Strain identifier

BacDive ID: 11478

Type strain: Yes

Species: Paenibacillus pabuli

Strain Designation: NRS-924, P 1

Strain history: CIP <- 1988, L.K. Nakamura, NRRL: strain 924, Bacillus circulans

NCBI tax ID(s): 1349782 (strain), 1472 (species)

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General

@ref: 1278

BacDive-ID: 11478

DSM-Number: 3036

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

description: Paenibacillus pabuli NRS-924 is a spore-forming, mesophilic bacterium that was isolated from green or fermenting fodder.

NCBI tax id

NCBI tax idMatching level
1349782strain
1472species

strain history

@refhistory
405311988, L.K. Nakamura, NRRL: strain 924, Bacillus circulans
1278<- NRRL, NRS-924 <- N.R. Smith, 924 (Bacillus circulans) <- J.R. Porter <- M. Schieblich (Bacillus pabuli, P 1)
67770NRRL NRS-924 <-- N. R. Smith NRS-924 <-- J. R. Porter P1 <-- M. Schieblich.
121495CIP <- 1988, L.K. Nakamura, NRRL: strain 924, Bacillus circulans

doi: 10.13145/bacdive11478.20250331.9.3

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 pabuli
  • full scientific name: Paenibacillus pabuli (Nakamura 1984 ex Schieblich 1923) Ash et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Bacillus pabuli

@ref: 1278

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus pabuli

full scientific name: Paenibacillus pabuli (Nakamura 1984) Ash et al. 1994

strain designation: NRS-924, P 1

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • motility: yes
  • confidence: 92.4

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1278NUTRIENT 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
40531MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121495CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
1278positivegrowth30
40531positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 96.9

spore formation

@refspore formationconfidence
125438yes93.129
125439yes96.2

Isolation, sampling and environmental information

isolation

@refsample type
1278green or fermenting fodder
121495Other, Green or fermenting fodder

isolation source categories

Cat1Cat2
#Engineered#Agriculture
#Host#Plants

taxonmaps

  • @ref: 69479
  • File name: preview.99_2243.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_141;97_152;98_1747;99_2243&stattab=map
  • Last taxonomy: Paenibacillus
  • 16S sequence: AB073191
  • Sequence Identity:
  • Total samples: 2870
  • soil counts: 1643
  • aquatic counts: 208
  • animal counts: 410
  • plant counts: 609

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
12781Risk group (German classification)
1214951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus pabuli clone JS-4F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478102547nuccore1472
20218Paenibacillus pabuli gene for 16S rRNA, partial sequenceAB0450941500nuccore1472
20218Paenibacillus pabuli gene for 16S rRNA, partial sequenceAB0731911507nuccore1472
20218Paenibacillus pabuli gene for 16S rRNA, partial sequence, strain: NBRC 13638AB6804751477nuccore1472
20218B.pabuli 16S ribosomal RNAX606301435nuccore1472

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus pabuli NBRC 136381349782.3wgspatric1349782
66792Paenibacillus pabuli NBRC 136382681813001draftimg1349782
67770Paenibacillus pabuli NBRC 13638 NBRC 13638GCA_001514495contigncbi1349782

GC content

@refGC-contentmethod
127849.9
6777049Buoyant density centrifugation (BD)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes60.086no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.724no
125438spore-formingspore-formingAbility to form endo- or exosporesyes93.129no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes50.618no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.355no
125438motile2+flagellatedAbility to perform flagellated movementyes84.648no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes96.2
125439BacteriaNetmotilityAbility to perform movementyes92.4
125439BacteriaNetgram_stainReaction to gram-stainingvariable87.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.9

External links

@ref: 1278

culture collection no.: CCUG 27415, NRRL NRS-924, DSM 3036, ATCC 43899, LMG 11158, NCIMB 12781, NRS 924, JCM 9074, CCM 3893, CIP 103119, IFO 13638, KCTC 3398, LMG 15970, NBRC 13638

straininfo link

  • @ref: 80712
  • straininfo: 1158

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653909Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium.Rivas R, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.63173-02005*Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Rods/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Xylans/*metabolismGenetics
Phylogeny18319478Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine.Roux V, Fenner L, Raoult DInt J Syst Evol Microbiol10.1099/ijs.0.65228-02008Adult, Bacterial Typing Techniques, Cerebrospinal Fluid/*microbiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Female, Genes, rRNA, Genotype, Gram-Negative Bacteria/*classification/genetics/*isolation & purification, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Urine/*microbiologyGenetics
Phylogeny31483753Paenibacillus xylanivorans sp. nov., a xylan-degrading bacterium isolated from decaying forest soil.Ghio S, Sauka DH, Ferrari AE, Piccini FE, Ontanon OM, Campos EInt J Syst Evol Microbiol10.1099/ijsem.0.0036862019Argentina, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Paenibacillus/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Xylans/*metabolismTranscriptome
Cultivation34406433Isolation, Identification and Characterization of Paenibacillus pabuli E1 to Explore Its Aflatoxin B1 Degradation Potential.Li G, Li X, Dong L, Li C, Zou P, Saleemi MK, Murtaza B, Jin B, Zhao H, Wang L, Li S, Yang H, Xu YCurr Microbiol10.1007/s00284-021-02624-42021*Aflatoxin B1, Animals, Biodegradation, Environmental, Culture Media, Humans, *Paenibacillus/geneticsPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1278Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3036)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3036
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
40531Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14882
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/
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
80712Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1158.1StrainInfo: A central database for resolving microbial strain identifiers
121495Curators of the CIPCollection of Institut Pasteur (CIP 103119)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103119
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1