Prokaryotic endophytic community characterization

Co-amplification of host DNA represents a major technical challenge in plant-associated prokaryotic microbial community surveys using amplicon-based high throughput sequencing, as it prevents the thorough description of the associated microbial communities. In this work, we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rDNA in order to reduce plant DNA co-amplification and increase diversity coverage of associated prokaryotic diversity.