Lyophilisation improves the extraction of PCR-quality community DNA from pig faecal samples

BACKGROUND: Faeces are increasingly used as sources of DNA for genetic and ecological studies. Although multiple methods to preserve faecal samples prior to DNA extraction have been used (e.g., 70% or absolute ethanol, freezing at -20 degrees C or in liquid nitrogen) no information is at present available in the literature on the use of lyophilised faeces. Accordingly, the yield and quality of the community DNA obtained by using four different commercial DNA extraction kits (QlAamp DNA Stool Mini Kit, REALPURE Spin Kit, SPEEDTOOLS Tissue DNA Extraction Kit, and JETQUICK Tissue DNA Spin Kit) from fresh and lyophilised samples of faeces were studied here. RESULTS: The use of lyophilised faeces resulted in a 1.5- to 2-fold increase in DNA recovery relative to the use of fresh faeces regardless of the kit used. Among the four kits tested, the best results were obtained with the QlAamp DNA Stool Mini Kit. Community DNA obtained from lyophilised faeces also provided the best restriction fragment length polymorphism (PCR-RFLP) profiles, which should guarantee a better representation of the microbial diversity present in faecal samples. CONCLUSION: As compared with using fresh faecal samples for pig faecal microbiota studies, lyophilisation improved both DNA yield and quality of the information arising from the PCR-RFLP method of analysis. (C) 2009 Society of Chemical industry