These protocols describe three methods for DNA extraction from rat stool pellets. We recommend the QIAGEN DNeasy Blood and Tissue Kit when targeting the host (e.g. rat). 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.

The method using the QIAamp PowerFecal DNA Kit was suitable when targeting the microbiome, however this product has been discontinued by the manufacturer. Please use this legacy method to inform decisions and development going forward. Alternative kit replacements may be available, however these have not been validated by our internal teams.

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.