Saponin treatment for eukaryotic DNA depletion alter the microbial DNA profiles

Here, we have investigated a DNA isolation saponin-based protocol applied to different biological matrices to deplete the released host DNA. The bacterial DNA obtained was used in order to assess the relative abundance of bacterial and human DNA, revealing that the inclusion of 2.5 % (wt/vol) saponin allowed the depletion of most of the host's DNA in favor of an enrichment of bacterial DNA. However, shotgun metagenomic sequencing showed counterfeit microbial profiles of the DNA samples, highlighting an erroneous increase in the level of Gram-positive reads.