Strain identifier
BacDive ID: 11482
Type strain: 
Species: Paenibacillus polymyxa
Strain Designation: II
Strain history: <- D. Claus, II
NCBI tax ID(s): 1406 (species)
version 9.3 (current version)
General
@ref: 155
BacDive-ID: 11482
DSM-Number: 365
keywords: genome sequence, Bacteria, spore-forming, mesophilic
description: Paenibacillus polymyxa II is a spore-forming, mesophilic bacterium that was isolated from garden soil.
NCBI tax id
- NCBI tax id: 1406
- Matching level: species
strain history
- @ref: 155
- history: <- D. Claus, II
doi: 10.13145/bacdive11482.20250331.9.3
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 polymyxa
- full scientific name: Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994
synonyms
@ref synonym 20215 Clostridium polymyxa 20215 Aerobacillus polymyxa 20215 Paenibacillus jamilae 20215 Bacillus polymyxa
@ref: 155
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus polymyxa
full scientific name: Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994
strain designation: II
type strain: no
Culture and growth conditions
culture medium
- @ref: 155
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
- @ref: 155
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | yes | 90.524 |
| 125439 | yes | 90.2 |
compound production
- @ref: 155
- compound: inhibitors for glycoside hydrolases
Isolation, sampling and environmental information
isolation
- @ref: 155
- sample type: garden soil
- geographic location: Göttingen
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Engineered | #Agriculture | #Garden |
Safety information
risk assessment
- @ref: 155
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paenibacillus polymyxa strain DSM 365 | 1406.47 | wgs | patric | 1406 |
| 66792 | Paenibacillus polymyxa DSM 365 | 2585427968 | draft | img | 1406 |
| 66792 | Paenibacillus polymyxa DSM 365 | GCA_022537985 | scaffold | ncbi | 1406 |
| 66792 | Paenibacillus polymyxa DSM 365 | GCA_000714835 | contig | ncbi | 1406 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 67.463 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.545 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 90.524 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 65.916 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 94.189 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 85.148 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 90.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 83.9 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 80.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 79.2 |
External links
@ref: 155
culture collection no.: DSM 365
straininfo link
- @ref: 80716
- straininfo: 1163
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 22989651 | Enhanced fed-batch fermentation of 2,3-butanediol by Paenibacillus polymyxa DSM 365. | Hassler T, Schieder D, Pfaller R, Faulstich M, Sieber V | Bioresour Technol | 10.1016/j.biortech.2012.08.047 | 2012 | Butylene Glycols/*metabolism, *Fermentation, Paenibacillus/*metabolism, Viscosity | |
| Genetics | 25450636 | Genome sequence of type strain Paenibacillus polymyxa DSM 365, a highly efficient producer of optically active (R,R)-2,3-butanediol. | Xie NZ, Li JX, Song LF, Hou JF, Guo L, Du QS, Yu B, Huang RB | J Biotechnol | 10.1016/j.jbiotec.2014.07.441 | 2014 | Butylene Glycols/chemistry/isolation & purification/*metabolism, Genome, Bacterial/*genetics, Molecular Sequence Data, Paenibacillus/*genetics/*metabolism, Stereoisomerism | Metabolism |
| Biotechnology | 27765680 | Investigation of relationship between 2,3-butanediol toxicity and production during growth of Paenibacillus polymyxa. | Okonkwo CC, Ujor V, Ezeji TC | N Biotechnol | 10.1016/j.nbt.2016.10.006 | 2016 | Acetoin/metabolism, Batch Cell Culture Techniques, Biofuels, Bioreactors, Biotechnology, Butylene Glycols/chemistry/*metabolism/*toxicity, Feedback, Physiological, Fermentation, Metabolic Engineering, Paenibacillus polymyxa/*drug effects/growth & development/*metabolism, Stereoisomerism | Metabolism |
| Metabolism | 32144108 | Inactivation of the Levansucrase Gene in Paenibacillus polymyxa DSM 365 Diminishes Exopolysaccharide Biosynthesis during 2,3-Butanediol Fermentation. | Okonkwo CC, Ujor V, Cornish K, Ezeji TC | Appl Environ Microbiol | 10.1128/AEM.00196-20 | 2020 | Bacterial Proteins/*metabolism, Butylene Glycols/*metabolism, Fermentation, *Gene Silencing, Genes, Bacterial, Hexosyltransferases/*metabolism, Paenibacillus polymyxa/enzymology/genetics/*metabolism, Polysaccharides, Bacterial/*biosynthesis | Enzymology |
| Metabolism | 32771627 | Engineering of the 2,3-butanediol pathway of Paenibacillus polymyxa DSM 365. | Schilling C, Ciccone R, Sieber V, Schmid J | Metab Eng | 10.1016/j.ymben.2020.07.009 | 2020 | Butylene Glycols/*metabolism, *CRISPR-Cas Systems, *Gene Editing, *Metabolic Engineering, *Paenibacillus polymyxa/genetics/metabolism | Biotechnology |
| 32995508 | Tailor-made exopolysaccharides-CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa. | Rutering M, Cress BF, Schilling M, Ruhmann B, Koffas MAG, Sieber V, Schmid J | Synth Biol (Oxf) | 10.1093/synbio/ysx007 | 2017 | |||
| 34973768 | Structural elucidation of the fucose containing polysaccharide of Paenibacillus polymyxa DSM 365. | Schilling C, Klau LJ, Aachmann FL, Ruhmann B, Schmid J, Sieber V | Carbohydr Polym | 10.1016/j.carbpol.2021.118951 | 2021 | Carbohydrate Conformation, Fucose/*chemistry, Paenibacillus polymyxa/*chemistry, Polysaccharides, Bacterial/*chemistry | ||
| Genetics | 35575559 | Complete Genome Sequence of Paenibacillus polymyxa DSM 365, a Soil Bacterium of Agricultural and Industrial Importance. | Kumar S, Ujor VC | Microbiol Resour Announc | 10.1128/mra.00329-22 | 2022 | ||
| Metabolism | 35588272 | Insights in the Complex DegU, DegS, and Spo0A Regulation System of Paenibacillus polymyxa by CRISPR-Cas9-Based Targeted Point Mutations. | Meliawati M, May T, Eckerlin J, Heinrich D, Herold A, Schmid J | Appl Environ Microbiol | 10.1128/aem.00164-22 | 2022 | Bacillus subtilis/genetics, Bacterial Proteins/genetics/metabolism, CRISPR-Cas Systems, *Paenibacillus polymyxa/genetics/metabolism, Point Mutation |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 155 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 365) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-365 | |
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 80716 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1163.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |