Pulsed-field gel electrophoresis (PFGE) is a technique for producing fingerprints of large DNA-molecules, such as bacterial genomes. Using PFGE, Biosafe is currently preparing a European standard, requested by the European Committee for Standardization (CEN), for identification of the probiotics Lactobacillus, Enterococcus, Pediococcus, Bacillus, and yeast in animal feeds, premixes, and additives. Most interlaboratory tests for the method have been already performed, and a comparison of results is currently in process. The standard will be finalized by the end of 2020.
The method is based on the digestion of genomic DNA of the strain with specified rare-cutting restriction enzymes to ideally produce 15–30 fragments. The samples are then applied to a gel matrix under the electric field that periodically changes direction, resulting in representation of the entire bacterial chromosome in a single gel. The method is highly reproducible and produces individual fragment patterns for each strain.
Although the price of whole genome sequencing (WGS) has decreased dramatically during the last decade, the old workhorse PFGE still has a strong foothold in strain identification in certain special cases. In fact, the combination of both techniques may produce the best results, because WGS data can be utilized in PFGE-analysis to select the optimal rare-cutting restriction enzymes by mapping the potential restriction sites in the genome.
PFGE is an excellent approach if you need to confirm:
- The presence of the strain in a feed additive from several batches
- Genetic stability of the production strain during the production process
- The presence of the strain among the background bacterial growth, for example while analyzing the intestinal samples of in vivo compatibility trials
Therefore, PFGE is a useful method for feed additive manufacturers, R&D and the authorities.
Contact us to discover how you could utilize PFGE in your projects!