Detected composition of microbial sequences in human, cattle, pig and avian faecal samples is affected by DNA isolation protocol

Human and animal faeces differ in microbial composition and presence of PCR inhibitors, which affect DNA isolation. While many protocols have been developed for human faeces, not all are equally suitable for animal faecal samples. Here we compared three commercial DNA isolation kits for isolation of DNA from human, cattle, pig and avian (swan) faecal samples: QIAamp FAST DNA Stool Mini Kit (Qiagen), NucleoSpin Soil Mini Kit (Macherey-Nagel) and QIAamp PowerFecal Pro DNA Kit (Qiagen).