Strain identifier

BacDive ID: 11488

Type strain: Yes

Species: Paenibacillus validus

Strain history: CIP <- 1988, L.K. Nakamura, Nat. Center Agri. Util. Res., Illinois, USA: strain NRS-1000, Bacillus validus

NCBI tax ID(s): 1349783 (strain), 44253 (species)

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General

@ref: 1279

BacDive-ID: 11488

DSM-Number: 3037

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

description: Paenibacillus validus DSM 3037 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
44253species
1349783strain

strain history

@refhistory
1279<- NRRL <- N.R. Smith, 1000 (Bacillus circulans) <- J.R. Porter <- G. Bredemann (Bacillus validus, 1)
67770NRRL NRS-1000 <-- N. R. Smith NRS-1000 <-- J. R. Porter V1 <-- G. Bredemann.
123787CIP <- 1988, L.K. Nakamura, Nat. Center Agri. Util. Res., Illinois, USA: strain NRS-1000, Bacillus validus

doi: 10.13145/bacdive11488.20230509.8.1

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 validus
  • full scientific name: Paenibacillus validus (Nakamura 1984 ex Bredemann and Heigener 1935) Ash et al. 1994

  • synonyms

    @refsynonym
    20215Paenibacillus gordonae
    20215Bacillus gordonae
    20215Bacillus validus

@ref: 1279

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus validus

full scientific name: Paenibacillus validus (Nakamura 1984) Ash et al. 1994 emend. Heyndrickx et al. 1995

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.949
69480100positive
123787yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1279NUTRIENT 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
34116MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123787CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123787CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1279positivegrowth30mesophilic
34116positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123787
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12378717632nitrate+reduction
12378716301nitrite-reduction

metabolite production

  • @ref: 123787
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123787oxidase-
123787catalase+1.11.1.6
123787urease+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
123787--+--+-----+----+---

Isolation, sampling and environmental information

isolation

@refsample type
1279soil
123787Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_41553.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_6869;97_8235;98_10106;99_41553&stattab=map
  • Last taxonomy: Paenibacillus validus subclade
  • 16S sequence: AB073203
  • Sequence Identity:
  • Total samples: 3802
  • soil counts: 2020
  • aquatic counts: 577
  • animal counts: 722
  • plant counts: 483

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
12791Risk group (German classification)
1237871Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus validus clone JJ-1F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478103437ena44253
20218Paenibacillus validus strain DSM3037 DNA for 16S ribosomal RNA, partial sequenceD783201424ena44253
20218Paenibacillus validus gene for 16S rRNA, partial sequenceAB0732031487ena44253
20218Paenibacillus validus gene for 16S rRNA, partial sequence, strain: NBRC 15382AB6808541466ena44253
20218Paenibacillus validus ribosomal RNA small subunit ribosomal RNA gene, complete sequenceM774891418ena44253

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus validus NBRC 153821349783.3wgspatric1349783
67770Paenibacillus validus NBRC 15382GCA_004000985contigncbi1349783

GC content

@refGC-contentmethod
127953.9
6777054Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes91.683no
gram-positiveyes77.32no
anaerobicno97.379no
halophileno92.509no
spore-formingyes94.487no
glucose-utilyes86.974no
thermophileno97.49yes
flagellatedyes87.718no
aerobicyes74.59no
glucose-fermentno93no

External links

@ref: 1279

culture collection no.: DSM 3037, ATCC 43897, LMG 11161, NCIMB 12782, NRRL NRS-1000, NRS 1000, JCM 9077, BCRC 15911, CCM 3894, CCUG 27416, CFBP 4263, CIP 103120, IFO 15382, KCTC 3401, KCTC 3859, NBRC 15382, NRRL B-14484

straininfo link

  • @ref: 80722
  • straininfo: 1210

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology7547285Paenibacillus (formerly Bacillus) gordonae (Pichinoty et al. 1986) Ash et al. 1994 is a later subjective synonym of Paenibacillus (formerly Bacillus) validus (Nakamura 1984) Ash et al. 1994: emended description of P. validus.Heyndrickx M, Vandemeulebroecke K, Scheldeman P, Hoste B, Kersters K, De Vos P, Logan NA, Aziz AM, Ali N, Berkeley RCInt J Syst Bacteriol10.1099/00207713-45-4-6611995Bacillus/chemistry/*classification/genetics, Base Sequence, DNA, Bacterial/analysis, Electrophoresis, Polyacrylamide Gel, Molecular Sequence Data, RNA, Ribosomal/chemistryGenetics
Metabolism16284749Isolation and characterization of a gene cluster for dibenzofuran degradation in a new dibenzofuran-utilizing bacterium, Paenibacillus sp. strain YK5.Iida T, Nakamura K, Izumi A, Mukouzaka Y, Kudo TArch Microbiol10.1007/s00203-005-0045-92005Base Composition, Benzofurans/*metabolism, Cloning, Molecular, Dioxygenases/genetics/metabolism, Gram-Positive Bacteria/classification/*enzymology/genetics/physiology, Hydrocarbons, Aromatic/metabolism, Hydrolases/genetics/metabolism, Molecular Sequence Data, *Multigene Family, Oxygenases/genetics/metabolism, Sequence Analysis, DNA, Spores, Bacterial/physiologyEnzymology
Metabolism16445754The bacterium Paenibacillus validus stimulates growth of the arbuscular mycorrhizal fungus Glomus intraradices up to the formation of fertile spores.Hildebrandt U, Ouziad F, Marner FJ, Bothe HFEMS Microbiol Lett10.1111/j.1574-6968.2005.00027.x2006Bacteria/*growth & development, Fungal Proteins/genetics/*metabolism, Fungi/genetics/*growth & development/metabolism/physiology, *Gene Expression Regulation, Fungal, *Mycorrhizae, Nucleic Acid Hybridization/methods, Raffinose/metabolism, Spores, Fungal/physiologyPhylogeny
Phylogeny18450707Paenibacillus ginsengihumi sp. nov., a bacterium isolated from soil in a ginseng field.Kim MK, Kim YA, Park MJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.65378-02008Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Rods/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, *Panax, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny20190026Paenibacillus xylanisolvens sp. nov., a xylan-degrading bacterium from soil.Khianngam S, Tanasupawat S, Akaracharanya A, Kim KK, Lee KC, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.022269-02010Aerobiosis, Anaerobiosis, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Thailand, Vitamin K 2/analysis, Xylans/*metabolismGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1279Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3037)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3037
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
34116Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14883
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/
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
80722Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1210.1StrainInfo: A central database for resolving microbial strain identifiers
123787Curators of the CIPCollection of Institut Pasteur (CIP 103120)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103120