These protocols describe four methods for DNA extraction from rat stool pellets. We recommend the QIAGEN DNeasy Blood and Tissue Kit when targeting the host (e.g. rat) and the QIAamp PowerFecal DNA Kit when targeting the microbiome. An even mix of host and microbiome was observed with the QIAGEN Genomic-tip 20/G and the QIAGEN MagAttract HMW DNA Kit: the Genomic-tip method yielded longer read lengths, while the MagAttract HMW DNA Kit had a shorter extraction procedure. We also recommend the use of SPRI size selection prior to sequencing.

Please see below a comparison of DNA fragment lengths and sequencing read lengths for the four protocols. Click on the panel of your choice to view the protocol.