Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44621Risk group (German classification)
1182311Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus chibensis gene for 16S rRNA, partial sequenceAB0731941505ena59846
20218Paenibacillus chibensis gene for 16S rRNA, partial sequence, strain: NBRC 15958AB6810061480ena59846
20218B.amylolyticus 16S ribosomal RNAX606061435ena1451
20218Paenibacillus chibensis DNA for 16S rRNAD853951436ena59846

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus chibensis strain NBRC 1595859846.3wgspatric59846
66792Paenibacillus chibensis NBRC 159582925295060draftimg59846
67770Paenibacillus chibensis NBRC 15958GCA_004001045contigncbi59846

GC content

  • @ref: 67770
  • GC-content: 52.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes79.49no
anaerobicno98.579no
halophileno93.971no
spore-formingyes96.869no
glucose-utilyes89.848no
thermophileno98.359yes
flagellatedyes76.246no
aerobicyes80.955no
motileyes88.775no
glucose-fermentno83.425no

External links

@ref: 4462

culture collection no.: DSM 11731, IFO 15958, JCM 9905, NBRC 15958, NRRL B-142, HSCC 442, PCI 221, ATCC 9966, ATCC BAA 725, CCM 1084, CECT 375, CIP 105254, IAM 1112, IFO 3329, KCTC 3758, LMG 14457, NBRC 3329, NCIMB 8144

straininfo link

  • @ref: 80775
  • straininfo: 9916

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21887645Paenibacillus telluris sp. nov., a novel phosphate-solubilizing bacterium isolated from soil.Lee JC, Kim CJ, Yoon KHJ Microbiol10.1007/s12275-011-0471-02011Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial, Fatty Acids/chemistry, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/ultrastructure, Phenotype, Phosphates/*chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, SolubilityGenetics
Phylogeny24556633Paenibacillus shirakamiensis sp. nov., isolated from the trunk surface of a Japanese oak (Quercus crispula).Tonouchi A, Tazawa D, Fujita TInt J Syst Evol Microbiol10.1099/ijs.0.055772-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Stems/microbiology, Quercus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26373452Paenibacillus zeae sp. nov., isolated from maize (Zea mays L.) seeds.Liu Y, Zhai L, Wang R, Zhao R, Zhang X, Chen C, Cao Y, Cao Y, Xu T, Ge Y, Zhao J, Cheng CInt J Syst Evol Microbiol10.1099/ijsem.0.0006082015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyEnzymology
Phylogeny27498790Paenibacillus solani sp. nov., isolated from potato rhizosphere soil.Liu B, Liu GH, Sengonca C, Schumann P, Lan JL, Chen DJ, Cui WD, Lin NQInt J Syst Evol Microbiol10.1099/ijsem.0.0013782016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Solanum tuberosum/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33595431Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil.Paek J, Bai L, Shin Y, Kim H, Kook JK, Chang YHInt J Syst Evol Microbiol10.1099/ijsem.0.0047072021
Metabolism34822536Antifungal Activity of Biocontrol Agents In Vitro and Potential Application to Reduce Mycotoxins (Aflatoxin B1 and Ochratoxin A).Illueca F, Vila-Donat P, Calpe J, Luz C, Meca G, Quiles JMToxins (Basel)10.3390/toxins131107522021Aflatoxin B1/*metabolism, Antifungal Agents/*pharmacology, Bacillus amyloliquefaciens/metabolism, Cell-Free System, Fungicides, Industrial/*pharmacology, In Vitro Techniques, Ochratoxins/*metabolism, Paenibacillus/metabolism, Pantoea/metabolism, *Pest Control, Biological, Poisons/*metabolismBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4462Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11731)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11731
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
35797Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17253
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
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
80775Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9916.1StrainInfo: A central database for resolving microbial strain identifiers
118231Curators of the CIPCollection of Institut Pasteur (CIP 105254)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105254