Metagenomics for Monitoring Environmental Biodiversity: Challenges, Progress, and Opportunities

Metagenomics, as the genomic analysis of DNA materials from environmental samples containing multiple genomic components, is attracting more and more interests due to its wide applications on microbial, cancer, and immunology researches. This chapter provides an overview on the topic covering the major steps involved in data collection, processing, and analysis. We describe and discuss experiment design, sample processing and quality control, sequencing and assembly, annotation, and downstream analyses. For each step, we summarize the current points of views, key issues, and popular tools. A step-by-step tutorial is then given using the popular QIIME pipeline on a bacterial 16S rRNA study case, which would benefit new scientists of the field for the startup of a successful metagenome project.