In a healthy gut, the immune system tolerates a diverse microbial commensal community avoiding inappropriate inflammation responses and minimizing the presence of pathogens. When the balance between host and microbes is disrupted, risk for disease increases. There is mounting evidence that microbial dysbiosis is a substantial risk factor for common gut diseases including IBS, IBD and colorectal cancer. Understanding this dysbiosis is challenging because of the extraordinary complexity of the gut ecosystem and the tremendous variability between healthy individuals in the taxa that make up the human microbiome. Advances in technology, especially sequencing technology, are beginning to allow for a full description of this complexity. In this review, we consider how new "omics" technology can be applied to the study of the gut ecosystem in human and animal models with special consideration given to factors that should be considered in the design of experiments and clinical trials.