I recently wrote up a review with Dr. Elizabeth Grice of next-generation sequencing technologies. We specifically focused on their applications for microbiome research. While it was published it in a wound care journal, the techniques outlined are broadly applicable to any system with a diversity of microbes. Please have a look at the manuscript below!
Hodkinson, B. P., and E. A. Grice. 2015. Next-generation sequencing: a review of technologies and tools for wound microbiome research. Advances in Wound Care 4(1): 50-58.
Download manuscript (PDF file)