Metagenomics is one of several genomics applications, which has benefited immensely from the high throughput and cost efficacy of Next Generation sequencers. And although hundreds of studies on metagenome analysis have been published over the past few years, the methodology for conducting them is still very much evolving. In this DSRG study we will evaluate the influence of various sample preparation methods, specifically DNA extraction and amplification approaches, on data output along with a comparative analysis of Next Generation sequencing platforms. We will study the effect of these different experimental and technical strategies on determination of sample biodiversity.