Microbes are abundant on earth and play a crucial role in the environment they inhabit. Before the dawn of metagenomics, the study of the effect of microorganisms on their environment was limited due to use of low throughput techniques that could only examine single organisms or a few at a time. Metagenomics is a fast growing field of science that permits investigation of microbes by directly extracting DNA from the environment. A lot of environments, ranging in complexity from the ocean to acid mines, from wastewater communities to the human body have been targeted by metagenomics studies, and these studies generate tremendous amounts of data and newer and more efficient bioinformatic tools and methods are needed to interpret this complex data. In this dissertation we used bioinformatic tools to enrich our understanding of the role that microorganisms play within some important but understudied microbial environments. In Chapter # 1, we report an increased microbial richness associated with colorectal cancer. This is an important finding that could lead to the development of diagnostic methods to identify individuals at high risk of developing colorectal cancer and this early detection could help devise preventive strategies. In Chapter # 2 we discuss a batch- effect we discovered in our colorectal cancer project and how filtering out the batch- effect helped us in revealing the true biological signal. In Chapter #3 we report results of a metagenomic survey where we analyzed the pyrosequences obtained from a wastewater community. In Chapter # 4 of this dissertation we perform a systematic comparison of some of the methods used in taxonomic profiling of microbial communities and show how the choice of method can have an effect on the community's taxonomic profile reported.Overall this dissertation demonstrates the value of using bioinformatic tools, during the course of analysis of complex communities, in not only filtering out artifacts and in choice of analysis pathways but also in discovering important biological effects.