Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract

A crucial step in the analyses of the microbial community of the porcine gastrointestinal tract is the extraction of DNA from the different section. The chosen method should allow to the identification of the majority of microorganisms present. Due to sample heterogeneity it is complicated to equally lyse cells of all species present, so it is important to investigate the best method to cover the highest number of microorganisms. Several methods use mechanical lysis that may increase the DNA degradation, while others have a gentle approach that may underestimate the existent species. There is a huge offer in the market regarding DNA extraction kits and several robust methods for DNA extraction were used in the literature. Standardisation of methods is important to gain reliable knowledge on bacterial community profiles and to make porcine studies more comparable. The aim of this project is to test different DNA extraction methods and analyse the bacterial community composition with terminal restriction fragment length polymorphism (T-RFLP) and Illumina amplicon sequencing in order to identify the most suitable method for a comprehensive investigation of the porcine gastrointestinal microbiota.