The unseen world of microbes has a profound affect on everyday life. Complex microbial communities play a role in everything from climate regulation to human health and disease pathogenesis. Advancements in the field of Metagenomics are providing a window into the world of microbial communities with an unprecedented resolution. Next-generation sequencing technology is allowing researchers to describe the relationships between these complex microbial communities and their host environments. The research in this dissertation investigates these complex microbial host relationships and the various tools and techniques needed to conduct metagenomic research. Chapter 1 presents a current overview of techniques at the disposal of researchers conducting metagenomics experiments. Topics discussed include qualitative DNA fingerprinting techniques, comparison between Next-generation sequencing platforms, and how to handle statistical analysis of large metagenomic datasets. Chapter 2 deals with the development of Peak Studio, a platform independent graphical user interface, intended to be a pre-processing tool for researchers conducting DNA fingerprinting experiments. Chapter 3 explores how time and microenvironment influence the structure of gut microbial communities in a mouse model. Two experimental cohorts of mice are analyzed through the use of Illumina HiSeq sequencing of the 16S rRNA targeted V6 hypervariable region. Also considered are the effects over time of inoculating mice with a founder microbial community. In total, this dissertation emphasizes the importance of experimental design and the development and use of technology in the exploration of complex microbial communities.