Choice of method for purification of bacterial DNA from faecal material influences community structure as detected by next generation sequencing

In this study we conducted a systematic comparison of the DNA extraction methods on feacal samples used by the two major collaborative efforts: The European MetaHIT and the American Human Microbiome Project. Additionally, effects of homogenizing the samples before extraction were addressed. We observed significant differences in distribution of bacterial taxa depending on the method. While eukaryotic DNA was most efficiently extracted by the MetaHIT protocol, DNA from bacteria within the Bacteroidetes phylum was most efficiently extracted by the HMP protocol. Whereas it is comforting that the inter-individual variation clearly exceeded the variation resulting from choice of extraction method, our data highlights the challenge of comparing data across studies applying different methodologies.