Challenges in bacterial DNA enrichment and quantification in tissues

We evaluated the effects of bacterial DNA enrichment, based on selective lysis of host cells and removal of their DNA, on detection and quantification of bacteria. For that purpose, we spiked pig muscle tissue with a mock community consisting of four bacterial species from different phyla. The accuracy of taxonomic profiling and bacterial quantification results varied among extraction procedures and sample storage conditions. Compared to the original enrichment protocol, the modified procedure improved detection of bacteria and their abundance estimate.